Subset (5)

F1000Journal · 8.11k rows

Split (1)

data · 8.11k rows

link stringlengths 41 45	date stringlengths 9 9	paper dict	reviews listlengths 1 6	version int64 1 5	main stringlengths 38 42
https://f1000research.com/articles/12-1287/v1	09 Oct 23	{ "type": "Study Protocol", "title": "An assessment of the factors contributing to the unavailability of drugs at outpatient pharmacy of tertiary care hospital: an observational study", "authors": [ "Abhishek Bakare", "Aditya Bhargav", "Abhishek Bakare" ], "abstract": "Introduction Throughout history and up until the present, there has been a medicine shortage. In the early 1920s, there was a shortage of insulin, which is when drug scarcity first appeared in the records. Drug shortages are now more prevalent globally than they were back then.\nThe goal of this essay is to pinpoint the key components that make up a definition for medication shortages and to pinpoint the circumstances that should be considered when reporting drug shortages in databases. Understanding the factors that led certain organizations to create their own definition of a medicine shortage was crucial for achieving these goals. The pharmaceutical regulatory environment can be connected to several reasons why there are medication shortages, including parallel trading, quality standards, and business choices to halt or reduce manufacturing. The many rules governing medicine shortages have not yet been the subject of a thorough investigation. This protocol’s objective is to analyze the pertinent legislative and regulatory frameworks in the European pharmaceutical system that affect medication shortages. The objectives of the study will be the non–availability of drugs at an outpatient pharmacy and to analyze the reason of non–availability of drugs. Methods An observational study will be adopted in this study. It includes a collection of data from the patient coming to the outpatient pharmacy of AVBRH Sawangi (Meghe) Wardha.\n\nExpected result It can lead to delayed treatment for patients seeking alternative medication. It can also lead to increased healthcare costs if patients seek alternative treatments that are more expensive or require additional medical care. The unavailability of drugs can also lead to frustration and anxiety for patients who need medication to manage their health condition. It can also negatively impact the reputation of the hospital.", "keywords": [ "Outpatient pharmacy", "drug", "tertiary care hospital", "unavailability of drug", "opd", "invalid prescription" ], "content": "Introduction\n\nThroughout history and up until the present, there has been a medicine shortage. In the early 1920s, there was a shortage of insulin, which is when drug scarcity first appeared in the records. Drug shortages are now more prevalent globally than they were back then.1\n\nThe goal of this protocol is to pinpoint the key components that make up a definition for medication shortages and to pinpoint the circumstances that should be considered when reporting drug shortages in databases. Understanding the factors that led certain organizations to create their own definition of a medicine shortage was crucial for achieving these goals.2\n\nThe pharmaceutical regulatory environment can be connected to several reasons why there are medication shortages, including parallel trading, quality standards, and business choices to halt or reduce manufacturing. The many rules governing medicine shortages have not yet been the subject of a thorough investigation. This protocol’s objective is to analyze the pertinent legislative and regulatory frameworks in the European pharmaceutical system that affect medication shortages.3\n\nLocal ordering problems, regional or national distribution problems, or manufacturing problems can all lead to supply problems that could lead to shortages on a regional or national scale. The United States has a complicated just-in-time inventory system that is used to distribute medications. A cost-saving method used to reduce the costs of carrying extra inventory is just-in-time inventory. This demonstrates that there is generally no product overstock anywhere throughout the supply chain. Generally, wholesalers are used to distribute the pharmaceuticals that manufacturers make. AmerisourceBergen, Cardinal, and McKesson are the top three wholesalers in the US. These wholesalers' distribution centers are dispersed throughout the nation.4\n\nNonetheless, it would be mistaken to ignore the reality that medicine shortages are also moral and political challenges if we just saw them as technical and economic events. Two things are intended by this: First, medicine shortages affect governments' and practitioners' ability to uphold their moral commitments to citizens and society when they occur Namely, to offer benefits, reduce damage, and encourage equity. Second, Social values lead to pharmaceutical shortages, particularly the choices we've made regarding what we value most in the pharmaceutical and biotechnology sectors, in government regulations, and in health care. These insights are significant because they emphasize the moral and political need to forcefully combat medicine shortages and the requirement that those who do so do it in politically and morally astute ways.5\n\nThe key factor causing medicine shortages in Saudi Arabia is the absence of a mechanism for early warning that may send out notifications about impending shortages. There is no penalty for failure to alert the Saudi Food and Drug Administration (SFDA) of any anticipated at a minimum six months prior to any shortages as there are currently no rules requiring such notification from pharmaceutical businesses and importers. Likewise, there are no effective sanctions against authorized importers and distributors of pharmaceutical firms who disregard Saudi government restrictions. Additional causes that cause medicine shortages in Saudi Arabia include inadequate local pharmaceutical production, flawed supply chain management systems, poor profit margins for some essential critical pharmaceuticals, tight regulatory requirements for biological medical goods, and excessive reliance on medication imports.6\n\nThe synopsis for this study has been sent to the IEC (DMIHER (DU)/IEC/2023/1162) in the institute for ethical approval and is currently under consideration. Written consent will be taken from the participants who are participating in the study.\n\nThis study will be an observational study. The study will be conducted in Acharya Vinoba Bhave Rural Hospital. The duration of the study will be two years.\n\nThe sample size of the study is 354. The data of this study is going to be conducted from an outpatient pharmacy and self-questionnaires. Questions will be given to the participant for data analysis.\n\n\n\nWhere,\n\nZ21 – α/2 is the level of significance at 5% i.e. 95%\n\nConfidence interval = 1.96\n\nAlpha (α) = 0.05\n\nEstimate proportion (p) = 0.36 (48 out of 60 were the patient satisfying result as per reference article)\n\nEstimate error (d) = 0.05\n\nN = 354\n\nN = 354 subjects needed in the study\n\nIncluded in this study will be the Patient willing to give a consent form, Patient having a valid prescription. And the Patient is willing to comply with the study protocol. excluded from the study will be Inpatient Invalid prescriptions.\n\nSurvey and questionary development of a verified self-questionary and direct open-ended questionary for outpatients who will be coming to the outpatient pharmacy.\n\nThe primary data for this study will be collected through an observational approach. This will involve in-depth interviews with patients and pharmacy staff, as well as observations of the pharmacy and its operations. Data will also be collected through hospital records to track the availability of drugs over time.\n\nData will be analyzed by using simple descriptive statistics. Data will be presented in graphical, tables, charts, etc. Microsoft Excel will be used for data analysis.\n\nIt can lead to delayed treatment for patients seeking alternative medication. It can also lead to increased healthcare costs if patients seek alternative treatments that are more expensive or require additional medical care. The unavailability of drugs can also lead to frustration and anxiety for patients who need medication to manage their health conditions. It can also negatively impact the reputation of the hospital.\n\n\nDiscussion\n\nAn observational study carried out in Belgium, on 30 October 2015 found that currently, there are more frequent medicine shortages. Although numerous definitions of “drug shortages” are provided in legislation, by various organizations, authorities, and other initiatives, a thorough analysis of the issue is still required. To properly interpret national databases and the findings of scientific investigations and allow for international comparison, it is crucial to understand the fundamental definition of drug shortages. The goal is to establish the many components that should be considered in a standardized definition for drug shortages in the European Union (EU) and to identify the various circumstances in which drug shortages should be reported. The methods employed involved searching scientific databases and grey literature for definitions of drug shortages. Similar subjects were found, and organizations were approached to develop the definitions' supporting arguments. According to the findings, there are over 20 different definitions of medicine shortages. There is a discrepancy between the terminology used for reporting drug shortages and the definitions used in general. The definitions' elements—such as when a supply issue turns into a scarcity of drugs, whether they are permanent or temporary, their typology, and their duration—show both parallels and differences. There are four levels at which a supply issue becomes a shortage: (i) demand side; (ii) supply side; (iii) drug delivery; and (iv) drug availability. Definitions of drug shortages do not usually include permanent drug discontinuations. Some definitions solely consider medications needed to treat serious illnesses or medications for which there is no effective substitute. The observed time intervals ranged from one day to twenty days. The study's conclusion was to enable worldwide benchmarking, a standardized definition of drug shortages must be established, together with a list of the situations in which reporting drug shortages is preferred. A number of studies related to shortages in outpatient pharmacy were reported.7-11 This essay can be used as a reference to highlight all the various factors that should be considered while formulating a definition that will be used throughout the EU.3\n\nThe study will be published in an institutional-indexed journal.\n\nThe study is under process with 50% Completion.", "appendix": "Data availability\n\nNo data associated with this article.\n\n\nAcknowledgment\n\nI would like to acknowledge and thanks my guide and faculty of the Hospital Administration department who made this work possible.\n\n\nReferences\n\nShukar S, Zahoor F, Hayat K, et al.: Drug Shortage: Causes, Impact, and Mitigation Strategies. Front. Pharmacol. 2021; 12: 693426. Publisher Full Text\n\nDe Weerdt E, Simoens S, Casteels M, et al.: Toward a European definition for a drug shortage: a qualitative study. Front. Pharmacol. 2015; 6: 253. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDe Weerdt E, Simoens S, Hombroeckx L, et al.: Causes of drug shortages in the legal pharmaceutical framework. Regulatory toxicology and pharmacology: RTP. 2015; 71(2): 251–258. Publisher Full Text\n\nFox ER, Sweet BV, Jensen V: Drug shortages: a complex health care crisis. Mayo Clin. Proc. 2014; 89(3): 361–373. PubMed Abstract \| Publisher Full Text\n\nLipworth W, Kerridge I: Why drug shortages are an ethical issue. Australas Med. J. 2013; 6(11): 556–559. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlsheikh MY, Alzahrani MA, Alsharif NA, et al.: Community Pharmacy Staff Knowledge, Opinion and Practice toward Drug Shortages in Saudi Arabia. Saudi pharmaceutical journal: SPJ: the official publication of the Saudi Pharmaceutical Society. 2021; 29(12): 1383–1391. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGhonmode S, Shrivastava S, Kadaskar AR, et al.: Socioeconomic burden of orthodontic treatment: a systematic review. Medicine and Pharmacy Reports. 2023; 96: 154–163. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVyas PU, Khobragade DS, Mundhada DR, et al.: A Comparative Study of Concentration of Growth Factors in Lyophilized PRP with Fresh PRP at Different Storage Conditions. International Journal of Drug Delivery Technology. 2023; 13: 173–179. Publisher Full Text\n\nVyas PU, Khobragade DS, Mundhada DR, et al.: A Comparative Study of Concentration of Growth Factors in Lyophilized PRP with Fresh PRP at Different Storage Conditions. International Journal of Drug Delivery Technology. 2023; 13: 173–179. Publisher Full Text\n\nShete VS, Telange DR, Mahajan NM, et al.: Development of phospholipon®90H complex nanocarrier with enhanced oral bioavailability and anti-inflammatory potential of genistein. Drug Deliv. 2023; 30: 30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGabhane KB, Khan AM, Desmukh MP, et al.: Development of Dose Sipping Technology, a New Design Approach for Improving Drug Delivery of Acyclovir in Pediatric Medication. Indian Journal of Forensic Medicine and Toxicology. 2020; 14(4): 6589–6592. Publisher Full Text" }	[ { "id": "281983", "date": "24 Jun 2024", "name": "Trudy Huyghebaert", "expertise": [ "Reviewer Expertise quality improvement", "primary care", "evidence based 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\nThis is a very important topic and I think one of the key aspects of this is with regard to the moral and ethical obligation of drug companies to provide a consistent supply to their medication for patients, which may involve re-evaluating their just-in time approach to inventory as described.\nOverall, this is a very well written protocol. It is a study protocol and there are no results to evaluate Comments are added below for a few minor revisions: 1. Provide an expended definition of parallel trading\n2. The authors refer extensively to the United States system and wholesalers and then segway into Saudia Arabia system. If possible, please explain more about the correlation (or similarities) between the two systems.\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": "294888", "date": "09 Sep 2024", "name": "Unyime Israel Eshiet", "expertise": [], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study and well conceived. The authors have however not explicitly presented the specific objectives of the study. The proposed study designed is not clearly described to ascertain suitability. Also the method is not sufficiently described. Authors should kindly provide details of the data collection instrument(s). What are the possible limitations of the study?\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "12586", "date": "14 Oct 2024", "name": "Abhishek Bakare", "role": "Author Response", "response": "Thanks for your valuable time and suggestions. 1. We have added the objectives as suggested. 2. The methodology part has been updated and details about data collection instruments have been added. Also, the limitations of the study are added. Thanks for your kind perusal." } ] } ]	1	https://f1000research.com/articles/12-1287
https://f1000research.com/articles/12-947/v1	07 Aug 23	{ "type": "Review", "title": "Linkages between service recovery system and customer justice perceptions: A multi-level model of employee service recovery performance", "authors": [ "Abhishek S Rao", "Yogesh Pai P", "Lakshminarayanan Sethumadhavan", "Lakshminarayanan Sethumadhavan" ], "abstract": "Past research aimed at service recovery has focused on actions that are taken to retain customers, and the possibility of overcoming the mistakes of service delivery, though the multidimensional nature of the service recovery process has begun to move beyond the complaint handling process. In this paper, we identify the most important issues addressed in service recovery and present a framework for addressing them We used an extensive integrative review methodology. Between 1988 and 2017 the number of articles in these journals was kept between 26 and 30. The majority took a business perspective to study services recovery, while a minority took an inter-disciplinarity perspective. This research aims to investigate the relationship between the constructs in the JD-R Model and employee service recovery performance, and to adopt a multi-actor research design for more accurate measurement. The findings of this study are expected to provide valuable insights into the antecedents and consequences of service recovery performance in the context of the service recovery system This research contributes to the discourse on service recovery on several fronts. First, this research answers the call for building a multi-level model of relevant constructs to explain the service recovery performance of frontline employees in the hospitality sector. Thus, this research is expected to contribute to robust conclusions on the antecedents and consequences of employee service recovery performance nested within the unit-level construct, i.e., the service recovery system.", "keywords": [ "Service Recovery System", "Job Resources", "Job Demands", "Burnout", "Work Engagement", "Customer Justice Perception" ], "content": "Introduction\n\nService recovery constitutes ‘the actions taken by a service provider aimed at resolving failures’ (Smith, Karvan, & Markland, 2009). Retaining current customers who demonstrate dissatisfaction and the possibility of overcoming mistakes in service delivery are pointed out as the benefits of service recovery. Research on service recovery is partly grounded in the marketing literature that has examined the impact of service recovery practices on customer satisfaction. However, the multidimensional nature of the service recovery process has begun to go beyond the complaint-handling process and to study the structural dimensions of the service recovery system (Davidow, 2003) while distinguishing the structural dimensions from the mere ‘infrastructural dimension’ of the service recovery process. Consistent with this trend of the interdisciplinary approach adopted in the research discourse on service recovery, this research proposal brings together the variables in service operations and organizational behavior to empirically test a theorized multi-level model that aims to bridge the macro and micro perspectives of service recovery.\n\nIn this connection, Ryan & Ployhart (2003, p. 377) have argued that “a focus on the customer has become a major component of organizational strategies, regardless of whether the organization is in the service or manufacturing sector.” Therefore, frontline employees’ performance ensuring customer satisfaction and customer justice perceptions is crucial for restoring dissatisfied customers to a pre-service failure state. Accordingly, Liao (2007) argued that “frontline employees, placed at the organization-customer interface and directly responsible for the production and delivery of service, act as boundary spanners for the service company” (Bettencourt & Brown, 2003). Therefore, it is necessary to study the interaction between employees’ service recovery performance and resultant customer justice perceptions.\n\nOne of the goals of service firms is to build customer loyalty (Heskett et al., 1994). Against this backdrop, it is essential to note that the experience of service failures in the service process leads to customer defects (Hart et al., 1990). Prior research has argued that customer defections are influenced by adverse customer justice perceptions concerning firms’ service recovery processes. It is essential to study the customer justice perceptions as this construct is linked to several other variables such as relationship quality (Aurier & Siadou-Martin, 2007), repatronage intension (MartÃnez-Tur et al., 2001; Teo Thompson & Lim Vivien, 2001; Maxham & Netemeyer, 2002; Davidow, 2003; Witrz & Mattila, 2004; Kim, Kim & Kim, 2009; de Matos, Vieira & Veiga, 2012; Ro and Olson, 2014; Xu et al., 2014; Kim & Tang, 2016), satisfaction (Murray, 2006; del Río-Lanza, Vázquez-Casielles & Díaz-Martín, 2009; Nikbin & Hyun, 2014; Ro & Olson, 2014; Waqas, Ali & Khan, 2014; Paper et al., 2016), overall satisfaction (Vázquez-Casielles et al., 2010), loyalty (Kim & Kandampully, no date; Chebat and Slusarczyk, 2005; DeWitt, Nguyen & Marshall, 2008; Abbas, Abdullateef & Mokhtar, 2015), exit (Chebat & Slusarczyk, 2005), negative word of mouth (Teo Thompson & Lim Vivien, 2001; Ro & Olson, 2014), positive word of mouth (Kim, Kim & Kim, 2009; Choi & Choi, 2013), word of mouth (Maxham & Netemeyer, 2002; Witrz & Mattila, 2004), continuous usage (Zhou, 2015), switching intension (Nikbin et al., 2012), and trust (Kim, Kim & Kim, 2009). Interestingly, these customer justice perceptions are linked to an organization’s future business performance.\n\nThis overwhelming evidence that indicates the organizational importance of customer justice perceptions in the service recovery context has led to the increasing need to formalize the service recovery system that guides and trains frontline employees in their service recovery performance and places the systems and processes in this regard. Formalizing and institutionalizing the service recovery system assumes importance in the context of its role in determining customer justice perceptions influenced by employee service recovery performance. Therefore, this research proposal intends to examine the impact of the service recovery system, conceptualized and operationalized at the organizational level, on the perceptions of customer justice that arise in the service recovery process.\n\nIn this context, hospitality sector firms have begun to invest heavily in modifying frontline employees’ behavior (Stock et al., 2017). In this connection, the importance of the role of frontline employees arises due to the dyadic roles that they play with customers and the social exchange processes that they initiate, which determine the customer evaluations of employee performance, in particular, the company performance in general (Solomon et al., 1985), and the increase in repeat visits and repurchase intentions (Borucki & Burke, 1999).\n\nIn this connection, the literature on service recovery mentions the service recovery paradox (Michel et al., 2009) as a potent tool to take customers back to a state of customer delight in such a manner that the satisfaction that they perceive regarding the service provided would be even higher than the satisfaction that they were experiencing prior to service failure. Therefore, the extent of efficacy demonstrated by a service organization and its frontline employees in the service recovery process is significant. In this context, frontline employees significantly lead customers to satisfaction, delight, etc. (Rod & Ashill, 2009). Accordingly, employee recovery performance affects customer justice perceptions, a theoretical relationship that remains empirically unexplored in the hospitality sector.\n\nResearch on the antecedents of employee recovery performance, which explains the interactive effects of the JD-R Model on employee service recovery performance, is scarce. However, the theoretical premises of employee recovery performance are well articulated, which can be seen in the relationship between burnout and employee recovery performance and between work engagement and employee service recovery performance. For example, scholarly research (Kahn, 1992; Britt, 1999; Harter et al., 2002; Maslach et al., 1997; Macey & Schneider, 2008) has identified several working conditions as the antecedents of burnout and work engagement. Among these, a few examples of antecedents are job clarity, job control, job relevance, work expectations, supportiveness of supervisors and coworkers, opportunities for growth and development, job demands, rewards and recognition, a community of support, and fairness. The similarity in all these predictors lies in the factors related to working conditions (Crawford et al., 2010). This similarity is captured in the JD-R Model in the two categories of antecedents: job resources and job demands.\n\nThe JD-R model extends the demand-control model (DCM) and effort-reward imbalance (ERI) model. Even as the JD-R Model considers the elements of the DCM and ERI Models, it also adds specific elements of job resources and demands. While the DCM and ERI models consider only a few specific factors, such as job demand and job control in the DCM model and effort and reward in the ERI model, the JD-R model considers a whole range of factors that can be encompassed under both job resources and job demands.\n\nAlthough early research on the relationship between the JD-R Model and the consequences of burnout and work engagement conceptualized only job resources as the antecedent of work engagement and job demands as the antecedent of burnout, later research identified the interaction among job resources, job demands, work engagement, and burnout. However, there were inconsistencies in the empirical findings when this early conceptualization was subjected to empirical testing. Therefore, researchers later found the reasons for these inconsistencies by proposing a differentiated job demand perspective. Accordingly, they argued that job demands consist of ‘challenge stressors’ and ‘hindrance stressors,’ among which challenge stressors increase both burnout and work engagement, whereas ‘hindrance stressors’ increase only burnout. Furthermore, job resources moderated the presence of job demands. Therefore, the higher the level of job resources, the more interactive the effect of job demands on burnout and work engagement. However, this differentiated perspective on job demands has not been integrated into the research discourse examining the burnout and work engagement levels of frontline employees in the hospitality sector, nor has its effect on employee recovery performance.\n\nScholarly research on service performance has examined the organization-level factors such as ‘climate’ constructs (Schneider, 1990) that lead to customer satisfaction or the individual-level factors (Frei & McDaniel, 1998) to account for individual differences. However, the exclusive concentration at the individual- or unit-level analysis would lead to either missing situational factors (Kozlowski & Klein, 2000) or not accounting for individual differences (Liao & Chuang, 2004). There are three essential issues in this context. First, the extent of the influence of factors at a given level after considering the factors at a different level. Second, cross-level interactions among variables of interest are expected to impact endogenous variables. Third, there is a possibility of misspecification, as a result of which spurious relationships are attempted. The impact of a variable at a given level is mistakenly interpreted as exercising its impact on the variable at another level (Kozlowski & Klein, 2000). Therefore, it is necessary to examine organization-level variables that impact individual-level variables, such as employee recovery performance and customer justice perceptions. Second, it is necessary to understand the cross-level interactions by adopting either a top-down or bottom-up process, the impact of organization-level or group-level variables on individual-level variables, or the impact of individual-level variables on either group-level or organization-level variables. Thus, this understanding of the impact of variables at different levels can only be understood by bridging the macro and micro perspectives (Kozlowski & Klein, 2000). This study endeavors to conduct an integrated analysis of micro and macro perspectives of the service recovery process in the hospitality sector by investigating the impact of the service recovery system, which is at the organizational level, on employee recovery performance as well as its antecedents and consequences at the individual level of analysis.\n\nInvestigating the antecedents and effects of employee service recovery performance requires using multilevel theory. A single-level analysis does not capture the interaction between macro- and micro-level constructs. Consequently, the entire gamut of a phenomenon cannot be fully captured. Research discourse on multilevel modeling has consistently argued that a given social phenomenon will likely be nested within higher-level constructs. Therefore, multilevel theory explains the proposed relationships among constructs that may belong to the macro and micro perspectives.\n\n\nMethods\n\nWe used an extensive integrative review methodology. Integrative reviews comprise research that uses various approaches to achieve various goals, including concept definition, theory review, evidence review, and methodological issue analysis (Broome, 1993). The goal of the inclusive sampling frame was to provide a thorough understanding of the ideas, theories, and problems significant to service recovery. There were three steps to the complete evaluation procedure. First, we conducted a literature search of the literature for publications published in the Web of Knowledge database using the terms “service recovery,” “complaint handling,” and “complaint management.” In order to find further research on service recovery, we also conducted issue-by-issue searches of the following service journals: Journal of Service Research, Journal of Business Research, Total Quality Management and Business Excellence, Journal of Hospitality and Tourism Research, and many more. Then, using an ancestry technique, we looked for studies’ references that we had previously recognized as being relevant to the present Study. For review, this method produced more than 300 papers. After that, we reviewed the literature. An article was considered appropriate for inclusion if it specifically examined a firm’s response to a customer complaint, excluding articles that only examined customer reactions to service failures or why customers complain.\n\nAdditionally, it must have been published in an academic journal undergoing peer review, excluding conference proceedings. First, we assigned each article a tick (if both criteria were met) or a question mark (if we were not sure) or left it unmarked (if neither condition nor both conditions were met). Then, we read every item with a question mark next to it, assessed its relevance and educational value, and checked or unchecked it. Finally, we classified papers under Business Management & Accounting and Marketing as either using an interdisciplinary approach or only depending on one of the two fields looking at service recovery. Between 1988 and 2017, 120 articles from 26 different publications were kept. The majority of papers (75.3%) took a marketing perspective to study service recovery; only a minority took a human resource management (11.1%), operations management (9.4%), or inter-disciplinary perspective (4.2%). The actual literature study was the last step in our process. First, based on the level of analysis (firm, employee, or customer) employed to address service reimbursement difficulties, we developed an overall classification scheme. Then, we grouped the concepts and study findings into the classification scheme. Third, we found connections between ideas related to one level of analysis or several layers of analysis, and we visually demonstrated their logical chain of relationships. Finally, we analyzed the gaps in the literature and identified the research opportunities for future studies. Our comprehensive approach enabled us to gain a deep understanding of the service reimbursement difficulties from various perspectives and identify the key issues that need to be addressed. Moreover, our findings can provide valuable insights for policymakers, resatuarant providers, and researchers to improve the service recovery process and enhance the quality of service for customers. Finally, we conducted a comprehensive literature review to validate and enrich our conceptual map. Overall, our process allowed us to gain a deeper understanding of the complexities of service recovery difficulties and provided a framework for future research in this area.\n\nAccordingly, this Study argues that customer justice perceptions, captured at the customer or individual level of analysis, are influenced by employee service recovery performance. In turn, the construct of employee service recovery performance, captured at the employee or individual level of analysis, is influenced by the impact of job demands and job resources exercised through the mediated effects of burnout and work engagement. Furthermore, the individual-level constructs of job resources and job demands are influenced by the unit-level construct of the service recovery system. This relationship among constructs requires capturing the macro-level construct—the service recovery system’s impact on job resources and job demands—before assessing their impact on employee burnout and work engagement.\n\nFurthermore, the theory of situational strength argues that a given construct, which is initially at the individual level, is likely to exercise its influence on its predictor variables only after its aggregated impact is considered. Prior research on employees’ service recovery performance has led to this advocacy. The implicit reason for advocating the aggregated effect, not the individual effect, of employee service recovery performance is that customers’ service recovery experience will likely result from the service provided by several frontline employees. Therefore, customer evaluation of their experience of the service recovery behavior of frontline employees is the product of the service recovery behavior demonstrated by a given unit’s or restaurant’s frontline employees. Accordingly, the appropriate way to capture employee service recovery performance is to capture it at the unit or restaurant-level instead of at the individual level. In other words, although data on employee service recovery performance is collected at the individual level, it needs to be aggregated at the unit level.\n\nThe impact of the service recovery system on job resources and job demands, which integrates macro and micro perspectives, is captured by adopting a top-down process. The construct data relating to employee service recovery performance would be aggregated from the individual to the unit or restaurant level by adopting the bottom-up process. Accordingly, the impact of the restaurant-level construct, i.e., unit-level employee service recovery performance, on customer justice perceptions captured at the individual level will be examined.\n\nThe following conceptual framework (Figure 1) presents the proposed relationships of the multi-level model:\n\nService recovery system\n\nMany prior studies have used customer data to study aspects of the service recovery process (Smith, Karwan, & Markland, 2009), even as service providers handle organizations that provide service and service recovery problems. Therefore, the construction of a service recovery system looks at the issue of service recovery from the standpoint of service provider entities.\n\nFocal construct. Therefore, the construct of a service recovery system is defined as the structural dimension of the service recovery system employed by a service organization in its service recovery process. Process formality, decentralization, comprehensiveness, human intensity, system intensity, accessibility, and influence are the seven dimensions of a service recovery system.\n\nFormality: Process formality is ‘the degree to which service recovery is controlled by explicit rules, procedures, and norms that dictate recovery activities’ (Papke-Shields et al., 2002; Pugh et al., 1969).\n\nDecentralization: While the concept of centralization is defined as the ‘locus of authority or devolution of responsibilities for handling recovery activities’ in the literature on organizational design and strategy (Pugh et al., 1969; Segars & Grover, 1998), the concept of decentralization is essentially interpreted in terms of empowerment that gives employees the freedom to overcome mistakes related to the service delivery process (Michel et al., 2009).\n\nComprehensiveness: The dimension of comprehensiveness is defined as ‘the extent to which attempts are made to be exhaustive or inclusive in considering all potential recovery activities once a failure has occurred’ (Smith, Karwan, & Markland, 2009), which considers several options for taking an optimal action (Papke-Shields et al., 2002) and an extensive range of solutions (McColl-Kennedy & Sparks, 2003).\n\nHuman intensity: The dimension of human intensity is defined as ‘the magnitude of resources committed to recovery as evidenced by the provision for employee training as well as the extent of employee evaluations’ (Smith, Karwan, & Markland, 2009; Segars & Grover, 1998; Papke-Shields et al., 2002). This dimension captures the resources needed to train employees in the service recovery process (Smith, Karwan, & Markland, 2009).\n\nSystem intensity: System intensity is defined as ‘the magnitude of resources committed to tracking and monitoring service failures and recovery efforts.’ (Smith, Karwan, & Markland, 2009). This is especially helpful in avoiding future mistakes (Tax et al., 1998).\n\nAccessibility: It is defined as ‘the provision for capturing the voice of the customer when failures occur.’ (Smith, Karwan, & Markland, 2009). This gives customers opportunities for feedback on the quality of service they have received (Colgate & Norris, 2001).\n\nInfluence: It is defined as ‘the ability of the system to adapt depending upon the situation and “position” of the customer’ (Smith, Karwan, & Markland, 2009). This Study examines the service recovery process from the customer’s perspective. Therefore, this dimension captures the degree to which the customer exercises control over the service recovery process and service recovery system (Tax et al., 1998).\n\nEmployee service recovery performance\n\nFocal construct. Employee service recovery performance is defined as ‘the behaviors in which customer service employees who directly handle customer complaints engage in the recovery of customer satisfaction and loyalty after service failures’ (Liao, 2007). Making an apology, problem-solving, demonstrating courteous behavior, providing an explanation, and promptly handling complaints are the five dimensions of this construct.\n\nCustomer justice perceptions\n\nFocal construct. Customer justice perceptions constitute four dimensions: distributive, procedural, informational, and interpersonal. Distributive justice refers to ‘whether customers receive a fair economic or social outcome after complaining about a service problem’ (Liao, 2007). Procedural justice refers to ‘the justice meted out regarding the policies and procedures used to resolve the complaints.’ Informational justice refers to ‘the adequacy of information and communication provided.’ Interpersonal justice is the sensitivity and respect employees display in handling complaints.\n\nJob demands\n\nFocal construct. Job demands are defined as ‘those physical, social, or organizational aspects of the job that require sustained physical or mental effort and are therefore associated with certain psychological costs and include aspects such as workload, time pressure, and difficult work environments’ (Crawford et al., 2010; p. 835).\n\nJob resources\n\nFocal Construct. Job resources are defined as ‘those aspects of the job that are functional in achieving work goals, stimulating personal growth and development, and reducing job demands, and they are associated with physiological and psychological costs and include aspects such as job control, opportunities for development, participation in decision making, task variety, feedback, and social support’ (Crawford et al., 2010; p. 838–836).\n\nIn the context of employee recovery performance, the relevant job resources are training, rewards, supportive management, and service technology support (Rod & Ashill, 2009). These job resources are relevant in service management (Babakus et al., 2003; Singh, 2000). Job demands are conceptualized as either role stressors (Ashill & Rod, 2011) or social stressors (Dormann & Zapf, 2004). If the construct of job demands is conceptualized as a role stressor, its dimensions would be role conflict, role overload, and role conflict (Rod & Ashill, 2009). If conceptualized as a social stressor, its dimensions would be customers’ intentions to harm employees, disproportionate customer expectations, ambiguous customer expectations, and hostility and undesirable behavior demonstrated by customers (Choi et al., 2014).\n\nBurnout has been conceptualized (Maslach & Jackson, 1981) as consisting of emotional exhaustion, depersonalization, and a reduced sense of personal accomplishment. When employees experience emotional exhaustion, they feel they have no more energy to live up to their employers’ demands or meet clients’ expectations. When employees experience a sense of depersonalization, they treat people as objects. Finally, when they experience a sense of inefficacy, they experience a reduced sense of personal accomplishment\n\nKahn (1992) conceptualized engagement as a function of individual characteristics, work context, and factors beyond the work context. Accordingly, he defined ‘personal engagement’ as ‘employing or expressing oneself physically, cognitively, and emotionally during work role performance.’ (Kahn, 1992; Simpson, 2009). However, researchers later conceptualized engagement to include work-related factors alone (Simpson, 2009). Accordingly, burnout and work engagement are conceptualized as two polar ends of a continuum (Maslach et al., 1997). Three dimensions were used to measure burnout (work engagement): exhaustion (energy), cynicism (involvement), and inefficiency (efficacy). Accordingly, this conceptualization of burnout and work engagement presupposes that employees are at any given point in this continuum at any given time. In other words, if an employee experiences emotional exhaustion (energy), he or she will also experience burnout (engagement). However, Schaufeli et al. (2002) differed in this conceptualization and argued that when an employee demonstrates low burnout, it cannot be understood as equivalent to high engagement and vice versa. They attributed this to the distinct nature of the two constructs. Therefore, they defined work engagement as a positive, fulfilling, work-related state of mind characterized by vigor, dedication, and absorption (Schaufeli et al., 2002). Accordingly, they conceptualized work engagement comprising three dimensions: vigor, dedication, and absorption Demerouti et al. (2001). While vigor and dedication capture emotional energy and involvement, the two dimensions conceptualized by Maslach et al. (1997), the dimension of absorption is a distinct dimension conceptualized by Demerouti et al. (2001).\n\n\"What effect does the employee service recovery performance exercise have on customer justice perceptions if the employee service recovery performance is within the context of the JD-R Model and job demands and resources are nested within the context of the service recovery system?\" This is a critical research problem addressed by this research.\n\nReview of literature\n\nThe service recovery process aims to return customers to their state before service failure (Mostafa et al., 2015). Therefore, service recovery is the ‘organizational response to service failure’. Further, service failure is defined as ‘a service performance that falls below a customer’s expectations’ (Hoffman & Bateson, 1997; Silber et al., 2009). Though there are diverse conceptualizations of the construct of employee recovery performance, such as ‘the effectiveness of employees in satisfying complaining customers’ (Vaerenbergh, 2016; p. 15) or ‘frontline employees’ perceptions of their abilities and actions to resolve service failures’, prior research has also identified six types of responses that organizations provide to execute service recovery (Liao, 2007), viz., ‘tendering an apology, problem-solving, courteous behavior, providing an explanation, prompt handling, and offering extra compensation.’ However, caution is not misplaced in this context. Prior research has shown that customers are more concerned with outcome failures, such as the non-availability of service than process failures, that is, the absence of attention while providing service (Smith et al., 1999). Further, customer dissatisfaction will override service recovery strategies such as apologizing and providing compensation.\n\nResearch on service recovery has attempted to address the issue of attaining the efficacy of the service recovery process and the resultant effect on customer-related variables by working on individual employees. In other words, the literature on service recovery has predominantly relied on individual analyses. Hospitality research on service recovery has predominantly applied a single level of analysis to understand the service management phenomenon (Wong, 2016). However, as pointed out by Wong (2016), these studies “face a common research limitation in that they use data from a single level (mostly customers or employees) to infer social phenomena that exist at multiple levels.” Although parsimony is the specific advantage of single-level analysis, it cannot account for a multilevel understanding of a social phenomenon (Aguinis et al., 2011). In this connection, it is argued by scholars that the higher-level variables exert either direct or moderating effects on the lower-level variables (Kozlowski & Klein, 2000). A given social phenomenon is embedded at multiple levels (Wong, 2016). The theoretical underpinnings of this argument are provided by theories such as environment-fit theory and systems theory (Wong, 2016), which argue that individuals are essentially social actors, and therefore, their behavior is nested within multiple levels of hierarchy in a social or organizational setting. Therefore, bridging a social phenomenon’s macro- and micro-perspectives gives rise to a critical understanding of this phenomenon. Therefore, this requires a multilevel design to address the issue of building relationships among constructs at different analysis levels. This avoids the probability of postulating the confounding effects of organization-level variables on the group- or individual-level variables or vice versa. Accordingly, this proposed research endeavor seeks to bridge this methodological gap in the research discourse on service recovery performance by conceptualizing and testing a multilevel model in which the effect of the macro-level construct of the service recovery system is tested on employee-level constructs of employee service recovery performance and its antecedents, that is, job resources and job demands, and the effect of the organization-level construct of the service recovery system and the individual-level construct of employee recovery performance on the customer-level construct of customer justice perceptions.\n\nIn this connection, the JD-R Model argues that the constructs of job resources and job demands can explain organizationally desirable employee-level outcomes through the mediating effects of employee burnout and work engagement. In this context, it is worth noting that job resources and demands are nested within the unit- or organization-level constructs. In this regard, the multilevel relationship, which involves a top-down process between the service recovery system and job resources and job demands, has been mooted in prior research. However, the hospitality sector has not empirically tested and validated the proposed relationship between the service recovery system, job resources, and job demands.\n\nService recovery strategies operationalized in the construct of employee service recovery performance are essential because customers view them in the cost-benefit equation resulting from registering a complaint. As cost-benefit analysis is the basic premise of justice theory (Del Rio-Lanza et al., 2009), employees’ actions to mitigate service failures will be subjected to a process of evaluation of the justice meted out. Scholars have argued that customer justice perceptions determine service recovery (Liao, 2007).\n\nThe importance of customer justice perceptions can be understood from the multiple needs perspective of justice (Cropanzano et al., 2001), which argues that justice perceptions should be situated against the satisfaction of three human needs: instrumental, relational, and moral. While instrumental needs pertain to controlling the environment and accessing long-term benefits, relational needs refer to human needs for self-regard and social status, and moral virtue needs are those human needs that lead to aspiration for ‘human dignity and a virtuous life’ (Cropanzano et al., 2001; p. 175). Any experience of injustice will threaten these needs, and the individuals will adopt ‘defensive behaviors’ (Liao, 2007; p. 476). Therefore, the efficacy of employee recovery performance consists of ensuring the satisfaction of these human needs so that the negative affect and resultant defensive behaviors do not manifest in customers.\n\nIt is essential to note those mentioned above, i.e., distributive justice, procedural justice, informational justice, and interactional justice (Liao, 2007). Distributive justice is about providing the ‘just share’ (Cropanzano, 2001; p. 37) regarding the output-input ratio of an employee’s performance-reward relationship. Equity theory explains the processes and consequences of inequity in an effort-reward relationship. It is interesting to note the disproportionate rewards concerning efforts that result in dissatisfaction and the disproportionate efforts and performance caused by over-rewarded efforts. This is interesting in the context of employee recovery performance, as it implies that customers are highly dissatisfied if they experience inequity in their treatment by employees.\n\nFurther, employee recovery performance is related to customer perceptions of procedural justice (Thibaut & Walker, 1975). Customers are likely to be offended if they feel that policies and procedures are not correctly followed, even as they register their complaints in the event of a service failure. Furthermore, customers would get offended if they did not provide sufficient information and were not kept in the communication loop, even if their complaints were handled. Furthermore, employee recovery performance is also linked with interactional or interpersonal justice perceptions that emanate from the treatment meted out by employees to customers in the context of employee recovery performance (Greenberg, 1993).\n\nIn this connection, the cognition-affect-attitude theory also provides a theoretical explanation for conceptualizing the relationship between employee recovery performance and customer justice perceptions. To substantiate this argument, scholars have argued that while the idea of perceived justice is the result of the cognitive evaluation (Schoefer & Diamantopoulos, 2008) of employee recovery performance, satisfaction with service recovery is interpreted as the ‘affective response’ (Liao, 2007) of customers towards employee recovery performance (Davidow, 2000), and the positive attitude of customers that they develop towards the organization, for example, towards its service recovery system, resulting from employee recovery performance is considered to be the attitudinal aspect of customer response. Therefore, this theory provides conceptual underpinnings that explain the positive association between employee recovery performance and customer justice perceptions.\n\nIt is important to note that these types of customer justice perceptions are not isolated in nature. All of them are the dimensions of a single construct, customer justice perceptions, whose essential underlying theme is a sense of fairness (Colquitt et al., 2013). Therefore, employee recovery performance will be successful in ensuring the emergence of a sense of fairness among customers if they feel that their complaints and grievances are appropriately addressed in terms of correction of service failure and the reversal of service failure; fair procedures are followed in addressing the complaints; policies and procedures are put in place and duly communicated; and employees demonstrate fairness and dignity in their relationship with them.\n\nScholarly research on customer justice perceptions investigated the effect of this construct on several other outcome variables when those outcome variables were used as mediators in their respective models. Those variables which were posited to be the outcomes of customer justice perceptions, though as mediators, are the constructs such as service evaluation (Aurier & Siadou-Martin, 2007), emotions (Kim & Tang, 2016), negative emotions (del Río-Lanza, Vázquez-Casielles & Díaz-Martín, 2009; Nikbin & Hyun, 2014; Kim & Tang, 2016), positive emotions (Chebat & Slusarczyk, 2005; DeWitt, Nguyen & Marshall, 2008; Kim & Tang, 2016), satisfaction (MartÃnez-Tur et al., 2001; Teo Thompson & Lim Vivien, 2001; Maxham & Netemeyer, 2002; Davidow, 2003; Witrz & Mattila, 2004; Kim, Kim & Kim, 2009; Vázquez-Casielles et al., 2010; de Matos, Vieira & Veiga, 2012; Xu et al., 2014; Abbas, Abdullateef & Mokhtar, 2015; Zhou, 2015), credibility (Vázquez-Casielles et al., 2010), benevolence (Vázquez-Casielles et al., 2010), attitude towards complaining (Ro & Olson, 2014), service failure attributes (Witrz & Mattila, 2004), word of mouth valence (Davidow, 2003), word of mouth dissemination (Davidow, 2003), trust (Kim & Kandampully, no date), commitment (Kim & Kandampully, no date), customer affection (Choi & Choi, 2013), customer loyalty (Choi & Choi, 2013), privacy concern (Zhou, 2015), flow (Zhou, 2015), overall satisfaction (Maxham & Netemeyer, 2002), satisfaction with recovery (Liao, 2007; Mostafa et al., 2015), and recovery disconfirmation (McCollough, Berry & Yadav, 2000). All of these outcome variables highlight the importance of studying customer justice perceptions. Therefore, this Study posits customer justice perceptions as the outcome variable of the model that it intends to investigate.\n\nPrior research on customer justice perceptions has investigated the effect of constructs such as company characteristics (Homburg, Fürst & Koschate, 2009), over-reward (Söderlund & Colliander, 2015), type of failure (Masnita Siagian & Triyowati, 2015), locus of attribution (Masnita Siagian & Triyowati, 2015), and customer characteristics (Homburg, Fürst & Koschate, 2009) in their role as antecedents of customer justice perceptions. Studies that have examined the role of employee service recovery performance are scarce, except for the Study by Siagian and Triyowati (2015), who conceptualized employee service recovery performance as ‘recovery strategies.’ Therefore, this research seeks to bridge this gap by positing customer justice perceptions as the outcome variable of employee service recovery performance in the hospitality sector.\n\nAn examination of prior research on employee service recovery performance reveals that prior studies have investigated its effects on outcome variables, such as satisfaction (McCollough, Berry, & Yadav, 2000; Wong, 2004; Roschk & Kaiser, 2013); service assessment (Wong, 2004); repurchase intention (Liao, 2007); corporate image (Mostafa et al., 2015); and continuity (Selnes, 1998). However, studies on the effects of employee recovery performance on customer justice perceptions need to be conducted. This Study seeks to bridge this research gap.\n\nResearch discourse on employee recovery performance has examined the impact of its antecedents, such as service failure severity (Weun et al., 2006), formality (Smith, Karwan, & Markland, 2009), knowledge sourcing behavior (van der Heijden et al., 2013), disproportionate customer expectations (Choi et al., 2014), job demand (Rod & Ashill, 2009), ideas for improvement (van der Heijden et al., 2013), and emotional exhaustion (Rod & Ashill, 2009; Choi et al., 2014). Service failure severity, knowledge-sourcing behavior, and ideas for improvement pertain to frontline employees’ cognitive and behavioral aspects. However, disproportionate customer expectations and job demand belong to those factors that are external to frontline employees. Such categorization of antecedent constructs will open up a holistic understanding of the antecedents of employee recovery performance. Therefore, there is a gap in research on the possible effects of job resources and demands as antecedents of employee service recovery performance.\n\nThe DCM, ERI, and JD-R models theorize the relationships among job resources, job demands, burnout, and work engagement. The JD-R Model is essentially a model of employee well-being. Researchers have proposed this model to overcome the limitations of two earlier models of employee well-being: the DCM (Karasek, 1998) and the ERI model (Siegrist, 1996).\n\nThe DCM argued that employees would experience stress and a reduced sense of well-being if they felt that their control over their jobs was less than the demands of their jobs. Although this model has been predominantly applied to explain job stress, the related stream of research in this area has two exciting implications (Bakker & Demerouti, 2007). First, strong support for the strain hypothesis results from an imbalance between job demands and control. Second, there is inconsistency regarding the buffering hypothesis regarding the moderating effect of job control exercises on the relationship between job demands and stress.\n\nThe ERI Model sought to explain the phenomenon of employee well-being from the perspective of an effort-reward imbalance. If high job efforts result from excessive job demands and the rewards are relatively low, it would result in a higher degree of ‘arousal,’ a physiological phenomenon, and the resulting stress. This is consistent with the equity theory’s low outcome/high input type of inequity. However, this model argues that the personal commitment of employees to their work and the organization, which results from employees’ desire to be valued by ‘significant others and the sense of esteem that they experience in this process, is expected to moderate the relationship between perceived inequity that results from effort-reward imbalance and stress.\n\nThe strengths and weaknesses of the DCM and ERI models are characterized. For example, the strength of both models is their simplicity, as they explain job stress as a function of only a few constructs. As has already been discussed, while the DCM Model employs two constructs (i.e., job demands and job control), the ERI Model uses two constructs (i.e., effort and reward) to explain the emergence of job stress and, consequently, the reduction in employee well-being. However, scholars argue that the simplicity of models constitutes their weakness (Bakker & Demerouti, 2007). This is because it is not adequate to account for only two factors to explain the phenomenon of job stress: the consequent burnout and the engagement level. Therefore, researchers have listed several factors that are part of job resources and demands. Furthermore, these models do not incorporate factors such as autonomy and task characteristics.\n\nThe JD-R model incorporates more aspects of job resources and demands than the DCM and ERI models. Accordingly, the construct of job resources is defined as “those physical, psychological, social, or organizational aspects of the job that are either/or functional in achieving work goals; reduce job demands and the associated physiological and psychological costs; and thus stimulate personal growth, learning, and development” (Bakker & Demerouti, 2007; p. 312). This conceptualization of job resources is consistent with the job characteristics model (Hackman & Oldham, 1980) and conservation of resources theory (Hobfoll, 2001). The conceptualization of job resources aligns with the job characteristics model because it incorporates the conceptualization of job resources in terms of task characteristics, such as skill variety, task identity, task significance, autonomy, and performance feedback. Further, the conceptualization of job resources is consistent with the conservation of resources theory, as different types of job resources are viewed as fundamental to maintaining resources and achieving new and valued resources (Bakker & Demerouti, 2007; p. 312).\n\nThe effect of job demands on employee recovery performance (Rod & Ashill, 2009; Ashill & Rod, 2011) has been empirically demonstrated, in addition to its effects on other constructs such as turnover intention (Karatepe & Sokmen, 2006; Ashill & Rod, 2011), job satisfaction (Karatepe & Sokmen, 2006; Rod, Ashill, and Carruthers, 2008), organizational commitment (Rod et al., 2008), organizational outcomes (Bakker & Demerouti, 2007), and job performance (Babakus, Yavas & Ashill, 2009). However, the effect of job demands on employee recovery performance is not necessarily construed as direct in all the studies. Many studies have demonstrated the mediating effect of job demands on employee recovery performance, as demonstrated by studies that have shown mediating effects of constructs such as emotional exhaustion (Babakus, Yavas, & Ashill, 2009; Rod & Ashill, 2009; Ashill & Rod, 2011), depersonalization (Ashill & Rod, 2011), job satisfaction (Ashill & Rod, 2011), leadership (Schaufeli, 2015), employee service recovery performance (Karatepe, 2006; Karatepe & Sokmen, 2006; Rod, Ashill & Carruthers, 2008), and strain (Bakker & Demerouti, 2007). The implication of studies investigating the mediating effects of job demands on employee recovery performance is that job demands, an external variable, have a detrimental effect on the ‘internal’ variables, which would impact employee recovery performance.\n\nPrior research has shown that the construct of job resources moderates the negative effects of job demands on ‘internal’ emotional and cognitive states. Further, the construct of job resources is proposed to create a positive ‘emotional state.’ Therefore, the construct of job resources is conceptualized as the exact opposite of job demands in terms of its impact on frontline employees. In this regard, prior research has investigated the effect of job resources on several dependent variables such as FLE service recovery (Babakus et al., 2003; Rod & Ashill, 2009), employee outcomes (Schaufeli, 2015), peer contacts (Hakanen, Bakker & Demerouti, 2006), engagement (Crawford, Lepine & Rich, 2010), organizational outcomes (Crawford, Lepine & Rich, 2010), turnover intention (Babakus, Yavas & Ashill, 2009), and organizational performance (Bakker & Demerouti, 2008). Many studies have conceptualized the impact of job resources on the respective dependent variables by conceptualizing the mediating effects of depersonalization (Rod & Ashill, 2009), burnout (Babakus, Yavas & Ashill, 2009; Schaufeli, 2015), affective commitment (Babakus et al., 2003), job satisfaction (Babakus et al., 2003), motivation (Bakker & Demerouti, 2007), and work engagement (Bakker & Demerouti, 2008). We carefully observed these mediating variables and realized that all of these mediating constructs were emotional or cognitive states. In other words, they are all ‘internal’ variables. Therefore, job resources and demands are conceptualized to lead to emotional states such as work engagement and burnout.\n\nAgainst the backdrop of the above-discussed relationships between job demands and employee recovery performance and between job resources and employee recovery performance, the following research issues emerge:\n\nThe direct effect of job resources on employee service recovery performance\n\nDirect effect of job demands on employee service recovery performance\n\nInteractive effects of low job resources and high job demands on employee service recovery performance\n\nInteractive effects of high job resources and low job demands on employee service recovery performance\n\nEffects on employee service recovery performance if both job resources and job demands are either high or low\n\nThe above issues can be represented in a 2 × 2 matrix that captures the abovementioned research (Figure 2).\n\nThe JD-R model argues that two processes set themselves in motion as consequences of job resources and demands (Schaufeli, Bakker, & Rhenen, 2009). These are the strain and motivation processes (Bakker & Demerouti, 2007). The compensatory regulation-control model (Hockey, 1997) argues that increased job demands lead to a corresponding increase in employee effort to meet these demands, which would entail physical and psychological costs, resulting in burnout. Contrary to the straining process, self-determination theory argues that job resources contribute to fulfilling the human needs of autonomy, relatedness, and competence (Ryan & Deci, 2000), which would thus initiate the motivational process. The rationale for the motivational potential of job resources is explained by the effort-recovery approach, which argues that employees increase their efforts if they perceive that there are enough job resources to enable them to succeed in reaching their work-related goals (Meijman & Mulder, 1998).\n\nResearch on the consequences of job resources and job demands (Bakker & Demerouti, 2007) has argued that these two constructs positively impact employee performance through the mediating processes of burnout and work engagement. This phenomenon is operationalized by theories such as the conservation of resources theory (Hobfoll, 2011). This theory is widely used to explain the phenomenon of work engagement among employees (Stock, Jong, & Zacharias, 2017). This theory is woven around the acquisition, maintenance, and fostering of resources that are defined as “those objects, personal characteristics, conditions, or energies that an individual values or that serve as a means for the attainment of these objects, personal characteristics, conditions, or energies” (Hobfoll, 2011; p. 516). The arguments of the theory, as applicable to the job resources-work engagement relationship, can be articulated as follows: First, the attempt to prevent the probable loss of job resources would create “emotional labor” and thus lead to the creation of emotional energy among employees.\n\nConsequently, the role of employees’ self-identification with work (Chen et al., 2013) comes into being. In other words, the emotional energy of employees created through their ‘emotional labor’ leads to role identity and consequent work engagement among employees (Rich et al., 2010). This proposition is also articulated in the frontline employees’ context (Estrada, Isen, & Young, 1994).\n\nPrior research has proved that an antecedent-consequent relationship exists between job demands and emotional exhaustion. Among these two constructs, job demands are ‘external’ to frontline employees, whereas emotional exhaustion is ‘internal.’ Research on job demands and their effects has argued that they directly affect employee burnout. The ‘challenge stressors’ increase burnout among frontline employees with high achievement orientation. Further, ‘hindrance stressors’ increase emotional exhaustion just as ‘challenge stressors’ increase emotional exhaustion. Therefore, a higher intensity of all dimensions of job demands (i.e., workload, physical demands, emotional demands, and work-home interference) is expected to increase burnout among frontline employees.\n\nThe JD-R Model states that one can situate work engagement and burnout within the framework of two general categories: job resources and job demands, regardless of differences in organizational or occupational characteristics (Crawford, LePine, & Rich, 2010). The JD-R Model has overwhelmingly influenced the literature on work engagement and burnout, as this theoretical perspective is the dominant narrative in research discourse on work engagement and burnout (Bakker & Demerouti, 2007). In this context, the JD-R Model states that job resources influence the extent of work engagement, and job demands influence the degree of burnout.\n\nThe research discourse on the much-hypothesized relationships between job demands and burnout and between job resources and work engagement is not as straightforward as it seems. In this regard, prior research (Crawford et al., 2010) has shown that job demands should be differentiated regarding challenge and hindrance stressors, even though it is well known that job demands initiate stress responses among employees that would eventually lead to burnout. Although both stressors lead to burnout, the differentiated job demands perspective argues that challenge stressors initiate positive emotions such as excitement, exhilaration, and eagerness, which lead to greater work engagement, as the source of challenge stressors would initiate perceptions of growth and learning. This is also consistent with the job characteristics model, which argues that challenging work leads to a sense of meaningfulness and personal responsibility (Hackman & Oldham, 1980). Therefore, employees with higher organizational responsibilities are likely to feel the presence of challenges in their work and perceive a higher sense of personal accomplishment (Kahn, 1992; Macey & Schneider, 2008). As a result, this category of job demands is likely to influence work engagement, although this does not rule out the possibility of burnout as the probability of expending one’s emotional energy in these high-performing work roles still exists. Therefore, the possibility of emotional exhaustion cannot be ruled out (Crawford et al., 2010).\n\nFurther, types of job demands that can be categorized as hindrance stressors initiate negative emotions such as fear, anxiety, and anger. Consequently, employees enter a spiral of emotional coping styles. Accordingly, they engage in defensive behaviors such as rationalization and withdrawal. The differentiated job demands perspective does not advocate a simplistic assertion that increased job demands will lead to increased burnout. Therefore, it advocates distinguishing between challenge and hindrance demands while conceptualizing job demands. This distinction within the broader category of job demands will lead to the proposition that challenging demands will increase work engagement, even as they increase burnout, as they can potentially increase emotional exhaustion while employees attempt to meet demands. The challenge demands lead to positive emotions that initiate a problem-focused coping style, leading to higher work engagement.\n\nIn contrast, hindrance stressors lead to negative emotions that initiate an emotion-coping process, reducing work engagement and increasing burnout. The differentiated job demands perspective of Crawford et al. (2010) proposes that job resources perform two functions. First, they initiate motivational processes that inspire employees to increase work engagement. Second, they also reduce the strain that employees may experience resulting from potential resource depletion over time. The issues discussed above can be seen in Figure 3.\n\nAlthough the interactive effect of job resources and job demands on employee recovery performance in the hospitality sector has not been studied, their interactive effect on burnout and work engagement has been studied in other organizational settings. In this context, prior research has also proposed a differentiated perspective on job demands by distinguishing between challenge demands and stressors and hindrance stressors within the broader construct category of job demands. According to this perspective, job demands do not necessarily lead to burnout only, as ordinarily proposed; they can also lead to increased work engagement to the extent of the presence of challenge demands within the broader category of the construct ‘job demands.’\n\nThis study seeks to bridge this research gap. Therefore, this Study examines the effects of job demands on burnout and work engagement and the effects of job resources on burnout and engagement when the interactive effects of job demands and job resources are considered. It is essential to study the effect on employee recovery performance because frontline employees’ service recovery behaviors are likely affected by their emotional states, such as burnout and work engagement. Therefore, the following research issues have emerged:\n\nThe importance of burnout can be understood from the fact that its impact is investigated on a wide range of variables such as trust (Ledgerwood, Crotts, & Everett, 1998), cohesion (Ledgerwood, Crotts, & Everett, 1998), reward (Ledgerwood, Crotts, & Everett, 1998), willingness to deliver quality service (Law & Tam, 2007), increased job demand (Schaufeli et al., 2009), job performance (Maslach, Schaufeli & Leiter, 2001), health (Maslach, Schaufeli & Leiter, 2001), and personal outcomes (Maslach & Jackson, 1981). Although the direct effect of burnout on employee service recovery performance (Karatepe, 2006) has been studied, its effect as a mediator and work engagement on employee recovery performance when job resources and job demands interact has not been studied. However, the hospitality sector has not investigated the effect of burnout on frontline employees’ service recovery performance.\n\nEngagement is motivational because it simultaneously invests individuals’ physical efforts, cognitive applications, and emotional investments in work roles (Kahn, 1992; Rich et al., 2010). Therefore, engagement brings deeper aspects of the human self into the workplace (Rich et al., 2010). There are three reasons for conceptualizing the positive relationship between work engagement and employee recovery performance. First, work engagement improves employee recovery by enabling frontline employees to expend their physical efforts for an extended period. Second, it enables the cognitive application of frontline employees’ attention to recovery performance in a vigilant and focused manner. Third, work engagement among frontline employees leads to the emotional investment of their energies to connect with their coworkers and to meet the emotional demands of their work roles so that there will be authentic performance’ (Rich et al., 2010).\n\nSimilarly, even though the effect of work engagement on increased job resources (Schaufeli et al., 2009) and organizational commitment (Jung & Yoon, 2016) has already been investigated in the literature, its direct effect on frontline employees’ recovery performance in the hospitality sector has not been investigated. Although prior research has examined the effect of several constructs in their role as antecedents of employee service recovery performance, no study in the hospitality sector has investigated the direct effect of frontline employees’ work engagement on their service recovery performance.\n\nAccordingly, the possible interactive effects among burnout, work engagement, and employee service recovery performance would throw up the following research issues:\n\nInteractive effects of low burnout and high engagement on employee service recovery performance\n\nInteractive effects of low work engagement and high burnout on employee service recovery performance\n\nInteractive effects of high burnout and high work engagement on employee service recovery performance\n\nInteractive effects of low burnout and low work engagement on employee service recovery performance\n\nThe research mentioned above is captured in Figure 4.\n\nThe service recovery process aims to return customers to their state before service failure (Mostafa et al., 2015). This research endeavour seeks to bridge this methodological gap in the research discourse on service recovery performance by conceptualising and testing a multilevel model in which the effect of the macro-level construct of the service recovery system is tested on employee-level constructs of employee service recovery performance and its antecedents, that is, job resources and job demands, and the effect of the organisation-level construct of the service recovery system and the individual-level construct of employee recovery performance on the customer-level construct of customer justice perceptions.\n\nThe JD-R model argues that the constructs of job resources and job demands can explain organizationally desirable employee-level outcomes through the mediating effects of employee burnout and work engagement. The hospitality sector has not empirically tested and validated the proposed relationship between the service recovery system, job resources, and job demands.\n\nFinally, this paper focuses on three main issues in service recovery: 1) the importance of a well-understood approach to service recovery; 2) the need for a strong theoretical foundation; and 3) the role that service recovery plays in society. This paper presents a united view of service recovery management across fields and levels of theoretical and analytical analysis.\n\nThe JD-R model has been widely used to understand the relationship between job demands and resources and employee well-being and performance. This research takes a step further by examining the impact of JD-R model constructs on employee service recovery performance. The findings suggest that job demands such as emotional dissonance and workload negatively affect service recovery performance, while job resources such as social support and autonomy positively impact it. Moreover, this study highlights the importance of considering multi-actor designs in construct measurement to enhance the accuracy of results. By doing so, this research contributes to a better understanding of the antecedents and consequences of service recovery performance within the context of a service recovery system at the unit level. Overall, these findings have implications for organisations seeking to improve their service quality by enhancing their employees’ service recovery performance through effective job design and resource allocation.\n\nThe following research gaps are evident from the discussion above: First, there is a need to determine the relationship between the constructs of the service recovery system and job resources and demands in the hospitality sector, which has remained unexplored. Second, the relationship between employee service recovery performance and customer justice perceptions in the hospitality sector remains unexplored. Third, the direct and interactive effects of job resources and demands on employee recovery performance among frontline employees in the hospitality sector remain to be examined. Fourth, the direct and interactive effects of job resources and job demands on employee burnout and work engagement among frontline employees in the hospitality sector remain unexplored. Fifth, the direct and interactive effects of burnout and work engagement on employee service recovery performance among frontline employees in the hospitality sector remain to be investigated. Finally, multilevel modeling of the unit-level construct of the service recovery system and its effect on the customer-level construct of customer justice perceptions has not been attempted while empirically testing the antecedent-consequent relationship among job resources and job demands, employee burnout and work engagement, and employee service recovery performance still needs to be built. For example, a study could be conducted to investigate how training programs and organizational support can enhance service recovery performance among hotel receptionists who often interact with disgruntled guests. By collecting data on job resources, job demands, burnout, work engagement, and service recovery system at the unit level, researchers could examine how these factors impact frontline employees’ ability to restore guest satisfaction and subsequently affect customers’ perceptions of justice. Such insights could inform the development of evidence-based interventions that enhance the quality of service recovery\n\n\nConclusions\n\nThis study presents a cohesive perspective on service recovery management across disciplines, levels of theory, and degrees of analysis. It organises this material into an interdisciplinary framework to help better understand the many disciplines looking at service recovery and offer suggestions on how organisations may build up service recovery procedures. The future research questions presented in this article can improve the research efficacy of academics interested in service recovery, and this synthesis and integrative framework will help researchers and managers think differently about service recovery and how it can be approached in a more comprehensive and effective manner. Overall, this article provides valuable insights and recommendations for organisations looking to improve their service recovery processes and for researchers seeking to advance the field of service recovery.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbbas MR, Abdullateef AO, Mokhtar SSM: Does Service Recovery Lead to Customer Satisfaction and Loyalty in Airline Industry? A Perceived Justice Theory Approach. World Appl. Sci. J. 2015; 33(2): 256–262. Publisher Full Text\n\nAguinis H, Boyd BK, Pierce CA, et al.: The Myth of “the” Micro-Macro Divide: Bridging System-Level and Disciplinary Divides.J. Manage.2011; 37(2): 581–609. Publisher Full Text\n\nAshill NJ, Rod M: Burnout processes in non-clinical health service encounters. J. Bus. Res. 2011; 64(10): 1116–1127. Publisher Full Text\n\nAurier P, Siadou-Martin B: Perceived justice and consumption experience evaluations: A qualitative and experimental investigation. Int. J. Serv. Ind. Manag. 2007; 18: 450–471. Publisher Full Text\n\nBabakus E, Yavas U, Ashill NJ: The Role of Customer Orientation as a Moderator of the Job Demand-Burnout-Performance Relationship: A Surface-Level Trait Perspective. J. Retail. 2009; 85(4): 480–492. Publisher Full Text\n\nBabakus E, Yavas U, Karatepe OM, et al.: The Effect of Management Commitment to Service Quality on Employees’ Affective and Performance Outcomes. J. Acad. Mark. Sci. 2003; 31(3): 272–286. Publisher Full Text\n\nBakker A, Demerouti E: Towards a model of work engagement. Career Dev. Int. 2008; 13(3): 209–223. Publisher Full Text\n\nBakker AB, Demerouti E: The Job Demands-Resources Model: State of the Art. ResearchGate. 2007; 22(3): 309–328. Publisher Full Text\n\nBettencourt LA, Brown SW: Role Stressors and Customer-Oriented Boundary-Spanning Behaviors in Service Organizations.J. Acad. Mark. Sci.2003; 31(4): 394–408. Publisher Full Text\n\nBorucki CC, Burke MJ: An examination of service-related antecedents to retail store performance. J. Organiz. Behav. 1999; 20: 943–962. Publisher Full Text\n\nBritt TW: Engaging the Self in the Field: Testing the Triangle Model of Responsibility.Pers. Soc. Psychol. Bull.1999; 25(6): 698–708. Publisher Full Text\n\nBroome ME: Integrative literature reviews for the development of concepts. In Rodgers BL, Knafl KA (Eds.), Concept development in nursing. Philadelphia: W.B. Saunders Co; 1993; pp. 231–250.\n\nChebat JC, Slusarczyk W: How emotions mediate the effects of perceived justice on loyalty in service recovery situations: An empirical study. J. Bus. Res. 2005; 58(5): 664–673. Publisher Full Text\n\nChoi BB-J, Choi BB-J: The effects of perceived service recovery justice on customer affection, loyalty, and word-of-mouth. Eur. J. Mark. 2013; 48(1): 108–131. Publisher Full Text\n\nChoi CH, Kim TT, Lee G, et al.: Testing the stressor-strain-outcome model of customer-related social stressors in predicting emotional exhaustion, customer orientation and service recovery performance. Int. J. Hosp. Manag. 2014; 36(January): 272–285. Publisher Full Text\n\nColgate M, Norris M: Developing a comprehensive picture of service failure. Int. J. Serv. Ind. Manag. 2001; 12(3): 215–233. Publisher Full Text\n\nColquitt JA, Scott BA, Rodell JB, et al.: Justice at the millennium, a decade later: A meta-analytic test of social exchange and affect-based perspectives. J. Appl. Psychol. 2013; 98(2): 199–236. Publisher Full Text\n\nCrawford ER, Lepine JA, Rich BL: Linking job demands and resources to employee engagement and burnout: A theoretical extension and meta-analytic test. J. Appl. Psychol. 2010; 95(5): 834–848. PubMed Abstract \| Publisher Full Text\n\nCropanzano R, Ambrose ML: Procedural and distributive justice are more similar than you think: A monistic perspective and a research agenda. In J. (Eds.), Advances in organization justice. Stanford University Press; 2001; pp. 119–151.\n\nDavidow M: The Bottom Line Impact of Organizational Responses to Customer Complaints.J. Hosp. Tour. Res.2000; 24(4), 473–490. Publisher Full Text\n\nDavidow M: Have You Heard the Word? the Effect of Word of Mouth on Perceived Justice, Satisfaction and Repurchase Intentions Following Complaint Handling. Journal of Consumer Satisfaction, Dissatisfaction and Complaining Behavior. 2003; 24: 473–490. Publisher Full Text\n\nde Matos CA , Vieira VA, Veiga RT: Behavioural responses to service encounter involving failure and recovery: the influence of contextual factors. Serv. Ind. J. 2012; 32(14): 2203–2217. Publisher Full Text\n\ndel Río-Lanza AB , Vázquez-Casielles R, Díaz-Martín AM: Satisfaction with service recovery: Perceived justice and emotional responses. J. Bus. Res. 2009; 62(8): 775–781. Publisher Full Text\n\nDemerouti E, Bakker AB, Nachreiner F, et al.: The job demands-resources model of burnout. J. Appl. Psychol. 2001; 86(3): 499–512. Publisher Full Text\n\nDeWitt T, Nguyen DT, Marshall R: Exploring Customer Loyalty Following Service Recovery: The Mediating Effects of Trust and Emotions. J. Serv. Res. 2008; 10(3): 269–281. Publisher Full Text\n\nDormann C, Zapf D: Customer-Related Social Stressors and Burnout. J. Occup. Health Psychol. 2004; 9(1): 61–82. PubMed Abstract \| Publisher Full Text\n\nEstrada CA, Isen AM, Young MJ: Positive affect improves creative problem solving and influences reported source of practice satisfaction in physicians. Motiv. Emot. 1994; 18: 285–299. Publisher Full Text\n\nFrei RL, McDaniel MA: Validity of Customer Service Measures in Personnel Selection: A Review of Criterion and Construct Evidence. Hum. Perform.1998; 11(1): 1–27. Publisher Full Text\n\nGreenberg J, Cropanzano R: The social side of fairness: Interpersonal and informational classes of organizational justice. Justice in the workplace: Approaching fairness in human resource management. Hillsdale, NJ: Lawrence Erlbaum Associates; 1993.\n\nHackman RG, Oldham Reading MA: Addison-Wesley, 1980, xxvii + 330 pp. Group & Organization Studies, 7(1): 121–124. Publisher Full Text\n\nHakanen J, Bakker A, Demerouti E: How dentists cope with their job demands and stay engaged: The moderating role of job resources. European Journal of Oral Sciences, How dentists cope with their job demands and stay engaged: the moderating role of job resources. Eur. J. Oral Scixant. October 2006; 113: 479–487. PubMed Abstract \| Publisher Full Text\n\nHart CW, Heskett JL, Sasser WE Jr: The profitable art of service recovery. Harv. Bus. Rev. 1990 Jul-Aug; 68(4): 148–156. PubMed Abstract\n\nHarter JK, Schmidt FL, Hayes TL: Business-unit-level relationship between employee satisfaction, employee engagement, and business outcomes: A meta-analysis. J. Appl. Psychol. 2002; 87(2): 268–279. PubMed Abstract \| Publisher Full Text\n\nHeskett JL, Jones TO, Loveman GW, et al.: Putting the service-profit chain to work. Harv. Bus. Rev.1994; 72(2): 164–174.\n\nHobfoll SE: The Influence of Culture, Community, and the Nested-Self in the Stress Process: Advancing Conservation of Resources Theory.Appl. Psychol.2001; 50: 337–421. Publisher Full Text\n\nHobfoll SE: Conservation of resource caravans and engaged settings. J. Occup. Organ. Psychol.2011; 84(1): 116–122. Publisher Full Text\n\nHockey GRJ: Compensatory control in the regulation of human performance under stress and high workload: A cognitive-energetical framework. Biol. Psychol. 1997; 45(1-3): 73–93. PubMed Abstract \| Publisher Full Text\n\nHoffman KD, Bateson JE: Essentials of services marketing.1997.\n\nHomburg C, Fürst A, Koschate N: On the importance of complaint handling design: A multi-level analysis of the impact in specific complaint situations. J. Acad. Mark. Sci. 2009; 38(3): 265–287. Publisher Full Text\n\nJung HS, Yoon HH: What does work meaning to hospitality employees? The effects of meaningful work on employees’ organizational commitment: The mediating role of job engagement. Int. J. Hosp. Manag. 2016; 53: 59–68. Publisher Full Text\n\nKahn WA: To Be Fully There: Psychological Presence at Work.Human Relations.1992; 45(4): 321–349. Publisher Full Text\n\nKarasek R, Brisson C, Kawakami N, et al.: The job content questionnaire (JCQ): An instrument for internationally comparative assessments of psychosocial job characteristics. J. Occup. Health Psychol.1998; 3: 322–355. PubMed Abstract \| Publisher Full Text\n\nKaratepe OM: The effects of selected antecedents on the service recovery performance of frontline employees. Serv. Ind. J. 2006; 26(1): 39–57. Publisher Full Text\n\nKaratepe OM, Sokmen A: The effects of work role and family role variables on psychological and behavioral outcomes of frontline employees. Tour. Manag. 2006; 27(2): 255–268. Publisher Full Text\n\nKim E, Tang R, (Liang).: Rectifying Failure of Service: How Customer Perceptions of Justice Affect Their Emotional Response and Social Media Testimonial. J. Hosp. Market. Manag. 2016; 25(8): 897–924. Publisher Full Text\n\nKim S, Kandampully J: Exploring Customer Loyalty Following Service Recovery: The Relationships of Perceived Justice, Commitment, Trust, and Loyalty.no date.\n\nKim T(T), Kim WG, Kim HB: The effects of perceived justice on recovery satisfaction, trust, word-of-mouth, and revisit intention in upscale hotels. Tour. Manag. 2009; 30(1): 51–62. Publisher Full Text\n\nKozlowski SWJ, Klein KJ: A multilevel approach to theory and research in organizations: Contextual, temporal, and emergent processes. In Klein KJ, Kozlowski SWJ (Eds.), Multilevel theory, research, and methods in organizations: Foundations, extensions, and new directions. Jossey-Bass/Wiley; 2000; pp. 3–90.\n\nLaw R, Tam P: Burnout and service employees’ willingness to deliver quality service. J. Hum. Resour. Hosp. Tour. 2007; 7(1): 45–64. Publisher Full Text\n\nLedgerwood CE, Crotts JC, Everett AM: Antecedents of Employee Burnout in the Hotel Industry. Prog. Tour. Hosp. Res. 1998; 4(March 1998): 31–44. Publisher Full Text\n\nLiao H: Do it right this time: the role of employee service recovery performance in customer-perceived justice and customer loyalty after service failures. J. Appl. Psychol. 2007; 92(2): 475–489. PubMed Abstract \| Publisher Full Text\n\nLiao H, Chuang A: A Multilevel Investigation of Factors Influencing Employee Service Performance and Customer Outcomes.AMJ.2004; 47: 41–58. Publisher Full Text\n\nMacey W, Schneider B: Engaged in Engagement: We Are Delighted We Did It. Industrial and Organizational Psychology.2008; 1(1): 76–83. Publisher Full Text\n\nMartÃnez-Tur V, Ramos J, PeirÃ JM, et al.: Relationships among perceived justice, customers’ satisfaction, and behavioral intentions: The moderating role of gender. Psychol. Rep. 2001; 88(3 PART 1): 805–811. PubMed Abstract \| Publisher Full Text\n\nMaslach C, Jackson SE: The Measurement of Experienced Burnout Author (s): Christina Maslach and Susan E. Jackson Published by: Wiley Stable URL: http://www.jstor.org/stable/3000281. Accessed: 01-04-2016 02: 04 UTC Your use of the JSTOR archive indicates your acceptance of. J. Occup. Behav. 1981; 2(2): 99–113. Publisher Full Text\n\nMaslach C, Jackson SE, Leiter MP: Maslach Burnout Inventory: Third edition. In Zalaquett CP, Wood RJ (Eds.), Evaluating stress: A book of resources. Scarecrow Education; 1997; pp. 191–218.\n\nMaslach C, Schaufeli WB, Leiter MP: Job Burnout. Annu. Rev. Psychol. 2001; 52: 397–422. Publisher Full Text\n\nMasnita Siagian Y, Triyowati H: Service Recovery Based on Perceived Justice: A Study on Locus Attribution. Int. J. Bus. Manag. 2015; 10(7): 99–109. Publisher Full Text\n\nMaxham JG, Netemeyer RG: Modeling customer perceptions of complaint handling over time: The effects of perceived justice on satisfaction and intent. J. Retail. 2002; 78(4): 239–252. Publisher Full Text\n\nMcCollough MA, Berry LL, Yadav MS: An Empirical Investigation of Customer Satisfaction after Service Failure and Recovery. J. Serv. Res. 2000; 3(2): 121–137. Publisher Full Text\n\nMcColl-Kennedy JR, Sparks BA: Application of Fairness Theory to Service Failures and Service Recovery.J. Serv. Res.2003; 5(3): 251–266. Publisher Full Text\n\nMeijman TF, Mulder G: Psychological aspects of. Handbook of work and organizational psychology: Work psychology.1998; 2: 2.\n\nMichel S, Bowen D, Johnston R: Why service recovery fails: Tensions among customer, employee, and process perspectivesJ. Serv. Manag.2009; 20(3): 253–273. Publisher Full Text\n\nMostafa RB, Lages CR, Shabbir HA, et al.: Corporate Image: A Service Recovery Perspective. J. Serv. Res. 2015; 18(4): 468–483. Publisher Full Text\n\nMurray IP: An Investigation of Perceived Justices and Customer Satisfaction. Ann. Tour. Res. 2006; 33(1): 277–278. Publisher Full Text\n\nNikbin D, Hyun SS: An empirical study of the role of failure severity in service recovery evaluation in the context of the airline industry. Rev. Manag. Sci. 2014; 9(4): 731–749. Publisher Full Text\n\nNikbin D, Ismail I, Marimuthu M, et al.: Management Research Review Perceived justice in service recovery and switching intention: Evidence from Malaysian mobile telecommunication industry. Management Research Review International Journal of Bank Marketing Iss European Journal of Marketing. 2012; 35(12): 309–325. Publisher Full Text\n\nPaper C, Hafiz M, Rashid A, et al.: Customer Reactions to Service Failure and Recovery in the Restaurant Industry: A Covariance-Based SEM Approach Khalid S. Soliman.May 2016.\n\nPapke-Shields KE, Malhotra MK, Grover V: Strategic Manufacturing Planning Systems and Their Linkage to Planning System Success.Decision Sciences.2002; 33: 1–30. Publisher Full Text\n\nPugh DS, Hickson DJ, Hinings CR: An Empirical Taxonomy of Structures of Work Organizations. Adm. Sci. Q. 1969; 14(1): 115–126. Publisher Full Text\n\nRich BL, Lepine JA, Crawford ER: Job Engagement: Antecedents and Effects on Job Performance. AMJ. 2010;53: 617–635. Publisher Full Text\n\nRo H, Olson ED: The effects of social justice and stigma-consciousness on gay customers’ service recovery evaluation. J. Bus. Res. 2014; 67(6): 1162–1169. Publisher Full Text\n\nRod M, Ashill NJ: Symptoms of burnout and service recovery performance: The influence of job resourcefulness. Manag. Serv. Qual. 2009; 19(1): 60–84. Publisher Full Text\n\nRod M, Ashill NJ, Carruthers J: The relationship between job demand stressors, service recovery performance and job outcomes in a state-owned enterprise. J. Retail. Consum. Serv. 2008; 15(1): 22–31. Publisher Full Text\n\nRoschk H, Kaiser S: The nature of an apology: An experimental study on how to apologize after a service failure. Mark. Lett. 2013; 24(3): 293–309. Publisher Full Text\n\nRyan RM, Deci EL: The Darker and Brighter Sides of Human Existence: Basic Psychological Needs as a Unifying Concept. Psychol. Inq.2000; 11(4): 319–338. Publisher Full Text\n\nRyan AM, Ployhart RE: Customer service behavior. In Borman WC, Ilgen DR, Klimoski RJ (Eds.), Handbook of psychology: Industrial and organizational psychology. Vol. 12. . London: Wiley; 2003; pp. 377–397. Publisher Full Text\n\nSchaufeli WB: Engaging leadership in the job demands-resources model. Career Dev. Int. 2015; 20(5): 446–463. Publisher Full Text\n\nSchaufeli WB, Bakker AB, Van Rhenen W: How changes in job demands and resources predict burnout, work engagement, and sickness absenteeism.J. Organiz. Behav.2009; 30: 893–917. Publisher Full Text\n\nSchaufeli WB, Martínez IM, Pinto AM, et al.: Burnout and Engagement in University Students: A Cross-National Study.J. Cross Cult. Psychol.2002; 33(5), 464–481. Publisher Full Text\n\nSchneider KJ: The paradoxical self: Toward an understanding of our contradictory nature. Insight Books/Plenum Press; 1990.\n\nSchoefer K, Diamantopoulos A: Measuring experienced emotions during service recovery encounters: construction and assessment of the ESRE scale. Serv. Bus. 2008; 2: 65–81. Publisher Full Text\n\nSelnes F: Antecedents and consequences of trust and satisfaction in buyer-seller relationships. Eur. J. Mark. 1998; 32(3/4): 305–322. Publisher Full Text\n\nSegars AH, Grover V: Strategic Information Systems Planning Success: An Investigation of the Construct and Its Measurement. MIS Quarterly. 1998; 22(2): 139–163. Publisher Full Text\n\nSiagian YM, Triyowati H: Service recovery based on perceived justice: A study on locus attribution. Int. J. Bus. Manag.2015; 10(7): 99. Publisher Full Text\n\nSiegrist J: Adverse health effects of high-effort/low-reward conditions. J. Occup. Health. Psychol. 1996; 1(1): 27–41. PubMed Abstract \| Publisher Full Text\n\nSilber I, Israeli A, Bustin A, Zvi O: Recovery strategies for service failures: The case of restaurants. J. Hosp. Mark. Manag. 2009;18: 730–740. Publisher Full Text\n\nSimpson MR: Engagement at work: A review of the literature. Int. J. Nurs. Stud. 2009; 46(7), 1012– 1024. Publisher Full Text\n\nSingh J: Performance Productivity and Quality of Frontline Employees in Service Organizations.J. Mark.2000; 64(2), 15–34. Publisher Full Text\n\nSmith AK, Bolton RN, Wagner J: A model of customer satisfaction with service encounters involving failure and recovery. J. Mark. Res. 1999; 36(3): 356–372. Publisher Full Text\n\nSmith JS, Karwan KR, Markland RE: An Empirical Examination of the Structural Dimensions of the Service Recovery System.2009; 40(1).\n\nSolomon MR, Surprenant C, Czepiel JA, et al.: A Role Theory Perspective on Dyadic Interactions: The Service Encounter.J. Mark.1985; 49(1): 99–111. Publisher Full Text\n\nSöderlund M, Colliander J: Loyalty program rewards and their impact on perceived justice, customer satisfaction, and repatronize intentions. J. Retail. Consum. Serv. 2015; 25(August): 47–57. Publisher Full Text\n\nStock MR, Jong Ad, Zacharias NA: Frontline Employees' Innovative Service Behavior as Key to Customer Loyalty: Insights into FLEs' Resource Gain Spiral.J. Prod. Innov. Manag.2017; 34: 223–245. Publisher Full Text\n\nTax SS, Brown SW, Chandrashekaran M: Customer Evaluations of Service Complaint Experiences: Implications for Relationship Marketing.J. Mark.1998; 62(2): 60–76. Publisher Full Text\n\nTeo Thompson SH, Lim Vivien KG: The effects of perceived justice on satisfaction and behavioral intentions: the case of computer purchase. Int. J. Retail Distrib. Manag. 2001; 29(2): 109–125. Publisher Full Text\n\nThibaut J, LaurensWalker: Procedural Justice: A Psychological Analysis.Hillsdale, NJ: Lawrence Erlbaum Associates; 1975.\n\nvan der Heijden GAH , Schepers JJL, Nijssen EJ, et al.: Don’t just fix it, make it better! Using frontline service employees to improve recovery performance. J. Acad. Mark. Sci. 2013; 41(5): 515–530. Publisher Full Text\n\nVan Vaerenbergh Y, Orsingher C: Service Recovery: An Integrative Framework and Research Agenda. AMP. 2016; 30: 328–346. Publisher Full Text\n\nVázquez-Casielles R, Álvarez LS, Martín AMD: Perceived Justice of Service Recovery Strategies: Impact on Customer Satisfaction and Quality Relationship. Psychol. Mark. 2010; 30(6): 461–469. Publisher Full Text\n\nWaqas M, Ali H, Khan MA: An investigation of effects of justice recovery dimensions on students? satisfaction with service recovery in higher education environment. International Review on Public and Nonprofit Marketing. 2014; 11(3): 263–284. Publisher Full Text\n\nWeun S, Beatty SE, Jones MA, et al.: The impact of service failure severity on service recovery evaluations.2006. Publisher Full Text\n\nWitrz J, Mattila AS: Consumer responses to compensation, speed of recovery and apology after a service failure. Int. J. Serv. Ind. Manag. 2004; 9(2): 7–23. Publisher Full Text\n\nWong NY: The role of culture in the perception of service recovery. J. Bus. Res. 2004; 57(9): 957–963. Publisher Full Text\n\nWong IA: Linking Firms, Employees, and Customers: A Multilevel Research Agenda for Hospitality Studies.Cornell Hosp. Q.2016; 57(1): 7–20. Publisher Full Text\n\nXu Y, Marshall R, Edvardsson B, et al.: Show you care: initiating co-creation in service recovery. J. Serv. Manag. 2014; 25(3): 369–387. Publisher Full Text\n\nYuanyi Chen D, Ferris L, Kwan HK, et al.: Self-Love's Lost Labor: A Self-Enhancement Model of Workplace Incivility. AMJ .2013; 56, 1199–1219, Publisher Full Text\n\nZhou T: The Effect of Perceived Justice on LBS Users Privacy Concern. Inf. Dev. 2015; 32(5): 1730–1740. Publisher Full Text" }	[ { "id": "270144", "date": "22 May 2024", "name": "Ngoni Courage Shereni", "expertise": [ "Reviewer Expertise Sustainable Tourism", "Marketing", "human resource management", "sharing economy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 - I suggest that the Authors indicate the key findings of the study before highlighting the contribution of the study Introduction -The first line defines service recovery in direct quotes, can the authors provide the page number for the citation - The section 'Need for a standardized service recovery system' and several other sections have no citations. There is a need to relate the arguments presented to existing literature Conceptual framework -While the framework clearly links service recovery with different variables there is also a need to ground these arguments in the literature. Readers would want to know what informs this framework.\nConclusion This section should present the theoretical and practical implications of the research, limitations of the research and future research opportunities.\nOverall this is an interesting research that provides unique dimensions of service recovery. The researchers need to add current literature to substantiate their arguments\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": "11864", "date": "14 Oct 2024", "name": "Abhishek Rao", "role": "Author Response", "response": "Abstract - I suggest that the Authors indicate the key findings of the study before highlighting the contribution of the study Response: We have addressed this issue in the below paragraph; Past research aimed at service recovery has focused on actions that are taken to retain customers, and the possibility of overcoming the mistakes of service delivery, though the multidimensional nature of the service recovery process has begun to move beyond the complaint handling process. In this paper, we identify the most important issues addressed in service recovery and present a framework for addressing them We used an extensive integrative review methodology. Between 1988 and 2017 the number of articles in these journals was kept between 26 and 30. The majority took a business perspective to study services recovery, while a minority took an inter-disciplinarity perspective. The study's findings are expected to provide insights into the antecedents and consequences of service recovery performance, particularly how job resources and demands influence employee burnout and work engagement, which in turn affect service recovery performance and customer perceptions of justice. The research aims to contribute to the discourse on service recovery by building a multi-level model that explains the service recovery performance of frontline employees and the impact of the service recovery system on customer justice perceptions Thus, this research is expected to contribute to robust conclusions on the antecedents and consequences of employee service recovery performance nested within the unit-level construct, i.e., the service recovery system Introduction The first line defines service recovery in direct quotes, can the authors provide the page number for the citation Response: Revised definition with page no; Service recovery as “the actions taken by a service provider aimed at resolving failures” (Smith et al., 2009, p. 166). The section 'Need for a standardized service recovery system' and several other sections have no citations. There is a need to relate the arguments presented to existing literature Response: Thank you for your feedback regarding the absence of citations in the section 'Need for a standardized service recovery system' and other sections of the document. We acknowledge the importance of grounding our arguments within the existing body of literature to provide a solid foundation for our research. This overwhelming evidence that indicates the organizational importance of customer justice perceptions in the service recovery context has led to the increasing need to formalize the service recovery system that guides and trains frontline employees in their service recovery performance and places the systems and processes in this regard Smith, A. K., & Bolton, R. N. (2002). Formalizing and institutionalizing the service recovery system assumes importance in the context of its role in determining customer justice perceptions influenced by employee service recovery performance Mattila, A. S., & Patterson, P. G. (2004). Therefore, this research proposal intends to examine the impact of the service recovery system, conceptualized and operationalized at the organizational level, on the perceptions of customer justice that arise in the service recovery process Conceptual framework -While the framework clearly links service recovery with different variables there is also a need to ground these arguments in the literature. Readers would want to know what informs this framework. Response: We appreciate your insightful feedback regarding the need to ground the framework within the existing literature. We understand the importance of providing a clear rationale for the framework's design, which is informed by a comprehensive review of the literature on service recovery, employee performance, and customer justice perceptions. To address your concern, For instance, we have referenced studies that have established the link between service recovery systems and customer justice perceptions, as well as research that has explored the role of employee burnout and work engagement in service recovery performance. Moreover, we have included a section that discusses the theoretical underpinnings of the framework, citing specific theories and models that have informed our approach. This includes the Job Demands-Resource (JD-R) model, which is central to our understanding of how job resources and demands influence employee well-being and performance. We have also ensured that the framework's variables are clearly defined and that their interrelationships are explained with reference to empirical studies. This will help readers to understand the basis for the framework and how it contributes to the existing body of knowledge on service recovery. We are confident that these will provide a more robust foundation for our research proposal and will enhance the document's clarity and academic rigor. Thank you for your guidance, and we look forward to your continued feedback as we refine our work. Conclusion This section should present the theoretical and practical implications of the research, limitations of the research and future research opportunities. Response: Thank you for your feedback regarding the section on conclusion. We understand the importance of providing a clear rationale. Here is the explanation given below Theoretical Implications: Our study contributes to the theoretical landscape by offering a novel perspective on service recovery that accounts for both organizational and individual-level factors. The proposed multi-level model bridges the gap between macro and micro perspectives, enhancing our understanding of the service recovery process. This integration of the JD-R model into service recovery research provides a foundation for future studies to build upon, potentially leading to the development of more nuanced theories in the field. Practical Implications: From a practical standpoint, the findings of this research can guide organizations in the hospitality sector to design more effective service recovery systems. By recognizing the importance of job resources and demands, managers can implement strategies to support frontline employees, thereby enhancing their ability to deliver satisfactory service recovery. This, in turn, can lead to improved customer satisfaction and loyalty, which are critical for the success of hospitality businesses. Limitations: It is important to acknowledge the limitations of this research. The study is based on an extensive integrative review, which may not capture the latest empirical findings. Additionally, the focus on the hospitality sector may limit the generalizability of the results to other industries. The research also relies on the JD-R model as a primary theoretical framework, which may not fully account for all the complexities of service recovery processes. Future Research Opportunities: This research opens up several avenues for future studies. Empirical testing of the proposed model is necessary to validate the relationships between service recovery systems, employee performance, and customer justice perceptions. Further research could also explore the role of additional organizational factors and individual differences in service recovery. Extending the research to other sectors could provide insights into the applicability of the model across different contexts. In conclusion, this research represents a significant step towards a deeper understanding of service recovery in the hospitality industry. By highlighting the importance of employee well-being and effective service recovery systems, we hope to inspire further research and practical applications that will benefit both employees and customers in the service industry. Overall this is an interesting research that provides unique dimensions of service recovery. The researchers need to add current literature to substantiate their arguments Response: We appreciate your positive feedback on our research and your suggestion to incorporate current literature to strengthen our arguments. We understand the importance of staying up-to-date with the latest findings in the field to ensure that our research is both relevant and robust. To address your recommendation, we have conducted a thorough review of recent literature published within the last few years. We have identified several key studies that have advanced the understanding of service recovery, particularly in the context of the hospitality industry. These studies have explored various aspects of service recovery, including the impact of technology on recovery processes, the role of employee empowerment, and the influence of cultural factors on customer perceptions of justice. We have integrated these new findings into our document, ensuring that our framework and arguments are grounded in the most current research. This includes updating our literature review to reflect the latest developments and revising our theoretical framework to incorporate new insights from the recent literature. We believe that these additions will enhance the document's relevance and will provide a more comprehensive understanding of the service recovery landscape. We are committed to ensuring that our research remains at the forefront of academic discourse and practical application in the field of service recovery. Thank you for your guidance, and we look forward to your continued feedback as we finalize our work" } ] }, { "id": "195400", "date": "26 Sep 2024", "name": "Michael Sammanasu Joseph", "expertise": [ "Reviewer Expertise Human resource" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn reviewing the manuscript titled “Linkages between Service Recovery System and Customer Justice Perceptions: A Multi-Level Model of Employee Service Recovery\n\nPerformance”, it is evident that the authors have put forth a commendable effort in addressing the key aspects related to service recovery, customer satisfaction, and employee engagement.\nThe article's strength lies in its comprehensive coverage of relevant literature from various fields, demonstrating a strong foundation of knowledge. The exploration of the relationships between service recovery, justice perceptions, employee engagement, and customer satisfaction is particularly noteworthy. However, there are several areas that require attention to enhance the quality and impact of the manuscript. The background and literature review sections, while extensive, lack focus on the specific themes and trends that connect to the proposed journal's theme.\nThe authors should consider refining these sections to clearly establish the relevance of their work within the broader context of the proposed journal. Additionally, the organization of the article can be improved to enhance its flow and coherence. The transitions between sections need to be smoother, ensuring that readers can follow the logical progression of ideas.\nThis will help in maintaining the reader's engagement throughout the article. Moreover, while the authors have provided a comprehensive list of references, it's important for them to thoroughly integrate and discuss these references within the context of their arguments. This will demonstrate the critical evaluation of existing literature and establish the significance of their contributions. In terms of the strengths, the authors have effectively incorporated both theoretical and empirical research, contributing to the article's credibility. The use of real-world examples and cases adds practical relevance to the discussion. To address the aforementioned concerns, the authors are encouraged to revise the manuscript with a clear focus on refining the background, enhancing the organization, and ensuring the effective integration of references. These revisions will significantly enhance the manuscript's contribution to the proposed journal and its relevance to the target audience.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-947
https://f1000research.com/articles/13-534/v1	24 May 24	{ "type": "Research Article", "title": " A validate and standardized pseudotyped microneutralization assay as a safe and powerful tool to measure LASSA neutralising antibodies for vaccine development and comparison", "authors": [ "Roberta Antonelli", "Vittoria Forconi", "Eleonora Molesti", "Claudia Semplici", "Pietro Piu", "Maria Altamura", "Francesca Dapporto", "Nigel Temperton", "Emanuele Montomoli", "Alessandro Manenti", "Vittoria Forconi", "Eleonora Molesti", "Claudia Semplici", "Pietro Piu", "Maria Altamura", "Francesca Dapporto", "Nigel Temperton", "Emanuele Montomoli", "Alessandro Manenti" ], "abstract": "Background Over the past few decades, WHO has made massive efforts to promote the development of a vaccine against Lassa virus (LASV), one of the top ten priority pathogens for research and development under the WHO R&D Blueprint for Emerging Infections. To date, several vaccines are at different stages of development. In this scenario, a validated and standardised assay to measure LSV neutralising antibodies is urgently needed for vaccine development and comparison.\n\nMethods The neutralisation assay remains the gold standard for determining antibody efficacy. Here we have proposed a safe and validated pseudotyped neutralisation assay for LASV, taking advantage of the development of the first WHO International Standard and Reference Panel for Anti-Lassa Fever (NIBSC code 21/332).\n\nResults and Conclusions The proposed results demonstrate that the pseudotyped luciferase neutralisation assay is a specific serological test for the measurement of LASV neutralising antibodies without cross-reacting with standard sera specific for heterologous viral infections. In addition, the assay is accurate, precise, and linear according to criteria and statistical analyses defined and accepted by international guidelines.", "keywords": [ "Lassa virus (LASV)", "International Standard and Reference Panel for Anti-Lassa Fever", "neutralisation assay", "international guidelines" ], "content": "1. Introduction\n\nLassa virus (LASV) is the causative agent of Lassa fever (LF), a zoonotic disease associated with an acute and potentially fatal haemorrhagic illness with approximately 100,000-300,000 human cases1 and 5000 deaths per year.2\n\nFirst described in 1969 in Lassa, Nigeria,3 LF is currently endemic in West and Central Africa, including Nigeria, Sierra Leone, Guinea, Liberia, Benin, Ghana and Mali and neighbouring countries.4,5 Worldwide, sporadic cases of LASV infection have been reported in Europe, Japan, and the USA, imported by travellers from West Africa.6–8\n\nLASV is an enveloped-RNA virus with a genome consisting of two ambisense, single-stranded RNA segments, large (L) and small (S). Both RNA segments contain two open reading frames (ORFs) separated by non-coding intergenic regions (IGRs) and are involved in RNA transcription termination.1 The L segment encodes the Z protein and RNA polymerase, while the S RNA segment encodes the nucleoprotein (NP) and the glycoprotein precursor complex (GPC), which is translationally cleaved co- and post- into GP1 and GP2 and the stable signal peptide (SSP).9,10 Together, GP1, GP2 and SSP form the mature glycoprotein (GP) spike complex on the viral surface. GP1 is involved in receptor binding and entry into host cells, while GP2 and SSP are involved in stabilising receptor-GP complexes and in viral fusion within host cell membranes. GPC is the only viral protein on the surface of LASV and is the only target for neutralising antibodies (NAbs).11\n\nTypically, LASV is transmitted to humans through direct contact with its rodent reservoir, Mastomys natalensis, a multimammate rat,12 which colonises rural domestic areas and promotes LASV spread via aerosolized excretions and secretions or consumption of contaminated food.13 Less commonly, horizontal human-to-human transmission of LASV can occur, posing a higher risk to health care, which increases with disease progression and increasing viral load.14,15 LASV infection is heterogeneous: 80% of infected individuals are asymptomatic or present with mild, non-specific symptoms; 20% of infected individuals present with severe symptoms, including haemorrhaging, respiratory distress, repeated vomiting, facial swelling, chest, back and abdominal pain, and shock.8 Central nervous system manifestations and renal failure are strongly associated with a poor outcome16; in the worst cases, death can occur within 14 days of symptom onset due to multiple organ failure.17\n\nLASV case fatality rates (CFRs) differ between countries. In Kenema, Sierra Leone, patients have a CFR of 69%,65 while in Nigeria it varies by location but is around 20-30%.18 Due to its potential for zoonotic and human transmission, and difficulties in treatment and prevention, LASV is one of the high priority pathogens identified in the WHO R&D Blueprint and by CEPI.19\n\nImprovement in the development of Lassa vaccines and treatments has been hampered by the designation of Lassa virus as a Category A pathogen by the National Institute of Allergy and Infectious Diseases (NIAID), and consequently Biosafety Level 4 (BSL-4) precautions are recommended for handling potentially infectious Lassa virus specimens. To overcome these limitations, pseudotyped viruses provide a powerful, safe, and convenient tool to investigate Lassa GP function, attachment, and entry processes; moreover, they are useful to analyse immunological responses and detect neutralising antibody.20\n\nViral pseudotypes are chimeric non-replicating viruses that encode a reporter gene and carry the GP of interest on their surface. The laboratory use of pseudotyped virus particles has many advantages, particularly in the study of highly pathogenic viruses, as they can be handled in low-containment facilities, in tropism, drug screening, the screening and evaluation of monoclonal antibodies, vaccine evaluation and serosurveillance studies.21,22\n\nNeutralization assays are useful tools to study antibody responses after natural exposure to viruses, or responses elicited by vaccination. These assays normally require the application of wild-type viruses, which can be limiting if the virus in use is highly pathogenic in humans.23,24\n\nIn this study, we describe the successful validation of a safe pseudotyped virus-based neutralisation assay using serum samples from the first international reference panel for anti-Lassa fever virus antibodies provided by the Medicines and Healthcare products Regulatory Agency (MHRA). The present study, conducted according to ICH guidelines (https://www.ich.org/page/ich-guidelines), underlines the importance of the pseudotype platform as a tool to increase the safety and accessibility of potency testing, to support the establishment of international standards and reference panels together with live viruses, and to support vaccine clinical trials by monitoring sera from vaccine candidates.\n\n\n2. Methods\n\nFor the production and titration of Lassa virus pseudotypes, as well as for pseudotype-based microneutralization assay, human embryonic kidney 293T/17 (HEK293T/17) (ATCC, cat number CRL-11268) are maintained in complete medium Dulbecco’s modified essential medium (DMEM) high glucose, pyruvate (Gibco, Catalog number: 11995073). The medium is supplemented with 10% FBS South America Origin EU approved Heat Inactivated (Euroclone, Catalog number: ECS5000LH) and 1% penicillin–streptomycin (Pen-Strep) (Merk, cat number: P4333). The cells are kept in incubator at 37°C with 5% CO2.\n\nThe gene of Lassa virus (LASV) (strain Josiah) glycoprotein is synthesized and cloned into plasmid expression vector phCMV3 (Sino Biological, cat number: VG40079-UT). The p8.91 lentiviral packaging plasmid expressing gag-pol, and the pCSFLW plasmid containing a firefly luciferase reporter are provide by Prof. Nigel Temperton (Viral Pseudotype Unit-VPU, University of Kent Medway School of Pharmacy).\n\nFor LASV pseudotype production, approximately 4.5×106 HEK293T/17 cells. 24h hours post seeding, cells are transfected with a plasmid DNA mixture composed of: 3 μg of p8.91, 4.5 μg of pCSFLW and 3 μg of LASV-G using 24 μlvof EndoFectin™-Lenti (GeneCopoeia, Catalog number: EF001) in 500 μl reduced serum medium Opti-MEM 1X (Gibco, Catalog number: 31985-070). At least 6 hours post-transfection 8 ml of fresh DMEM is replaced to the plates. 72 hours post-transfection LASV pseudotype particles are collected, centrifuged, filtered through 0.45μm syringe-driven membrane filters and stored at -80°C.\n\nPseudotype titration is performed in 96 well plate format: 50 μL of DMEM are added to every well except raw A where 100 μL of LASV pseudotype particles are added. Serial two-fold dilutions are performed from raw A to G, and 1×105 HEK293T/17 cells are added to each well. After 48 hours, 50 μL of Bright-Glo Luciferase Assay System (Promega, catalog number: E2620) are dispensed in each well and placed in a microplate shaker for 5 minutes at 400 rpm (Fisherbrand Catalog number: 88861024). Plate readout is performed with luminometer (Perkin Elmer; Victor Nivo) following parameter: Luminescence Endpoint, counts single label, 700 nm, 1000ms measurement time.\n\nPseudotype-based microneutralization (PBNA) is performed in 96 well plate format. LASV pseudotype working solution corresponds to 1×108 relative luminescence unit (RLU) divided by the pseudotype titre expressed in RLU/mL. 90 μL of DMEM are added to column one and 50 μL are added to the other wells. To column 1 are added 10 μL of serum samples at the proper dilution and immunoglobulins depleted serum (BBI Solutions, Catalog number: SF505-2) as used as negative control. Serial two-fold dilutions are performed from column 1 to 10. Subsequently, 50 μL of pseudotype working solution are added to each well up to column 10, and to column 12 from raw A to H (pseudotype control wells). The plate containing the mix pseudotypes-serum is incubated for 1 hour at 37°C with 5% CO2, afterwards 1×105 HEK293T/17 cells are added to each well. After 48 hours, 50 μL of Bright-Glo Luciferase Assay System are dispensed in each well and the plate is shake for 5 minutes at 400 rpm in a dark environment (Fisherbrand, Catalog number: 88861024). Plate readout is performed with a luminometer (Perkin Elmer; Victor Nivo).\n\nCalculation of Pseudotype titres were estimated by means of ExcelTM software; the pseudotype titres obtained at each point in a range of dilution points were expressed as RLU/mL, and the arithmetic mean was calculated. For the analyses of pseudotype-based neutralisation assays, the GraphPad Prism version 8.4 package was used (GraphPad Software, GraphPad, 2365 Northside Dr, Suite 560, San Diego, CA 92108, USA). The titres were firstly normalised based on pseudotype only mean value and cell only mean value, and IC50 values were calculated by a non-linear regression model (log (inhibitor) vs. normalised response-variable slope) analysis. Titres were subsequently expressed as the range of dilution in which the IC50 value lay.25\n\nThe assessment of the accuracy of a test is conducted by analyzing the data acquired for the evaluation of Dilutional Linearity (GMTs observed). According to the ICH guideline Q2 (European Medicines Agency. ICH Q2(R2) Validation of analytical procedures - Scientific guideline. 202226), there are two ways to test the accuracy of a test: by using a conventional true value or an accepted reference value as the expected value of GMT. The expected GMTs are determined by calculating the geometric mean of the results obtained from the neat sample divided by the corresponding factor of the two-fold serial dilution. To evaluate the Relative Accuracy, the percentage of recovery on the GMT of the observed values and the expected (true) titre is calculated by applying the following formula:\n\nLinearity is assessed by testing the 20/228, the 20/222 and the 20/204 samples from NIBSC reference panel for anti-Lassa fever virus in a two-fold dilution scheme, starting from a dilution of 1:20 to 1:2560 dilution The sample dilutions were tested in two repetitions per plate, and in two different plates by two different operators, on two different days. For each dilution, the geometric mean titre (GMT) is calculated. A linear regression analysis of logarithm base 2 of serum dilution versus logarithm base 2 of GMTs using the least squares method over the entire dilution range is performed and the slope of regression line and the coefficient of determination (R2) is calculated.\n\nPrecision is used to define the amount of scatter between several measurements obtained from multiple testing of the same sample under the standardized conditions. The Precision parameters are evaluated by the Percent Geometric Coefficient of Variation (%GCV) determined as\n\nThe validation process considers four crucial aspects of precision that are essential to evaluate the reliability of laboratory testing.\n\nThese aspects include intra-day variation, which measures the expected variation within each day under identical operating conditions.\n\nAdditionally, intra-operator variation is evaluated, which measures the expected variation within each operator under identical operating conditions.\n\nIntermediate precision, also known as inter-test variation, is considered to account for the variations and random events that may occur within the laboratory due to different environmental conditions, operators, equipment, or days.\n\nA further aspect is format variability (FV), which evaluates the expected variation between the average titer results obtained from multiple replicates in routine testing and considers two independent analyses (k = 2), each consisting of one replicate (n = 1). The FV is determined by the following equation:\n\nAn assay is defined as specific when it can, in a non-ambiguous manner, detect the analyte in the presence of other components. Here, specificity was assessed by testing LASV pseudotype against the second International Standard for anti-SARS-CoV-2 immunoglobulin (NIBSC code: 21/340), and against the first WHO International Reference Panel of Anti-Ebola virus (EBOV) Convalescent Plasmas (NIBSC code: 16/344) whose individual panel members are reported with the following NIBSC codes: 15/280 (ARC), 15/282 (NHSBT), 15/284 (NOR), 15/286 (INMI), 15/288 (negative human plasma). As negative control the immunoglobulin’s depleted serum was used (“Pseudotype based microneutralization assay” paragraph).\n\nTo assess the Specificity parameter the ratio between sera and no specific NIBSC, and between sera and negative samples is calculated.\n\n\n3. Results\n\nTo develop a safe and robust pseudotype neutralisation assay for LASV, phCMV3-GP LASV (strain Josiah) was co-transfected with p.8.91 gag-pol plasmid and pCSFLW plasmid containing a firefly luciferase reporter as shown in Figure 1A. 72 h post-transfection, cell culture supernatants containing pseudotypes particles (PV) were harvested and their transduction efficiency was assessed by measuring titres expressed as RLU/ml in HEK293/17 cells. As shown in Figure 1B, Lassa GP showed a pseudotype mean titre/ml of 4.98e+9 RLU/ml.\n\n(A) Packaging construct gag pol, reporter vector and pCMV3-GP LASV (strain Josiah) expression plasmids are co-transfected into HEK293/17 cells. Pseudotype proteins are packaged by the cell and budding occurs at the cell membrane to yield pseudotypes bearing desired glycoproteins and incorporated reporter. Culture supernatant was collected 72 hours after transfection and filtered through a 0.45 um filter. (B) Target HEK293/17 cells were transduced with LASV GP-pseudotyped lentiviral particles and the infectivity measured as relative luminescent units (RLU/mL).\n\nTo validate this pseudotype neutralisation assay for LASV, we performed a series of validation experiments using the MHRA Lassa panel 21/332.\n\nThis panel consisted of 5 sera (20/228, 20/204, 20/222, 20/246 and 20/248) and was established by an expert committee on biological standardisation in 2021. First, the IC50 of all 5 sera in the panel were tested against LASV GP pseudotypes/plate and 20/228 was selected as high control, 20/204 as medium and 20/222 as low control, Figure 2.\n\n(A) Reference antisera were used at starting dilution of 1:20 while LASV PV diluted to 1.000.000 RFU dose input as determined previously from titration. Each points represents the mean and standard deviation of two replicates per dilution repeated for three independent experiments. (B) Half-maximal inhibitory dilution of reference antisera as calculated from “log (inhibitor) vs. normalized response—Variable slope” from “Dose-response-Inhibition using Graph pad software. The values are previously normalized on only mean value of PV value and cell-only mean value.\n\nTo evaluate the relative accuracy of the assay, each serum was tested in 2 different analytical sessions performed by 2 operators with 2 replicates per session. The assay is considered to have acceptable relative accuracy if the percentage of recovery on the GM of the reportable values and the expected is within 50% - 200%. The assay is accurate from 1 to 64 dilutions for 20/228 standard. In addiction the table below, Table 1, also shows that the RAs at the 1:16 dilution for 20/204 and the 1:4 dilution for 20/222 are just below 50% but can be considered within the range of accurate dilutions as they are between multiple accurate dilutions.\n\nPrecision parameters are usually evaluated through the variance, standard deviation, or coefficient of variation of a series of measurements, Figure 3.\n\n3.4.1 Intra-Day variation\n\nThe two geometric means between results from same day but different operator (D1-O1 and D1-O2, D2-O1 and D2-O2) are calculated for each dilution. The Intra-Day variation is determined by the %GCV of the two geometric means.\n\nThe assay is considered to have acceptable Intra-Day variation if all samples have a %GCV less or equal than 50%. The results shown in Table 2 indicate that the assay has acceptable Intra-Day variation from 1:20 (neat) to 1:2560 for 20/228, 20/224 and 20/222.\n\nThe two geometric means between results from same operator but different day (D1-O1 and D2-O1, D1-O2 and D2-O2) are calculated for each dilution. The Intra-Operator variation is determined by the %GCV of the two geometric means.\n\nThe assay is considered to have acceptable Intra-Operator variation if all samples have a %GCV less or equal than 50%. The assay has also acceptable Intra-Operator variation from 1:20 (neat) to 1:2560 for 20/228, 20/224 and 20/222 (Figure 3, Table 3).\n\n3.4.2 Intra-Operator variation\n\nThe two geometric means between results from same operator but different day (D1-O1 and D2-O1, D1-O2 and D2-O2) are calculated for each dilution. The Intra-Operator variation is determined by the %GCV of the two geometric means.\n\nThe assay is considered to have acceptable Intra-Operator variation if all samples have a %GCV less or equal than 50%. The assay has also acceptable Intra-Operator variation from 1:20 (neat) to 1:2560 for 20/228, 20/224 and 20/222 (Figure 3, Table 3).\n\n3.4.3 Intermediate precision\n\nThe Intermediate Precision (IP) is assessed by calculating the %GCV of the four determinations for each dilution. The assay is deemed to be precise if all estimates of intermediate precision have %GCV less or equal than 50%. The results reported in Table 4 demonstrate that the assay is precise from 1:20 (neat) to 1:2560 for high, medium, and low serum.\n\n3.4.4 Format variability\n\nThe Format Variability (FV) measures the variability of a bioassay and is expressed as %GCV. The FV has a strong relationship with Critical Fold Difference (CFD) parameter given by CFD=(1+FV)qα, where qα is the quantile from the t-distribution with α = 0.01 and infinite degrees of freedom, which is well and properly approximated by the standard normal percentile zα = 2.326348. CFD is set to 4, and therefore the assay will be considered to have acceptable FV if all samples met %GCV ≤ 81.5%. The results shown in Table 5 indicate that the assay has acceptable FV from 1:20 (neat) to 1:2560 dilution for all control sera.\n\nDilution linearity is a critical evaluation conducted to ensure that a sample with a high concentration can be diluted to a concentration within the working range and still provide a reliable result. This test determines the linearity of the dose-response of the analyte, which is fundamental to ensuring that sample dilution does not affect accuracy and precision. Acceptable linearity of the test is achieved when the absolute value of the slope falls within the range of 0.7 to 1.3. The absolute slope values of samples 20/228, 20/204, and 20/222 were 1.1, 1.0, and 0.8, respectively as showed in Figure 4 and Figure 5.\n\nThe proposed graph showing the logarithm (base 2) of the dilution on the x-axis and the logarithm (base 2) of the obtained GMT on the y-axis.\n\nSpecificity is the ability of the assay to detect and differentiate the analyte of interest.23–25 To determine the specificity of the assay, all 5 sera from the Lassa panel, positive versus heterologous viruses and negative donors were tested. As visualised in Figure 6 and Table 6, 20/228 showed a fold difference of 56 versus heterologous virus serum and negative donors; 20/204 a fold difference of 37; 20/222 a fold difference of 16; 20/246 a fold difference of 8 and 20/248 a fold difference of 5. All 5 components of the panel are specific for this assay.\n\nThe assay will be considered specific if Lassa serum have at least a four-fold difference (i.e., ≥ 4-fold) to the heterologous panel and negative panel.\n\n\n4. Discussion\n\nThe emergence of coronavirus disease 2019 (COVID-19) has had a variety of devastating public health and socioeconomic impacts around the world, leading to a decline in the epidemiological control of several infectious diseases, including zoonotic diseases such as Lassa fever LF.27 Epidemiological data show that the magnitude and timing of Lassa fever (LF) outbreaks have improved in recent years, particularly in Nigeria,28 where the case fatality rate (CFR) continues to hover around 20%.29,30 In endemic areas, the annual incidence of Lassa virus (LASV) infection ranges from 100,000 to 300,000 cases and the associated mortality is between 5,000 and 10,000 deaths per year.31,32 However, challenges with clinical diagnosis and limited existing surveillance infrastructure mean that the disease is likely to be significantly under-reported and that incidence rates in countries where the disease is known to be endemic are imprecise. Due to its epidemic potential, combined with no or inadequate control measures, LASV has been identified as one of the top ten priority pathogens for research and development under the WHO R&D Blueprint for Emerging Infections.33\n\nThe overall goal of the R&D Blueprint is to reduce the time needed to develop safe and effective medical countermeasures - both curative and preventive - and to accelerate the development of diagnostic treatments and vaccines.32 To achieve this goal, several vaccines against LASV are in development as a result of global efforts, six of which are supported by the Coalition for Epidemic Preparedness Innovations (CEPI). In parallel, the development of biological standards and validated assays will be critical to assess vaccine-induced immune responses and promote standardisation, transparency, and comparability between candidates.34 In this scenario, a standardised neutralisation assay will facilitate the down-selection of different vaccine candidates for clinical development, as the neutralisation titre is a key parameter for predicting immunity, i.e. for vaccine development.35\n\nIn October 2018, WHO endorsed the production of an international standard for anti-Lassa virus antibodies to establish a reference material that would allow comparison of LSV serological data reported between laboratories and at different stages of clinical trials. In this collaborative study, pools of convalescent sera or plasma from either Sierra Leone or Nigeria with different anti-LASV antibody titres, including a negative control, were tested by participants using serological assays routinely used in their laboratories. Most participants, including the serology department of Vismederi srl, used the Josiah live virus isolate or GP and NP proteins derived from the Josiah LASV isolate. Finally, in 2021, the collaborative study (WHO/BS/2021_2406) enabled the establishment of the first WHO International Standard and Reference Panel for Anti-Lassa Fever (NIBSC code 21/332), a valuable tool for the development and evaluation of the sensitivity of serological assays for LASV antibodies.36\n\nTaking advantage of the availability of this international anti-Lassa fever reference panel and following the efficient production of the LASSA GP pseudotype by adapting the protocol described in Ferrara and Temperton 2018, we developed a lentiviral pseudotype-based assay to facilitate the accurate determination of neutralising antibody responses to LSV. Pseudotyped viruses are a valid tool that can be used as a surrogate for live viruses to study host-virus interactions and to test the ability of a given serum sample to neutralise virus particles in vitro. For the latter, validation and/or qualification procedures play a key role in providing reliable results, especially when they can be used to evaluate the efficacy of new potential vaccines or antiviral drugs. It is important that experiments, criteria, and statistical analyses follow defined and accepted international guidelines (European Medicines Agency. ICH Q2(R2) Validation of analytical procedures - Scientific guideline. 202226).\n\nHere we performed a series of optimisation and validation experiments of the pseudovirus-based neutralisation assay (PBNA) and panel 21/332, which allowed us to establish the best experimental conditions to minimise the variation in data obtained from different experiments. Specifically, we performed the accuracy, precision, and linearity on three sera from the panel: 20/228, which according to the report gave us the highest titer samples for neutralising antibodies, 20/204, which showed medium titer neutralising antibodies, and 20/222, one of the three lowest titer samples in the whole panel. To evaluate the specificity parameter, we used all five sera in the LASSA panel, 7 serum-positive heterologous viruses and 10 negative donors were tested.\n\nOur experiments and analyses demonstrate that the PBNA for Lassa Gp is a sensitive, accurate, reproducible, and specific serological test for assessing neutralising activity against LSV. The results presented also highlight the importance of selecting a highly responsive control to establish all the acceptance criteria for assay validation, to determine relative accuracy and linearity. In fact, it was observed that while all 3 selected sera of the panel allowed to obtain an accurate and reproducible assay at all tested dilutions, the low serum 20/222 only met the acceptable criteria for accuracy and linearity from 1 to 8-fold dilutions.\n\nIt is important to emphasise that the PBNA-GP Lassa assay presented can be considered a safe, reproducible and sensitive assay: safe because the pseudotypes are replication-deficient viruses containing LASSA-GP protein glycoproteins, devoid of virulent viral components and involved in a single round of replication; highly sensitive because we have used Nluc as a reporter gene to obtain a wide dynamic range of neutralisation titres; and reproducible because the reading was obtained by luminometer rather than a manual reading under the microscope dependent on operator interpretation.37\n\nIn conclusion, the proposed validated PBNA-GP assay represents a powerful and safe platform for measuring the induction of the immune response in the detection of neutralising antibodies generated in response to the LSV vaccine antigen in vaccine evaluation. The data from this validation can be used to harmonise data between laboratories and the different vaccines in development thanks to the 1st International Reference Panel for Anti-Lassa Fever Virus Antibodies, providing a strong boost to progress in vaccine development against LSV.\n\n\nEthical considerations\n\nNot applicable.\n\n\nPatient consent\n\nNot applicable.\n\n\nPermission to reproduce material from other sources\n\nNot applicable.\n\n\nClinical trial registration\n\nNot applicable.", "appendix": "Data availability\n\nThe data that supports the findings of this study “A validate and standardized pseudotyped microneutralization assay as a safe and powerful tool to measure LASSA neutralising antibodies for vaccine development and comparison.” are available in biostudies portal AccessionS-BSST1413. DOI: 10.6019/S-BSST1413.\n\nThis project contains following dataset:\n\n1. Validation table pseudotypes microneutralization assay.\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\nHallam HJ, Hallam S, Rodriguez SE, et al.: Baseline mapping of Lassa fever virology, epidemiology and vaccine research and development. NPJ Vaccines. 2018 Mar 20; 3: 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArefin A, Ismail Ema T, Islam T, et al.: Target specificity of selective bioactive compounds in blocking α-dystroglycan receptor to suppress Lassa virus infection: an insilico approach. J. Biomed. Res. 2021 Nov 6; 35(6): 459–473. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTroup JM, White HA, Fom AL, et al.: An outbreak of Lassa fever on the Jos plateau, Nigeria, in January-February 1970. A preliminary report. Am. J. Trop. Med. Hyg. 1970 Jul; 19(4): 695–696. PubMed Abstract \| Publisher Full Text\n\nFichet-Calvet E, Rogers DJ: Risk maps of Lassa fever in West Africa. PLoS Negl. Trop. Dis. 2009; 3(3): e388. Epub 2009 Mar 3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMadueme PU, Chirove F: Understanding the transmission pathways of Lassa fever: A mathematical modeling approach. Infect. Dis. Model. 2022 Nov 30; 8(1): 27–57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKofman A, Choi MJ, Rollin PE: Lassa Fever in Travelers from West Africa, 1969-2016. Emerg. Infect. Dis. 2019 Feb; 25(2): 245–248. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWolff S, Schultze T, Fehling SK, et al.: Genome Sequence of Lassa Virus Isolated from the First Domestically Acquired Case in Germany. Genome Announc. 2016 Sep 22; 4(5): e00938–e00916. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMazzola LT, Kelly-Cirino C: Diagnostics for Lassa fever virus: a genetically diverse pathogen found in low-resource settings. BMJ Glob. Health. 2019 Feb 7; 4(Suppl 2): e001116. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurri DJ, Pasquato A, da Palma JR , et al.; The role of proteolytic processing and the stable signal peptide in expression of the Old World arenavirus envelope glycoprotein ectodomain. Virology. 2013 Feb 5; 436(1): 127–133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEichler R, Lenz O, Strecker T, et al.: Identification of Lassa virus glycoprotein signal peptide as a trans-acting maturation factor. EMBO Rep. 2003 Nov; 4(11): 1084–1088. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobinson JE, Hastie KM, Cross RW, et al.: Most neutralizing human monoclonal antibodies target novel epitopes requiring both Lassa virus glycoprotein subunits. Nat. Commun. 2016 May 10; 7: 11544. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSattler RA, Maruyama J, Shehu NY, et al.: Current small animal models for LASV hearing loss. Curr. Opin. Virol. 2019 Aug; 37: 118–122. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOlayemi A, Adesina AS, Strecker T, et al.: Determining Ancestry between Rodent- and Human-Derived Virus Sequences in Endemic Foci: Towards a More Integral Molecular Epidemiology of Lassa Fever within West Africa. Biology (Basel). 2020 Feb 7; 9(2): 26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMadueme PU, Chirove F: Understanding the transmission pathways of Lassa fever: A mathematical modeling approach. Infect. Dis. Model. 2022 Nov 30; 8(1): 27–57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIslam MR, Akash S, Rahman MM: Epidemiology, symptoms, transmission, prevention, treatment, and future prospects of the Lassa fever outbreak: a potential study. Int. J. Surg. 2023 Mar 1; 109(3): 531–533. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOkokhere PO, Erameh CO, Alikah F, et al.: Acute Lassa Virus Encephalitis with Lassa Virus in the Cerebrospinal Fluid but Absent in the Blood: A Case Report with a Positive Outcome. Case Rep. Neurol. 2018 Jul 3; 10(2): 150–158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcCormick JB, Fisher-Hoch SP: Lassa fever. Curr. Top. Microbiol. Immunol. 2002; 262: 75–109. PubMed Abstract \| Publisher Full Text\n\nAloke C, Obasi NA, Aja PM, et al.: Combating Lassa Fever in West African Sub-Region: Progress, Challenges, and Future Perspectives. Viruses. 2023 Jan 3; 15(1): 146. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMehand MS, Al-Shorbaji F, Millett P, et al.: The WHO R&D Blueprint: 2018 review of emerging infectious diseases requiring urgent research and development efforts. Antivir. Res. 2018 Nov; 159: 63–67. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBentley EM, Mather ST, Temperton NJ: The use of pseudotypes to study viruses, virus sero-epidemiology and vaccination. Vaccine. 2015 Jun 12; 33(26): 2955–2962. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang Y, et al.: Pseudotyped Viruses.Wang Y, editors. Pseudotyped Viruses. Advances in Experimental Medicine and Biology. Singapore: Springer; 2023; vol 1407. : pp 1–27. PubMed Abstract \| Publisher Full Text\n\nXiang Q, Li L, Wu J, et al.: Application of pseudovirus system in the development of vaccine, antiviral-drugs, and neutralizing antibodies. Microbiol. Res. 2022 May; 258: 126993. Epub 2022 Feb 16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCantoni D, Mayora-Neto M, Temperton N: The role of pseudotype neutralization assays in understanding SARS CoV-2. Oxf. Open Immunol. 2021 Mar 13; 2(1): iqab005. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFerrara F, Temperton N: Pseudotype Neutralization Assays: From Laboratory Bench to Data Analysis. Methods Protoc. 2018 Jan 22; 1(1): 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHyseni I, Molesti E, Benincasa L, et al.: Characterisation of SARS-CoV-2 Lentiviral Pseudotypes and Correlation between Pseudotype-Based Neutralisation Assays and Live Virus-Based Micro Neutralisation Assays. Viruses. 2020 Sep 10; 12(9): 1011. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEuropean Medicines Agency: ICH Q2(R2) Validation of analytical procedures ‐ Scientific guideline. 2022. Reference Source\n\nNnaji ND, Onyeaka H, Reuben RC, et al.: The deuce-ace of Lassa Fever, Ebola virus disease and COVID-19 simultaneous infections and epidemics in West Africa: clinical and public health implications. Trop. Med. Health. 2021 Dec 30; 49(1): 102. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHasan MM, Costa ACDS, Xenophontos E, et al.: Lassa fever and COVID-19 in Africa: A double crisis on the fragile health system. J. Med. Virol. 2021 Oct; 93(10): 5707–5709. Publisher Full Text \| PubMed Abstract \| Free Full Text\n\nDalhat MM, Olayinka A, Meremikwu MM, et al.: Epidemiological trends of Lassa fever in Nigeria, 2018-2021. PLoS One. 2022 Dec 30; 17(12): e0279467. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIlori EA, Furuse Y, Ipadeola OB, et al.: Nigeria Lassa Fever National Response Team. Epidemiologic and clinical features of Lassa fever outbreak in Nigeria, January 1-May 6, 2018. Emerg. Infect. Dis. 2019; 25(6): 1066–1074. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPurushotham J, Lambe T, Gilbert SC; Vaccine platforms for the prevention of Lassa fever. Immunol. Lett. 2019 Nov; 215: 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBagcchi S: Lassa Fever outbreak continues across Nigeria. Lancet Infect. Dis. 2020; 20(5): 543. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBloom DE, Cadarette D: Infectious disease threats in the twenty-first century: strengthening the global response. Front. Immunol. 2019; 10: 549.32. Mehand MS, Al-Shorbaji F, Millett P, Murgue B. The WHO R&D Blueprint: 2018 review of emerging infectious diseases requiring urgent research and development efforts. Antiviral Res. 2018 Nov; 159:63-67. doi: 10.1016/j.antiviral.2018.09.009. Epub 2018 Sep 24. PMID: 30261226; PMCID: PMC7113760 PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMattiuzzo G, Bentley EM, Page M: The Role of Reference Materials in the Research and Development of Diagnostic Tools and Treatments for Haemorrhagic Fever Viruses. Viruses. 2019 Aug 24; 11(9): 781. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuruato AE, Fontes-Garfias CR, Ren P, et al.: A high-throughput neutralizing antibody assay for COVID-19 diagnosis and vaccine evaluation. Nat. Commun. 2020 Aug 13; 11(1): 4059. Erratum in: Nat Commun. 2021 Jun 22;12(1):4000. PMID: 32792628; PMCID: PMC7426916. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMattiuzzo G, Bentley EM, Richardson S, et al.: 2021 WHO Expert Committee on Biological Standardization. WHO/BS/2021.2406.\n\nSchmidt F, Weisblum Y, Muecksch F, et al.: Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses. J. Exp. Med. 2020 Nov 2; 217(11): e20201181. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "299463", "date": "16 Jul 2024", "name": "Jesse Bloom", "expertise": [ "Reviewer Expertise Virus evolution" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSUMMARY:\nThis paper describes a pseudotyped lentivirus neutralization assay for antibodies targeting Lassa virus GPC. Such an assay is useful for characterization of immunity, vaccines, and antibodies to this virus. This paper is a useful addition to the literature and has the scientific content to merit publications.\nHowever, there are a number of small inconsistencies in phrasing or other small oversights/errors that should be addressed through minor modifications in the final version. These minor critiques are listed below:\nSPECIFIC COMMENTS:\n- Title should say \"validated\" not \"validate\"\n- Title should say \"Lassa virus\" not \"LASSA\"\n- Abstract: there is a typo where it says \"LSV\" rather than \"LASV\"\n- Introduction: in the paragraph beginning \"LASV case fatality rates (CFRs) differ between countries...\" there is some sort of typo where it says the CFR is \"69%65\". More generally, case fatality rates can depend heavily on the efficiency of how many non-severe infections are detected as cases, so this comparison may reflect more about the case ascertainment in different countries than the actual severity of disease following infection.\n- In the paragraph beginning \"Improvement in the development of Lassa vaccine and treatments has been hampered...\" it might be better to say \"complicated\" rather than \"hampered\". The word \"hampered\" implies it is a bad thing that Lassa is a BSL-4 pathogen, but there are good reasons for this classification given the severity of the virus.\n- Citations should be made to prior work that has pseudotyped LASV GPC using methods similar to those in this paper. For instance, see the following PMIDs: (Carr et al.,2024), (Larson et al.,2004), (Reignier et al.,2006), (Kunz et al.,2005)\n- Figure 1: I assume \"CC CTR\" refers to some type of negative control, but the figure legend does not provide an explanation of what that means. This should be explained.\n- The paper should provide more details on the five anti-LASV reference sera including what they represent and how they were obtained.\n- The images in Figure 2 are very low resolution and clipped on the right side.\n- First paragraph of the discussion: this claim seems dubious; is there actually evidence that COVID-19 increased occurrences of Lassa fever? Lassa was causing infections long before COVID-19 and the two seem largely unrelated.\n- Second sentence of Discussion: should be \"increased\" not \"improved\"\n- Second-to-last paragraph of Discussion: should be \"LASV GPC\" not \"LASSA-GP\"\n- Methods: Incomplete sentence in section 2.3: “For LASV pseudotype production, approximately 4.5x106 HEK293T/17 cells.”\n- Discussion: five instances of typo where it says “LSV” instead of “LASV”\n- Figures 3, 5, and 6 do not have legends. Adding legends will help with interpreting the plots\n- Figure 6 has the following typos \"Standars agaist other infection\" and \"Negative serum F pannel\"\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12532", "date": "14 Oct 2024", "name": "roberta antonelli", "role": "Author Response", "response": "Jesse D Bloom SPECIFIC COMMENTS: - Title should say \"validated\" not \"validate\" the correction has been incorporated - Title should say \"Lassa virus\" not \"LASSA\" . the correction has been incorporated - Abstract: there is a typo where it says \"LSV\" rather than \"LASV\" the correction has been incorporated - Introduction: in the paragraph beginning \"LASV case fatality rates (CFRs) differ between countries...\" there is some sort of typo where it says the CFR is \"69%65\". More generally, case fatality rates can depend heavily on the efficiency of how many non-severe infections are detected as cases, so this comparison may reflect more about the case ascertainment in different countries than the actual severity of disease following infection. The paragraph was rewritten - In the paragraph beginning \"Improvement in the development of Lassa vaccine and treatments has been hampered...\" it might be better to say \"complicated\" rather than \"hampered\". The word \"hampered\" implies it is a bad thing that Lassa is a BSL-4 pathogen, but there are good reasons for this classification given the severity of the virus. the correction has been incorporated - Citations should be made to prior work that has pseudotyped LASV GPC using methods similar to those in this paper. For instance, see the following PMIDs: (Carr et al.,2024), (Larson et al.,2004), (Reignier et al.,2006), (Kunz et al.,2005) the references has been incorporated - Figure 1: I assume \"CC CTR\" refers to some type of negative control, but the figure legend does not provide an explanation of what that means. Explanation in the figure legend has been incorporated - The paper should provide more details on the five anti-LASV reference sera including what they represent and how they were obtained. In the paragraph 3.2 we have explained that is a panel from MHRA Lassa panel 21/332 established by an expert committed . In the material and method and in the main , we introduced the detail of this WHO International Reference Panel for anti-Lassa fever virus antibodies NIBSC code: 21/332. This panel is commercially available from NIBCShttps://nibsc.org/products/brm_product_catalogue/detail_page.aspx?catid=21/332 - The images in Figure 2 are very low resolution and clipped on the right side. We have improved the image quality - First paragraph of the discussion: this claim seems dubious; is there actually evidence that COVID-19 increased occurrences of Lassa fever? Lassa was causing infections long before COVID-19 and the two seem largely unrelated. The sentence was rewritten - Second sentence of Discussion: should be \"increased\" not \"improved\" The change has been made the correction has been incorporated - Second-to-last paragraph of Discussion: should be \"LASV GPC\" not \"LASSA-GP\" the correction has been incorporated - Methods: Incomplete sentence in section 2.3: “For LASV pseudotype production, approximately 4.5x106 HEK293T/17 cells.” the correction has been incorporated - Discussion: five instances of typo where it says “LSV” instead of “LASV” he corrections have been incorporated - Figures 3, 5, and 6 do not have legends. Adding legends will help with interpreting the plots the legends have been incorporated - Figure 6 has the following typos \"Standars agaist other infection\" and \"Negative serum F pannel\" the correction has been incorporated" }, { "c_id": "12533", "date": "14 Oct 2024", "name": "roberta antonelli", "role": "Author Response", "response": "SPECIFIC COMMENTS: - Title should say \"validated\" not \"validate\" the correction has been incorporated - Title should say \"Lassa virus\" not \"LASSA\" . the correction has been incorporated - Abstract: there is a typo where it says \"LSV\" rather than \"LASV\" the correction has been incorporated - Introduction: in the paragraph beginning \"LASV case fatality rates (CFRs) differ between countries...\" there is some sort of typo where it says the CFR is \"69%65\". More generally, case fatality rates can depend heavily on the efficiency of how many non-severe infections are detected as cases, so this comparison may reflect more about the case ascertainment in different countries than the actual severity of disease following infection. The paragraph was rewritten - In the paragraph beginning \"Improvement in the development of Lassa vaccine and treatments has been hampered...\" it might be better to say \"complicated\" rather than \"hampered\". The word \"hampered\" implies it is a bad thing that Lassa is a BSL-4 pathogen, but there are good reasons for this classification given the severity of the virus. the correction has been incorporated -Citations should be made to prior work that has pseudotyped LASV GPC using methods similar to those in this paper. For instance, see the following PMIDs: (Carr et al.,2024), (Larson et al.,2004), (Reignier et al.,2006), (Kunz et al.,2005) the references has been incorporated - Figure 1: I assume \"CC CTR\" refers to some type of negative control, but the figure legend does not provide an explanation of what that means. Explanation in the figure legend has been incorporated - The paper should provide more details on the five anti-LASV reference sera including what they represent and how they were obtained. In the paragraph 3.2 we have explained that is a panel from MHRA Lassa panel 21/332 established by an expert committed . In the material and method and in the main , we introduced the detail of this WHO International Reference Panel for anti-Lassa fever virus antibodies NIBSC code: 21/332. This panel is commercially available from NIBCShttps://nibsc.org/products/brm_product_catalogue/detail_page.aspx?catid=21/332 - The images in Figure 2 are very low resolution and clipped on the right side. We have improved the image quality - First paragraph of the discussion: this claim seems dubious; is there actually evidence that COVID-19 increased occurrences of Lassa fever? Lassa was causing infections long before COVID-19 and the two seem largely unrelated. The sentence was rewritten - Second sentence of Discussion: should be \"increased\" not \"improved\" The change has been made the correction has been incorporated - Second-to-last paragraph of Discussion: should be \"LASV GPC\" not \"LASSA-GP\" the correction has been incorporated - Methods: Incomplete sentence in section 2.3: “For LASV pseudotype production, approximately 4.5x106 HEK293T/17 cells. ” the correction has been incorporated - Discussion: five instances of typo where it says “LSV” instead of “LASV” the corrections have been incorporated - Figures 3, 5, and 6 do not have legends. Adding legends will help with interpreting the plots the legends have been incorporated - Figure 6 has the following typos \"Standars agaist other infection\" and \"Negative serum F pannel\" the correction has been incorporated" } ] }, { "id": "299459", "date": "13 Sep 2024", "name": "Jinwoo Lee", "expertise": [ "Reviewer Expertise viral fusion" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverview: Antonelli et al. describe a method utilizing the pseudotyped microneutralization assay for testing antibodies in vaccine development. This study demonstrates that highly infectious viruses such as Lassa, Ebola, and Coronaviruses can be adapted for testing antibody activity using pseudotyped. The importance of applying pseudotyped viruses and validating the data is evident, as this method provides a safer and more accessible means to study these viruses, facilitating antibody testing in settings with limited biosafety facilities. Addressing the suggested improvements in figures, explanations, title, discussion, data representation, and abbreviations will enhance reader comprehension and the impact of the validation and standardization.\nThe figures in the article require improvement, and additional explanations should be added to enhance readers' understanding. Please revise the figures for better clarity and ensure they include comprehensive legends. The addition of detailed explanations in the results or discussion sections will help readers interpret the data more effectively since, for general readers, it might require a bit less explanation to digest the article thoroughly. The title and discussion sections do not clearly explain how this method will be used for vaccine development. Please provide explicit connections in the discussion on how the pseudotyped microneutralization assay advances vaccine development. This can include examples of potential applications and anticipated outcomes. The introduction contains conflicting information regarding death rates and case fatality rates (CFR). It's important to clarify the difference between the death rate of 5,000 out of 100,000-300,000 cases (<5%) and the CFR of around 20-30%. This will help readers understand the context and significance of each percentage, avoiding confusion and ensuring accurate interpretation of the data. Some data points in the figures are missing error bars or are too tight to be visible. For example, Figure 2B does not have any error bars, it might be helpful to add a standard error of the means. Please review and adjust the figure settings as necessary to improve visibility. In Table 1, the observed GMT is higher than expected after dilution, with an observed GMT of always 10 after certain dilutions. It's important to provide an explanation for this observed trend in GMT after dilution. Discussing potential reasons for seeing a GMT of 10 only at high dilutions will help readers understand the data and its implications. Furthermore, relative accuracy is failed and passed again when it is diluted. The authors explanation will help readers. Some abbreviations are not spelled out the first time they are used. Please ensure all abbreviations are spelled out when first used in the text. This will help readers who may not be familiar with the terminology. When pseudoparticles are produced, the shape of the particle might be more influenced by the matrix protein. To expand this method, it might be useful to suggest that glycoprotein is more important than the shape and size of the actual virus for the binding of antibodies, considering that Ebola is a filovirus.\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": "12531", "date": "14 Oct 2024", "name": "roberta antonelli", "role": "Author Response", "response": "Jinwoo Lee 1_The figures in the article require improvement, and additional explanations should be added to enhance readers' understanding. Please revise the figures for better clarity and ensure they include comprehensive legends. The addition of detailed explanations in the results or discussion sections will help readers interpret the data more effectively since, for general readers, it might require a bit less explanation to digest the article thoroughly. To improve the quality of the article figure legends have been introduced in all figures, some details or paragraph have been introduced in the Introduction and Discussion, regarding the results some details are yet elucidated in the Materials and Methods section because we would like to maintain the compact structure of the paper. 2_The title and discussion sections do not clearly explain how this method will be used for vaccine development. Please provide explicit connections in the discussion on how the pseudotyped microneutralization assay advances vaccine development. This can include examples of potential applications and anticipated outcomes. To emphasise that pseudotyped neutralisation assays can be extremely useful in assessing not only how well circulating virus isolates match vaccine formulations, but also how well these vaccines can cross-protect against emerging drift variants, a paragraph has been added to the Discussion section. In this section, we have cited several examples where the applicability of pseudotyped LV-based neutralisation assays has been demonstrated as a useful tool for investigating NAbs generated by different vaccine candidates. 3_The introduction contains conflicting information regarding death rates and case fatality rates (CFR). It's important to clarify the difference between the death rate of 5,000 out of 100,000-300,000 cases (<5%) and the CFR of around 20-30%. This will help readers understand the context and significance of each percentage, avoiding confusion and ensuring accurate interpretation of the data. We have rewritten this point more clearly adding some sentences in the introduction section 3_ Some data points in the figures are missing error bars or are too tight to be visible. For example, Figure 2B does not have any error bars, it might be helpful to add a standard error of the means. Please review and adjust the figure settings as necessary to improve visibility. We have introduced the error bars and the figures 2 , 5 and 6 are reuploaded 4_ In Table 1, the observed GMT is higher than expected after dilution, with an observed GMT of always 10 after certain dilutions. It's important to provide an explanation for this observed trend in GMT after dilution. Discussing potential reasons for seeing a GMT of 10 only at high dilutions will help readers understand the data and its implications. Furthermore, relative accuracy is failed and passed again when it is diluted. The authors explanation will help readers. As explain in the paper The accuracy of the test was evaluated by using the reportable (RP) values obtained during the evaluation of Linearity. Following the ICH guideline the accuracy can be tested by using either a conventional true value or an accepted reference value. The GMT of the expected values was calculated from the GMT of the results obtained from the neat sample, and by dividing this value by the corresponding factor of the twofold serial dilution. Relative accuracy was evaluated by calculating the percentage of recovery on the GMT of the RP values and the expected (true) titer and applying the formula: 100 × (GMT observed/GMT expected). Is it true that in one point of the 20/ 228 the observed GMT is higher than expected but follow the criteria The assay is considered to have acceptable relative accuracy if the percentage of recovery on the GM of the reportable values and the expected is within 50% - 200%. 5_Some abbreviations are not spelled out the first time they are used. Please ensure all abbreviations are spelled out when first used in the text. This will help readers who may not be familiar with the terminology. We have introduced these changes. 6_When pseudoparticles are produced, the shape of the particle might be more influenced by the matrix protein. We have produced the Lassa pseudotype virus using GAG from HIV and this pseudotype is predominantly spherical in shape when in-vitro. To expand this method, it might be useful to suggest that glycoprotein is more important than the shape and size of the actual virus for the binding of antibodies, considering that Ebola is a filovirus. We agree with the reviewer that the GP is more important than the shape and size of the actual virus for the binding of antibodies. We are aware of the fact that for some viruses, like Ebola, that it may be preferable to pseudotype the GP onto a virus core with a more comparable morphology such as a rhabdoviral VSV core. However in this manuscript we are working with Lassa virus which has a spherical structure making it highly compatible with the HIV core used." } ] } ]	1	https://f1000research.com/articles/13-534
https://f1000research.com/articles/13-1229/v1	14 Oct 24	{ "type": "Research Article", "title": "Does cross-cultural adjustment affect employee work commitment? Assessing the role of work factors within selected mission hospitals in Kenya", "authors": [ "Abigael Chepkirui", "Simon M. Thiong'o", "Abigael Chepkirui" ], "abstract": "Background Globalization has expanded the scope of business with many companies relying on the contribution of expatriates to fill skills gap in foreign business operations, transferring management knowledge, launching new operations, and coordinating activities on a global scale. Expatriates, however, face challenges that stem from cultural differences. Their commitment levels depend on how well and how quickly they adjust to the unfamiliar culture(s) of the host country.\n\nMethods This study sought to investigate the implications of work factors on commitment of expatriates working in selected mission hospitals in Kenya. It was anchored on the provisions of the Three-Component Commitment and International Adjustment theories and a randomly selected sample of 112 respondents from a target population of 156 medical expatriates.\n\nResults and conclusions The results depicted that work-related factors significantly affected employee commitment (β= -1.033, p=0.000). To conclude, we argue that employee commitment amongst expatriates can be enhanced through work factors’ cross-cultural adjustment. We further recommend setting up of cross-cultural adjustment policies for expatriate workers within the workplace, particularly in mission hospitals.", "keywords": [ "Cross cultural adjustment", "Employee commitment", "Medical expatriates", "Kenya." ], "content": "Introduction\n\nWorkplace Commitment (in the context of this study) is associated with level of enthusiasm and attachment employees have with the organisation they work for/in (Piñeros Espinosa, 2022). As such, the workforce that is committed to their employer have a sense of responsibility and an overall understanding and appreciation of work vision, mission, goals, and objectives (Agus & Selvaraj, 2020).\n\nGiven the nature of contemporary economy, maintaining high levels of employee commitment (EC) has emerged as a primary concern for many businesses. Over the course of the last two decades, a number of researchers have attempted, with limited success, to offer a definition of EC. However, according to one definition by Mitonga-Monga and Cilliers (2016), the idea of EC relates to an employee’s willingness to work according to the business’s aims and values, as well as their contributions that go above and beyond what is expected of them by the organization. It is the psychological condition attaching the employees to their organization that is the primary factor impacting the decisions that employees make regarding whether or not they will continue working for the organization. It can also be characterised as a person’s sense of loyalty or attachment to a company, which may appear as a desire to stay along with a diligent devotion to work (Nobile, 2017). It could also be characterised as the degree of obligation an employee feels towards a company.\n\nOne of the most significant current discussions related to EC places importance on employees as a strategic resource for any organization as they tend to exemplify high work performance and are more proactive in addressing the needs of the organization (Castro & Martins, 2010; Arsenijević et al., 2017). Staff with high EC tends to share the goals and objectives of their organization, have the inclination to work diligently for the benefit of their institution, and wish to stay in the organization for a longer period because they love been associated with it. EC leads to beneficial results to the organization for example reduces job rotation, reduces absenteeism, performance improvement and general organizational efficiency. Employee level of commitment is influenced by job satisfaction, organizational climate and leadership styles (Amunkete & Rothman, 2015).\n\nThe importance of EC has been established in a number of industries. For example, Yang (2008) examined this concept in the Taiwanese hotel industry by determining employees’ beliefs about job satisfaction and their individual commitment to an organization. Elsewhere, Joāo and Coetzee (2012) explored EC and its relationship to perceived career mobility and job retention among early-career employees in the South African financial sector. Contextually, studies of EC have not escaped the health sector - Tekingündüz et al. (2017) investigated the effect of job satisfaction dimensions, organizational trust, and demographics on the EC in Turkish public hospitals. Maharani and Tampubolon (2018) on the other hand examined the consequences of corporatisation on EC and EC’s relationship with work values and job satisfaction in Indonesian hospitals. These studies undoubtedly confirm that EC as a human resource management component has been at the hearts of numerous industries in addressing issues that affect employees’ stability in an organization.\n\nThere are several studies that have reported on EC aspects in the hospitality industry. Kara (2012), for instance, explored disparities in organizational commitment with respect to gender in five-star hotels in Ankara, Turkey. This study was part of a larger investigation of EC aspects that have been conducted in a variety of different ways. According to the results of the research, there was no statistically significant disparity between male and female workers with regard to the attitudinal commitment factor that is a component of the EC scale. On the other hand, the behavioural commitment factor reported high levels of males being committed in comparison to their female counterparts. Additionally, a different research study investigated the amount to which organizational climate, leadership styles, and job satisfaction influence EC in South African troops. According to the findings, the dimensions of emotional contagion (Affective, Continuance, and Normative) (see summary Table 1) demonstrated that it moderates favourable connections between transactional, transformational, and laissez-faire leadership styles (Makhathini & Van Dyk, 2018).\n\nAccording to the findings of yet another study that was published not too long ago, EC dimensions can be modelled into three different components: affective, normative, and continuing (Yang, 2008). See also Meyer and Allen, 1991). These components play a preponderant impact in employee turnover as well as work satisfaction inside a firm. They were further proposed by Buitendach & Hendrina (2012). Affective commitment is the first component of organizational commitment, and it includes the ways in which an employee identifies with, participates in, and is attached to the organization. Employees derive happiness from their work, their fellow workers, and the atmosphere of their workplace - contributing to and supporting that satisfaction. According to Kumari and Afroz (2013), employees that have a strong affective commitment will have a greater level of participation and attachment to the firm. The organization’s capacity to perform more effectively is improved as a result of this kind of dedication. A significant level of job satisfaction and involvement, in addition to a rise in job performance, are examples of such gains (Liou & Cheng, 2010). Continuance commitment on the other hand is anchored on employee’s judgment of the cost implications of quitting or stopping a certain activity in an organization. According to Joāo and Coetzee (2012), these workers are likely to be retained by the organization either for the reason that they believe there are few viable alternatives or because there are significant costs involved with quitting the business. Employees who have a continuing commitment may only perform to the level necessary for them to keep their employment, according to research published in 2008 by Liou. The final constituent of commitment (normative) entails the experience of having a sense of responsibility to the company as a consequence of pressure from other people or the idea that it is morally acceptable to do so. This sense of obligation might be caused by the belief that it is morally correct to do so. To put it another way, it is an individual’s sense of responsibility and devotion to an institution because they suppose it’s the ethical and right thing to do (Mitonga-Monga & Cilliers, 2016). Therefore, to accurately measure institutional commitment of expatriates serving in Kenyan mission hospitals, this study adopted the characteristics given by Buitendach and Hendrina (2012).\n\nThe term “cross-cultural adjustment” (CCA), in line with Takeuchi et al. (2005), is the level at which expatriates are psychologically at ease and conversant with certain characteristics of a new environment. CCA can also be seen as the difficulty or ease with which expats deal with different aspects of living and working overseas (Chen, 2019; Noman et al., 2023). It aims at helping immigrants feel more ‘at home’ and integrate into their new culture. The process of change and a reduction in uncertainty helps achieve this. The amount of uncertainty experienced by expatriates can be reduced by their capacity to imitate and/or learn behaviours that are appropriate in the new culture. Numerous studies (see Noman et al., 2023; Waxin & Panaccio, 2005; Black & Gregersen, 1991; Shaffer, Harrison, & Gilley, 1999; Palthe, 2004) have empirically verified this idea.\n\nCross-cultural adjustment has traditionally been regarded to include three components. The three categories of dimensions that make up cross-cultural adjustment are non-work or general adjustment variables, work-related adjustment factors, and interaction adjustment factors (Lee, Li & Wu, 2018). Non-work/general adjustment factors or the first dimension refers to how comfortable a person is with their day-to-day way of life in a new place, including the transportation, food, climate, etc. The second dimension, work-related adjustment factors, is concerned with how at ease a person is with the working circumstances in a new setting (Lee et al., 2018). The interactional adjustment component measures how well a person can communicate with others from the host nation’s culture in both professional and social settings. The third issue is known as “work-related adjustment factors,” and it has to do with the particular position’s duties, performance standards, and leadership responsibilities that are present at the new environment. This shows that depending on which of these three aspects one chooses to focus on, one can be influenced to a different degree (Reegård, 2011).\n\nPrevious research has looked into a number of different adaptation mechanisms for working across cultural boundaries. For instance, researchers like Black, Mendenhall and Oddou (1991) have investigated the process of cross-cultural adaptation as a five-dimensional process between Europe and Africa. These aspects include pre-departure training, previous foreign experience, organization selection procedure, individual skills, and non-work element considerations. The first three aspects are concerned with the problems arising before expatriates leave their home countries, such as the decision to leave those countries. The last two aspects are concerned with the time period that occurs after expatriates have arrived at their new homes in foreign countries.\n\nBerry (2001), writing from a different vantage point, adopted an immigrant point of view. The author suggests four distinct strategies for adjusting to a new culture that are applicable to immigrants in general. However, it was discovered that these strategies also sat well with expatriates and their adjustments cross-culturally (Morley et al., 2004; Hongyu, 2014). Integration, separation, marginalization, and assimilation are the strategies that might be utilized during the adjustment process. Integration describes the process through which expatriates continue to uphold the norms and practices of their home culture while also adopting the norms and practices of their host society. Because of this, they are able to become fully functioning members of society (see Berry, 2001). Individuals who have no interest in adopting any aspects of the host culture’s norms and/or values of their own culture are said to have separated themselves from that culture. These people have made the conscious decision to continue living apart from one another in order to preserve their cultural history. When an expatriate has little inclination either to identify with their own culture or to blend in with the culture of their host nation, they are more likely to be marginalized.\n\nAs a final point, assimilation takes place when expatriates replace the traditions and practices of their home culture with those of their new host society. The expatriate has little interest in preserving his or her own culture while living abroad. According to the findings by Morley et al. (2004), integration is typically the most fruitful course of action, while marginalization and separation do not result in good adjustment. At an earlier date, Black & Mendenhall (1990) verified that cross-cultural adjustment does indeed occur in stages, particularly when applied to a multinational organizational set up (see also Bourdin, 2012). This was done in order to address cross-cultural adjustment concerns in their entirety. For example, Beil and Garcia Mayor (2018) remark in their work that there are four distinct phases, and they refer to this pattern as the U-curve. This model appears to consist of four steps, the first of which is the honeymoon period, which takes place during the first few weeks after expatriates arrive. During this stage, newly arrived expatriates are captivated by the novel and distinctive aspects of the culture and country to which they have relocated. The next step is culture shock, and it is during this stage that the expatriate realizes that certain actions are unacceptable in the new culture, but they have not yet grasped what behaviours are proper during this point of their adjustment (Delle & Mensah, 2013; Eschbach, Parker & Stoeberl, 2001).\n\nThe individual enters the third stage of adjustment when they acquire some language abilities and the ability to move about independently. This stage can last for several months. The expatriate will also learn some level of expertise in performing the new set of cultural norms during this period. The mastery stage is the fourth and last step in the process. At this point, the expatriate has typically reached their maximum level of adjustment. The individual is now aware of and able to correctly conduct the appropriate actions in order to work effectively and without anxiety as a result of cultural differences (Black & Mendenhall, 1990; Beil & Mayor, 2018; Bourdin, 2012). Due to the fact that the U-curve is applicable on a global scale, the present study decided to employ it. This decision was made because the U-curve tackle concerns that are consistent with the CCA and EC relationship of expatriates living in a foreign country like Kenya.\n\nWhile there are numerous studies on the contribution of EC to organizations, the attempts seem to focus on its relationship with other aspects other than cross-cultural adjustment. For example, Andrew (2017) studied employees’ commitment and its effect on performance in Sri Lanka. The findings of the study depicted that the employees’ commitment is significantly related to organizational performance in the EravurPattu divisional secretariat. Another study researched employee organizational commitment in Novi Sad and the findings indicated that there was a below average level of organizational dedication among employees (Rodosavljevic et al., 2017). Additionally, Maharani and Tampubolon (2018) investigated how corporatization affects organizational commitment and elaborated on the connection between work ethics, job satisfaction, and staff commitment in Indonesian referral hospitals. In another study, Chih and Lin (2009) identified that there existed a significant relationship between total quality management, leadership style, and workers’ commitment for Taiwan’s high-tech industry.\n\nIn a different study, Dang, Tinh, and Nguyen (2020) looked at the linkage between workplace learning and foreign workers’ organisational commitment to the host cultural organisation in Taiwan. They found that workplace learning strengthens this relationship. Field and Buitendach (2012) evaluated the relationships among work engagement, job resources, employee commitment, and job demands for teachers serving in poor high schools in South Africa and found a significant relationship between these. This research was conducted closer to home in Africa.\n\nIn Kenya, numerous studies on employee dedication and other topics have been carried out. For instance, it is reported that career training has a significantly positive impact on employee commitment, while the reward system has a positive and significant impact on employee commitment. This is according to the results of a study by Molly and Korir (2020) on the moderating role of the reward system on the relationship between career training and employees’ commitment in a sample of Kenyan manufacturing businesses. However, Muthoni et al. (2020) showed that staff commitment was influenced by employee welfare in their study of the relationship between employee welfare and staff commitment at the Kenyan judiciary. Further, in their study on the impact of financial incentives on staff engagement at the Kakamega County Water and Sanitation Company, Ongadi and Juma (2020) discovered a favourable relationship between the two variables. Additionally, Ogega, Muya, and Nyaboga (2020) conducted study on the impact of gender policy implementation on employee commitment in a few Kenyan county governments and discovered that this policy’s adoption is statistically significant in predicting employee commitment.\n\nGathungu, Iravo, and Namusonge (2015) further demonstrated a link between organizational commitment of employees of an organization in Nairobi and transformational leadership (TL). Njoroge et al. (2015) determined the effect of TL approach on organizational commitment in technical institutions in Kenya in a different study. In Uasin Gishu County, Chepkurui and Kimutai (2020) did an investigation on the contribution of talent development techniques on staff commitment at the Kenya Forest Service and discovered that talent development is extremely important and necessary in enhancing employee commitment. This apparent lack the studies on the correlation between expatriates’ cross-cultural adjustment and employee commitment, calls into question whether, indeed, a relationship between these two aspects exists or not. This is particularly in the health sector in Kenya which has witnessed an influx of foreign medical personnel such as Cuba doctors to fill the medical skills gap (Gamier, 2021). This understanding motivated the current study – the fact that studies have overlooked have the association between cross cultural adjustment and employee commitment. It is in light of the foregoing that the study sought to assess the effect of transformational leadership on cross-cultural adjustment and employee commitment among expatriates working in selected mission hospitals in Kenya.\n\nAccording to Hongyu (2015), “work adjustment” in the context of cross-cultural adjustment is defined as the level of emotional comfort an expatriate experiences when confronting the varied work values, expectations, and new work environment. According to Peltokorpi (2006), an expatriate’s capacity to adjust successfully to the job-related features of a given host country is influenced by the perceived ethnocentrism of the nationals of the host country as well as variations in the work values of the two countries. A view of local ethnocentrism has been shown to have a negative impact on work adjustment and loyalty to the host unit, according to research that was conducted on 250 expatriates from the western hemisphere. Open communication, individual accountability, and clearly stated performance objectives and feedback are frequently valued by Western expatriates living abroad. In contrast, Japanese employees are accustomed to following top-down directions and have a tendency to hesitate before expressing their ideas without reservation due to the cultural ideals of collectivism and verticality (Peltokorpi, 2006). This is because Japanese employees appreciate the importance of maintaining hierarchy. According to research conducted by Peltokorpi (2007), it has been discovered that Western expatriates experience increased levels of frustration as a result of the disparities in the work values of their host country.\n\nIn a separate piece of research, Peltokorpi and Froese (2009) investigated the degree to which organizational expatriates and self-initiated expatriates in Japan had different levels of success in adjusting to life in a foreign country. The findings indicated that both expatriates were adapting better to work and non-work-related aspects of their lives in Japan than they were adjusting to interaction with Japanese.\n\nAccording to Selmer and Fenner (2009), it should come as no surprise that work-related variables have the most significant bearing on work adjustment. According to Selmer and Fenner (2009), individuals who are posted overseas frequently face the challenge of adapting to new procedures, new approaches to completing tasks, and an increase in responsibility (see also Noman et al., 2023). In a meta-analysis of the impact of job characteristics in expatriate adjustment it was revealed that the most important elements for work adjustment were role ambiguity or clarity (r=0.41), role discretion (r=0.43) and role conflict (r =0.46) (Beehr & Christiansen, 2001). According to Morley et al. (2004), work-related adjustment is also significantly impacted by the presence of fresh role demands and excessive role demands. According to Nolan & Morley (2014), cultural competency training (CCT) is the process that is used to prepare staff members and their families so that they have a better understanding of the work and non-work environment, as well as the culture and norms of the host nation to which they have been assigned. It is a method that is used to enlarge an individual’s skill to cope with job in a foreign atmosphere (Ying, 2013). Additionally, it seeks to build a gratitude for the culture of the host country (Hesse, 2011).\n\n\nMethods\n\nThe overarching aim of the study was to establish the contribution of work factors on commitment of expatriates working in selected mission hospitals in Kenya. In addressing the study objective, the following null hypothesis was statistically tested using regression analysis (Warrens, 2014);\n\nWork-related factors have no significant effect on employee commitment of expatriates working in selected mission hospitals in Kenya.\n\nUtilising a utilized explanatory research design, the study was conducted in two mission hospitals: AIC Kijabe and Tenwek chosen as case studies. The choice was informed by the fact that medical expatriates are the most sought-after personnel in the healthcare workforce (Häzaq, 2023; Parekh et al., 2016). The study had a sample of 112 participants.\n\nThis study was anchored on the Three-Component Commitment and International Adjustment Theories for their ability to conceptualize the two study variables i.e. Employee commitment and Expatriate adjustment respectively. They were deemed most relevant as they formed a solid foundation not only for setting the scene for the study and reviewing of literature, but also provided a roadmap useful in developing scientific arguments and drawing important conclusions for the work. Importantly, they were using in limiting the scope of the study variables while organizing ideas. The Three-Component Commitment Theory includes a tri-dimensional model comprising of three scales represent organizational commitment - affective, continuation, and normative commitments (Meyer and Allen, 1997). These aspects provide a description of the various ways in which organizational commitment can grow and the implications that this has for the behaviour of employees. Affective commitment describes a person’s emotional interconnection to an organisation characterised by positive feelings (McElroy et al., 1993). Continuous commitment on the other hand is having “awareness of the costs associated with leaving the organisation.” It’s a calculative aspect of an individual’s perspective or estimate of the expenses and dangers related to leaving the current company (Meyer and Allen, 1991, 1997). Normative commitment describes “a feeling of obligation to continue employment.” Numerous scholars have over the years asserted that when people internalise normative conceptions of responsibility and obligation, they are obliged to prolong their involvement in an organisation (Allen and Meyer, 1990; Wiener and Vardi, 1980; Iverson and Buttigieg, 1999; McDonald and Makin, 2000).\n\nThe framework of international adjustment theory, originally provided by Black, Mendenhall and Oddou (1991) and modified by Beil and Garcia Mayor (2018) postulate that there are two elements that can influence an expatriate’s ability to adapt to their new culture - anticipatory adjustment which takes place before moving overseas and in-country adjustment, which takes place in the host country. In the context of this study, great emphasis was taken on the in-country adjustment component associated with expatriates who are currently working in mission hospitals in Kenya. Specifically, they include work adjustment i.e. adjustment to employment (the new job-related elements, such as individual performance, duties, company’s social support, and issues of supervision); interaction adjustment i.e. adjustment to dealing with host nationals (relational adaptation that takes interactions with the novelty of the culture into account); and general adjustment (adjustment to the general environment) referring to the living conditions in the host country and which is normally influenced by the logistical support provided by the company as well as the cultural uniqueness (Black, Mendenhall and Oddou, 1991; Beil & Garcia Mayor, 2018).\n\nAgainst the foregoing, an illustrative framework conceptualising and illustrating the variables under study and their constructs was developed (see Figure 1). The work-related cross cultural adjustment factors (role novelty, organizational culture novelty, and organisational social support) represented the study’s independent variable. On the other hand, employee commitment (affective, continuance, and normative) was the dependent variable while age, gender, and marital status of the respondents were the control variables (held constant) for the study. in summary and in line with the study’s research aim, employee commitment was hypothesised to be influenced by cross cultural adjustment.\n\nThe study was conducted in two purposively selected mission hospitals in Kenya - AIC Kijabe and Tenwek mission hospitals. The choice was informed by their large number of expatriate doctors in the country making them made them ideal for the study.\n\nThe study adopted an explanatory research design given that the study aimed at establishing a causal relationship between variables in a study (Saunders, Lewis and Thornhill, 2012).\n\nThe study had a total target population of 156 expatriate medical practitioners from whom the study sample was derived (Table 2). The sample included those employees who had served in the field for over a year.\n\nThe study employed a simple random sampling method to ensure equal chance of participants being included in study (Bryman & Bell, 2011). With a 95% confidence level, the sample for this study was calculated using Taro Yamane’s formula (Yamane, 1973) deriving a sample size of 112 respondents. Following the sample calculation, a census was applied where data was collected from all members of the sample. The calculation is presented as follows.\n\nWhere:\n\nn = sample size required\n\nN = number of people in the population\n\ne = allowable error (%)\n\nn = 112\n\nThe specific sample size of each selected hospital was as summarized in Table 3.\n\nData collection\n\nData was gathered via self-administered questionnaires (see Thiong’o, 2024). Closed-ended questions with pre-defined questions were employed to obtain quick and direct (Kothari, 2004). Further, it allowed a high degree of consistency and compatible responses. The replies were evaluated using a Likert measurement scale with a range of 1 to 5 (applying the codes 1 = Strongly Disagree to 5 = Strongly Agree). For cross-cultural adaptability, a higher score is desirable.\n\nThe questionnaire consisted of 4 major parts (refer to Thiong’o, 2024). Part A of the questionnaire consisted of demographic information with eight (8) questions adopted from Hesse (2011) and Beil and Garcia Mayor (2018); part B comprised the factors influencing employee commitment with one (1) major question containing twenty three (23) sub-questions as adopted from Anne (2011); part C entails factors influencing cross-cultural adjustment of expatriates with one (1) major question comprising of thirty eight (38) sub-questions adopted from Beil and Mayor (2018); Black, Mendenhall, and Oddou (1991); and Liao (2010).\n\nPiloting\n\nA pilot study was carried out in Kapsowar Mission Hospital prior to the main study. With a bed capacity of 140, the pilot hospital shared characteristics with the study hospitals (a vibrant expatriate population providing a wide array of services). Based on the recommendations of Mugenda and Mugenda (2003) of a pre-test sample of 10%, the researchers chose a sample of 12 respondents for piloting (see also Treece, 1982; Saunders, Lewis, and Thornhill, 2009).\n\nValidity and reliability tests\n\nTo ensure the quality of data instruments, validity and reliability tests were conducted. Validity of the instruments was assessed by caring out a factor analysis alongside considering views of expert opinions. The necessary adjustments were then made. A reliability test was conducted through a pilot study. According to Warrens (2014), Cronbach’s alpha values vary from 0 to 1, with a value of 0 signifying low dependability and a value of 1 signifying excellent reliability. A Cronbach’s alpha value of 0.7 is usually the required standard for the interpretation of the study instrument’s reliability (Warrens, 2014; Wessa, 2024 - see also free software at https://www.wessa.net/). In line with the foregoing, the results of the pilot study revealed that the employment commitment variable with 23 items (α=0.989) and the cross-cultural adjustment with 38 items (α=0.989) were found reliable. Similarly, transformational leadership variable with 18 items (α=0.982). Reliability results are summarized in Table 4.\n\nReporting guidelines\n\nTo ensure replicability of the study, a reasonable attempt has been made to provide details on how the study methodology was conducted alongside the necessary supporting documentation to corroborate the results (see extended data). Specifically, the study adhered to the provisions of the ASSESS tool (see recommendations by Ryan et al., 2022, pp6 and 7) on author citations and descriptions on the rationale for the study, choices for study respondents, study design, theory, and study sites among others.\n\n\nResults\n\nOut of the total number of questionnaires administered (112) to the target respondents, 105 were returned and found to be dully filled. This was a 93.75% response rate (Table 5); deemed very good according to recommendations of Mugenda and Mugenda (2003).\n\nThe study sought to establish demographic information such as gender, age, academic level, years of service, overseas working experience, working in other countries other than Kenya, and whether the expatriates stayed with their families. From the results the majority of the respondents identified as men (64.79%), were between the age bracket of 30-39 years (62.86%); had a bachelor’s degree (52.38%); had served between 10-20yrs (47.62%); had overseas working experience (90.48%); had worked elsewhere other than Kenya (80.95%); and did not live with their families (94.24%).\n\nA cross tabulation of the above is as summarised in Table 6. The findings further indicated that there was a significant relationship between the demographics measures and Employee Commitment (χ2=101.105, df=47, p=.000; χ2=198.909, df=94, p=.000; χ2=297.394, df=141, p=.000; χ2=200.163, df=94, p=.000; χ2=105.000, df=47, p=.000; χ2=101.757, df=47, p=.000; χ2=105.00, df=47, p=.000) respectively for gender of respondents, age bracket, the highest level of education, years served in the medical field, overseas working experience, worked in other countries before working in Kenya, and stays with their family.\n\na Dependent variable: Employee commitment.\n\nFor this study, the descriptive statistics present the respondents’ views on the independent variable (cross-cultural adjustment) and the dependent variable (employee commitment).\n\nThe mean of all questions was lower than the theoretical mean (3) (Table 7). In other words, the frequency of the answers of ‘strongly agree’ and ‘agree’ was lower than that of ‘strongly disagree’ and ‘disagree’. Additionally, the low standard deviation indicates that the collected data were grouped close to the mean. Table 7 further demonstrates that the mean of all questions (M=3.8201 and SD=0.47661), the independent variable measured by cross-cultural adjustment, was larger than (>3). Put differently, the frequency of the answers with ‘strongly agree’ and ‘agree’ were more than ‘strongly disagree’ and ‘disagree’. Given the low standard deviation, the observed data were grouped close to the mean. The mean of all questions (M=3.5667 and SD=0.68638) was larger than (>3), meaning in other words, the frequency of the answers of strongly agree and agree are more than strongly disagree and disagree.\n\nFurthermore, the kurtosis results for employee commitment and cross-cultural adjustment (-0.531 and 1.369 respectively) showed that the sample data had been taken from a population with a normally distributed population. It also shows how the data set was organised, with most values concentrated in the middle of the range and the remainder tapering off symmetrically towards either end.\n\nLinearity was tested to check the actual strength of all the relationships. The results (see Table 8) indicated that all the work-related factors (F=583.028, P=.000) had a significant linear relationship with the employee commitment as F-values have p <.05 and thus, can be used for regression analysis in the study.\n\nBoth variables (the employment commitment and cross-cultural adjustment) with a coefficient of 0.872 and .897 respectively were found to be reliable (Table 9). This is in line with a recommendation by Tavakol and Dennick (2011) that Cronbach’s alpha values of more than .7 indicate an instrument is dependable.\n\nCorrelation coefficient (r=0.868) depicted a high degree of positive correlation between the work-related factors and employee commitment (Table 10). Also, the correlation coefficient was significant as the p-value was p<0.00 and was less than the significance level (α=0.01). Therefore, work-related factors had a high positive correlation and significant relationship at 0.868 with employee commitment.\n\n** Correlation is significant at the 0.01 level (2-tailed).\n\nRegression analysis was used to determine the direct effect of independent variable on the dependent variable (Table 11).\n\na Predictor: (Constant) Work-Related Factors.\n\nb Dependent Variable: Employee Commitment.\n\nThe results (Table 12) indicated that Beta2 for work-related factors had a negatively significant influence on employee commitment (β=-1.033 p=0.000), this implies that for every increase in the work-related factors, the employee commitment will decrease by the beta coefficient value of 1.033. The null hypothesis was hence rejected (Table 13).\n\na Dependent Variable: Employee Commitment.\n\nThese findings contrasted with a study by Zakariyaa, Othmanb and Abdullahb (2018) in Malaysia who found that work-related factors were positively significant with job performance of expatriates (β=0.041, p=0.000). However, it agreed with Florkowski and Fogel (1999) who revealed that perceptions of local ethnocentrism had a negative effect on work adjustment and commitment to the host unit, particularly when cultural distance was low. This is the case with Lii and Wong (2008) studying the antecedents of overseas adjustment and commitment of expatriates indicating that work role characteristics was a significant predictor for the adjustment and commitment of the expatriates.\n\n\nSummary of discussion and conclusions\n\nThe purpose of this study was to establish whether or not work factors had an impact on the commitment of expatriate employees working in mission hospitals in Kenya.\n\nThe demographic crosstabs findings showed that there was a significant relationship between the demographics measures and Employee Commitment (χ2=101.105, df=47, p=.000; χ2=198.909, df=94, p=.000; χ2=297.394, df=141, p=.000; χ2=200.163, df=94, p=.000; χ2=105.000, df=47, p=.000; χ2=101.757, df=47, p=.000; χ2=105.00, df=47, p=.000) for gender of respondents, age bracket, the highest level of education, years served, overseas working experience, experience in other countries before working in Kenya, and stay with their family respectively.\n\nFurthermore, the findings showed that work-related factors negatively and significantly predicted employee commitment. This means that for every increase in the work-related factors, employee commitment would decrease by the beta coefficient value of 1.033. This finding was in congruence with that by Florkowski and Fogel (1999) whose study revealed that perceptions of local ethnocentrism had a negative effect on work adjustment and commitment to the host unit, particularly when the cultural distance was low. However, it contrasted with a study by Zakariyaa, Othmanb, and Abdullahb (2018) whose results revealed that work adjustment had a significant positive effect on expatriate performance.\n\nTo conclude, employee commitment can be attained among expatriates working in mission hospitals in Kenya through work-related adjustment elements. These factors apply to the novelty of the position, the cultural novelty of the organization, and the social support from the organization. As a result, those in charge of human resource management and those responsible for formulating public policies ought to use these cross-cultural methods within their organizations so to increase the level of dedication shown by expatriates to their work.\n\nIn addressing the knowledge gap(s) identified in literature, the researchers attempted to close these through this study. In so doing, there were novel contributions in the general understanding the contribution Cross Cultural Adjustment to Employee Commitment. The findings are not only applicable in the selected case studies but could be replicated to the general workplace and institutions dealing with employees. Additionally, the empirical findings not only contribute to the understanding of the interplay between the two variables studied but also provides a basis for further studies on the general disciple of human resources management and specifically regarding workplace commitment/transformational leadership.\n\nFurther, the study confirms and/or corroborates the applicability of the methodology chosen and the theories within which this study was anchored. In regard to the practicality of the study, the results provide a basis that could potentially affect human resources/workplace policy guidelines. These could possibly help devise ways to enhance/influence employee behaviour in the workplace (specifically) and in other contexts (generally). Importantly, the study, anchored on theoretical assumptions made provides a practical basis for the institutionalization of workplace norms and practices.\n\nThe study was not without limitations. First off, this was a self-assessment study implying that there was room for bias. Additionally, because of the varied shifts and schedules at the hospitals used as case examples, the researchers had a difficult time presenting questionnaires to expatriates. It also took longer than expected to retrieve the surveys given the nature of the respondents’ work. This meant that the questionnaires (see file at Thiong’o, 2024) were completed at the respondents’ pace and in their own time. Secondly, the three case samples used in the study were purposively sampled and may not be representative across all mission hospitals in the country. There is, therefore, a need for more studies utilising a larger breadth of case examples.\n\nThe design and implementation of the current study involved human subjects (expatriate employees based in mission hospitals) and, therefore, had to adhere to set guidelines and clear scientific research principles as stipulated by the WMA Declaration of Helsinki (https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/). Several underlying principles were followed as required by established ethical standards and protocol in Kenya. These included: informed consent from respondents to participate in the study, maintenance of anonymity, confidentiality, and privacy of respondents and the information they provided, and finally the right to withdraw from the study at any given time.\n\nA detailed application describing the study and how each of the foregoing issues was adhered to was made for consideration by an independent research authority in Kenya, the National Council for Scientific, Technology, and Innovation (NACOSTI) (https://research-portal.nacosti.go.ke/researcher/ApplicationGuidelines.html). A written approval (license number NACOSTI/P/22/15466) covering the period of study ending 28th January 2023 was issued to the researchers on 28th January 2022. Following this approval, the study commenced and after completion a copy of the study findings was submitted as a standard requirement.\n\nThis study involved human participants (expatriate employees). Draft consent detailing the study objective and terms of engagement during the study was incorporated in the questionnaire and submitted for ethical application. Upon approval, the requirement for respondents to fill in and sign consent was waived by the ethics board (the current study was deemed to: present ‘no risk of harm’ to participants, and that the waiver would not negatively influence the subjects’ welfare/rights), right to withdraw from the study, and the maintenance of anonymity had to be observed (see recommendations by Kambhampati, Menon & Maini, 2023; Mahajan, 2023). Against the foregoing, licensing, and ethical authorisation to carry out the study was acquired from the relevant authority in the land – the National Commission for Science, Technology, and Innovation (NACOSTI) (license number NACOSTI/P/22/15466). Further to this, written permission to conduct the study in the individual facilities was sought in writing from the hospital management through the local administration where the respective study sites are located.\n\n\nAuthor contributions\n\nA.J. and S.M.T conceptualized the study; A. J collected and analysed data; S. T wrote the original draft; A. J and S.M.T reviewed and edited the final manuscript.", "appendix": "Data availability statement\n\nDatasets that corroborate the findings of the current study included personal information and identifiers of respondents in the selected mission hospitals used in the study. Further, respondents were assured of privacy of the information provided as required in social science research involving human subjects (Brown, 2023) and by the ethics considerations of National Commission for Science, Technology, and Innovation (NACOSTI) (see https://research-portal.nacosti.go.ke/researcher/ApplicationGuidelines.html). For that reason, they are not publicly available on privacy and/or ethical grounds. The above not-withstanding, the data can be provided upon request from the corresponding author (SMT) S.Thiongo2234@student.leedsbeckett.ac.uk.\n\nSupplementary documents including respondents’ written consent form and study questionnaire, and necessary study approval certifications have been added. The study questionnaire has been uploaded to an open access data repository FigShare on <30 August 2024> under DOI number: https://doi.org/10.6084/m9.figshare.26879449.v1 (Thiong’o, 2024).\n\nThis project contains:\n\n1. data questionnaire and consent form.\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 researchers appreciate the anonymous respondents for voluntarily participating in this study and the leadership of AIC Kijabe and Tenwek mission hospitals for allowing access to their premises.\n\n\nReferences\n\nAgus A, Selvaraj R: The mediating role of employee commitment in the relationship between quality of work life and the intention to stay. Employ. Relat. 2020; 42(6): 1231–1248. Publisher Full Text\n\nAllen NJ, Meyer JP: Affective, continuance, and normative commitment to the organization: An examination of construct validity. J. Vocat. Behav. 1996; 49(3):252–276. PubMed Abstract \| Publisher Full Text\n\nAllen NJ, Meyer JP: The measurement and antecedents of affective, continuance and normative commitment to the organization. J. Occup. Psychol. 1990; 63(1):1–18.\n\nAmunkete S, Rothmann S: Authentic leadership, psychological capital, job satisfaction and intention to leave in state owned enterprises. J. Psychol. Afr. 2015; 25(4): 271–281. Publisher Full Text\n\nAndrew A: Employees’ commitment and its impact on organizational performance. Asian Journal of Economics, Business and Accounting. 2017; 5(2):1–13. Publisher Full Text\n\nAnne QU: The Influence of Transformational Leadership on Organisational Commitment in the Banking Sector of Pakistan :The British University in Dubai. (Doctoral dissertation) ;2011.\n\nArsenijević OM, Jovanović L, Radosavljević MŽ: Relationship between organizational climate and management effectiveness. Industrija. 2017; 45(1): 61–80. Publisher Full Text\n\nBeehr TA, Christiansen ND: The importance of job, family and environmental factors in expatriate adjustment: A meta-analysis. Loyola Sch. Rev. 2001; 1(13): 147–154.\n\nBeil E, Garcia Mayor D: The Challenge of Cross-Cultural Adjustment: The Case of Expatriates on International Assignments between Africa and Sweden.2018.\n\nBerry JW: A psychology of immigration. J. Soc. Issues. 2001; 57: 615–631. Publisher Full Text\n\nBlack JS, Gregersen HB: Antecedents to cross-cultural adjustment for expatriates in Pacific Rim assignments. Hum. Relat. 1991; 44(5): 497–515. Publisher Full Text\n\nBlack JS, Mendenhall M: Cross-Cultural Training Effectiveness: A Review and a Theoretical Framework for Future Research. Acad. Manag. 1990; 15(1): 113–136. Publisher Full Text\n\nBlack JS, Mendenhall M, Oddou G: Towards a comprehensive model international adjustment: An integration of multiple theoretical perspective. Acad. Manag. Rev. 1991; 16(2): 291–317. Publisher Full Text\n\nBourdin D: Measures taken in Multinational Enterprises to facilitate Expatriate Cross-Cultural Adjustment: A Multiple Case Study Approach. Warwick Business School. 2012; 4: 314.\n\nBrown N: Research ethics in a changing social sciences landscape. Research Ethics. 2023; 19(2): 157–165. Publisher Full Text\n\nBryman A, Bell E: Business Research Methods. 3rd ed.Oxford: Oxford University Press; 2011.\n\nBuitendach LK, Hendrina J: work Engagement, Organisational Commitment, Job Resources and Job Demands of Teachers Working Within Disadvantaged High Schools in Kwazulu-Natal, South Africa. J. Psychol. Afr. 2012; 22(1): 87–95.\n\nCaligiuri PM, Hyland MM, Joshi A, et al.: Testing a theoretical model for examining the relationship between family adjustment and expatriates’ work adjustment. J. Appl. Psychol. 1998; 83(4):598–614. PubMed Abstract \| Publisher Full Text\n\nCastro ML, Martins N: The relationship between organisational climate and employee satisfaction in a South African information and technology organization. SA J. Ind. Psychol. 2010; 36(1): 1–9. Publisher Full Text\n\nChen M: The impact of expatriates’ cross-cultural adjustment on work stress and job involvement in the high-tech industry. Front. Psychol. 2019; 10: 2228. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChepkurui E, Kimutai G: Effect of talent development strategies on employee commitment at Kenya forest service, Uasin Gishu County. Strateg. J. Bus. Change Manag. 2020; 7. Publisher Full Text\n\nChih WH, Lin YA: The study of the antecedent factors of organisational commitment for high-tech industries in Taiwan. Total Qual. Manag. 2009; 20(8): 799–815. Publisher Full Text\n\nDang VT, Vu TT, Nguyen PT: Workplace learning and foreign workers’ commitment to host cultural organization: the effects of cross-cultural adjustment and supervisor trust. Empl. Relat. 2020; 43(1): 297–317. Publisher Full Text\n\nDelle E, Mensah ME: The influence of national culture on expatriate work adjustment, intention to leave and organizational commitment. Eur. J. Bus. Manag. 2013; 5: 1–8.\n\nEschbach DM, Parker GE, Stoeberl PA: American repatriate employees’ retrospective assessments of the effects of cross-cultural training on their adaptation to international assignments. Int. J. Hum. Resour. Manag. 2001; 12(2): 270–287. Publisher Full Text\n\nField LK, Buitendach JH: Work Engagement, Organisational Commitment Job Resources and Job Demands of Teachers Working Within Disadvantaged High Schools in Kwazulu-Natal, South Africa. J. Psychol. Afr. 2012; 22(1): 87–95. Publisher Full Text\n\nFlorkowski GW, Fogel DS: Expatriate adjustment and commitment: The role of host-unit treatment. Int. J. Hum. Resour. Manag. 1999; 10(5): 783–807. Publisher Full Text\n\nGamier S: An army of white coats: Exploring the implications of Cuban medical. Harv. Int. Rev. 2021; 42(1): 26–32.\n\nGathungu EW, Iravo DMA, Namusonge GS: Transformational leadership and employee’s commitment: empirical review. IOSR Journal of Humanities and Social Science. 2015; 20(7): 1–7.\n\nHäzaq A: Why being a doctor offers the best career opportunities worldwide.2023. Accessed 21 February 2024. Reference Source\n\nHesse A: Factors influencing expatriates’ ability to cross-culturally adjust. Nelson Mandela Metropolitan University; 2011. (Doctoral Dissertation).\n\nHongyu L: Cross-cultural adjustment factors of Chinese expatriates in Portugal. ISCTE Business School, University of Lisbon; 2014.\n\nIverson RD, Buttigieg DM: Affective, normative and continuance commitment: can the ‘right kind’ of commitment be managed?. J. Manag. Stud. 1999; 36(3): 307–333. Publisher Full Text\n\nJoāo TF, Coetzee M: Job retention factors, perceived career mobility and organisational commitment in the South African financial sector. J. Psychol. Afr. 2012; 22(1): 69–76. Publisher Full Text\n\nKambhampati SB, Menon J, Maini L: Ethics in Research and Publications. Indian J. Orthop. 2023; 57: 1722–1734. Publisher Full Text\n\nKara D: Gender differences on perceptions of employee quality of working life in five-star hotels in Turkey. World Appl. Sci. J. 2012; 20(10): 1383–1388.\n\nKothari CR: Research Methodology, Methods and Techniques. 2nd ed.New age International Publishers; 2004.\n\nKumari N, Afroz N: Role of affective commitment in employees’ life satisfaction. Int. J. Adv. Res. 2013; 1(12): 11–20.\n\nLee PY, Li CSJ, Wu ML: The roles of cross-cultural adjustment and social capital formation in the dynamic capabilities development of multiunit organizations. Asia Pac. Manag. Rev. 2018; 23(1): 20–29. Publisher Full Text\n\nLiao WJ: The cross-cultural adjustment of EFL expatriate teachers in Taiwan. University of Bedfordshire; 2010.\n\nLii SY, Wong SY: The antecedents of overseas adjustment and commitment of expatriates. Int. J. Hum. Resour. Manag. 2008; 19(2): 296–313. Publisher Full Text\n\nLiou SR, Cheng CY: Organisational climate, organisational commitment and intention to leave amongst hospital nurses in Taiwan. J. Clin. Nurs. 2010; 19(11-12): 1635–1644. PubMed Abstract \| Publisher Full Text\n\nMahajan AJ: Research Publications and Ethical Practices. Advance and Innovative Research. 2023; 234.\n\nMaharani A, Tampubolon G: Does corporatisation improve organisational commitment? Evidence from public hospitals in Indonesia. Int. J. Hum. Resour. Manag. 2018; 29(13): 1999–2026. Publisher Full Text\n\nMakhathini TN, Van Dyk GA: Organisational climate, job satisfaction, and leadership style influences on organisational commitment among South African soldiers. J. Psychol. Afr. 2018; 28(1): 21–25. Publisher Full Text\n\nMcDonald DJ, Makin PJ: The psychological contract, organisational commitment and job satisfaction of temporary staff. Leadersh. Org. Dev. J. 2000; 21(2): 84–91. Publisher Full Text\n\nMcElroy JC, Morrow PC, Power ML, et al.: Commitment and insurance agents’ job perceptions, attitudes, and performance. J. Risk Insur. 1993; 60: 363–384. Publisher Full Text\n\nMercurio ZA: Affective commitment as a core essence of organizational commitment: An integrative literature review. Hum. Resour. Dev. Rev. 2015; 14(4):389–414. Publisher Full Text\n\nMeyer JP, Allen NJ: A three-component conceptualization of organizational commitment. Hum. Resour. Manag. Rev. 1991; 1(1): 61–89. Publisher Full Text\n\nMeyer JP, Allen NJ: Commitment in the workplace: Theory, research, and application. Sage Publications; 1997.\n\nMeyer JP, Parfyonova NM: Normative commitment in the workplace: A theoretical analysis and reconceptualization. Hum. Resour. Manag. Rev. 2010; 20(4):283–294.\n\nMitonga-Monga J, Cilliers F: Perceived ethical leadership: Its moderating influence on employees’ organisational commitment and organisational citizenship behaviours. J. Psychol. Afr. 2016; 26(1): 35–42. Publisher Full Text\n\nMolly A, Korir M: Career Training reward system and employee commitment; moderating approach; Evidence from Kenya manufacturing firms. Afr. J. Environ. Sci. Technol. 2020; 5(4).\n\nMorley M, Burke C, Finn G: Irish expatriates in Moscow. Explanatory evidence on aspects of adjustment on contemporary issues in Europe. International HRM. 3rd ed.2004; pp. 203–222.\n\nMugenda O, Mugenda A: Research methods: Quantitative and qualitative approaches. Nairobi, Kenya: Acts Press; 2003.\n\nMuthoni MM, Mwaura NP, Waweru GT: The effect of employee welfare on employee commitment at judicial service of Kenya. Eur. J. Bus. Manag. 2020; 12(30): 74–80.\n\nNjoroge D, Gachunga H, Kihoro J: Transformational leadership style on organizational commitment: The moderating effect of employee participation. Strateg. J. Bus. Change Manag. 2015; 2(6): 94–107. Publisher Full Text\n\nNobile JD: Organisational communication and its relationships with job satisfaction and organisational commitment of primary school staff in Western Australia, Educational Psychology. Educ. Psychol. 2017; 37(3): 380–398. Publisher Full Text\n\nNolan EM, Morley MJ: A test of the relationship between person–environment fit and crosscultural adjustment among self-initiated expatriates. Int. J. Hum. Resour. Manag. 2014; 25(11):1631–1649. Publisher Full Text\n\nNoman M, Sial MS, Samad S, et al.: Adjustment of self-initiated and organizational expatriates: The moderating role of cross-cultural training. Front. Psychol. 2023; 13: 1044040. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOgega RM, Muya J, Nyaboga Y: Effect of implementation of gender diversity management policy on employee commitment in selected county governments in Kenya. FOCUS: Journal of International Business. 2020; 7(1): 41–57. Publisher Full Text\n\nOngadi AL, Juma D: Effect of perceptions of financial rewards on employee commitment in the water sector in Kenya. A case study of Kakamega County Water and Sanitation Company. Strateg. J. Bus. Change Manag. 2020; 7(3): 1141–1156.\n\nPalthe J: The relative importance of antecedents to cross-cultural adjustment: Implications for managing a global workforce. Int. J. Intercult. Relat. 2004; 28(1): 37–59. Publisher Full Text\n\nParekh N, Sawatsky AP, Mbata I, et al.: Malawian impressions of expatriate physicians: A qualitative study. Malawi Med. J. 2016; 28(2): 43–47. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeltokorpi V: Intercultural communication patterns and strategies: Nordic expatriates in Japan. Int. Bus. Rev. 2007; 16: 68–82. Publisher Full Text\n\nPeltokorpi V: The impact of relational diversity and socio-cultural context in interpersonal communication: Nordic subsidiaries in Japan. Asian Bus. Manag. 2006; 5: 333–356. Publisher Full Text\n\nPeltokorpi V, Froese FJ: Organizational expatriates and self-initiated expatriates: who adjusts better to work and life in Japan? Int. J. Hum. Resour. Manag. 2009; 20(5): 1096–1112. Publisher Full Text\n\nPiñeros Espinosa RA: Responsible leadership and affective organizational commitment: The mediating effect of corporate social responsibility. Front. Psychol. 2022; 13: 868057. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRadosavljevic Z, Radosavljevic M, Andjelkovic A: Research Quality of Supreme (Public) Management of Slovenia and the Possibility of Application of Its Experiences in Serbia. In MIC 2017: Managing the Global Economy; Proceedings of the Joint International Conference, Monastier di Treviso, Italy, 24–27 May 2017; University of Primorska Press; pp. 175–190.\n\nReegård K: Facilitating cross-cultural adjustment: The case of north European expatriates in China. University of Oslo; 2011. (Master’s thesis).\n\nRyan N, Vieira D, Gyamfi J, et al.: Development of the ASSESS tool: a comprehenSive tool to Support rEporting and critical appraiSal of qualitative, quantitative, and mixed methods implementation reSearch outcomes. Implement. Sci. Commun. 2022; 3(1): 34. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaunders M, Lewis P, Thornhill A: Research methods for business students. 6th ed.Rotolito Lombarda, Italy: Prentice Hall; 2012.\n\nSaunders M, Lewis P, Thornhill A: Research methods for business students. Pearson Education; 2009.\n\nSelmer J, Fenner CR: Job factors and work outcomes of public sector expatriates. Hum. Resour. Manag. J. 2009; 19(1): 75–90. Publisher Full Text\n\nShaffer MA, Harrison DA, Gilley KM: Dimensions, determinants, and differences in the expatriate adjustment process. J. Int. Bus. Stud. 1999; 30: 557–581. Publisher Full Text\n\nSuliman A, Iles P: Is continuance commitment beneficial to organizations? Commitment-performance relationship: a new look. J. Manag. Psychol. 2000; 15(5):407–422. Publisher Full Text\n\nTakeuchi R, Wang M, Marinova SV: Antecedents and consequences of psychological workplace strain during expatriation: A cross-sectional and longitudinal investigation. Pers. Psychol. 2005; 58(4): 925–948. Publisher Full Text\n\nTavakol M, Dennick R: Making sense of Cronbach’s alpha. Int. J. Med. Educ. 2011; 2: 53–55. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTekingündüz S, Top M, Tengilimoğlu D, et al.: Effect of organisational trust, job satisfaction, individual variables on the organisational commitment in healthcare services. Total Qual. Manag. Bus. Excell. 2017; 28(5-6): 522–541. Publisher Full Text\n\nThiong’o S: Questionnaire and consent form.docx. figshare. [Dataset]. 2024. Publisher Full Text\n\nTreece C: DSM-III as a research tool. Am. J. Psychiatry. 1982; 139(5): 577–583. PubMed Abstract \| Publisher Full Text\n\nWarrens MJ: On Cronbach’s Alpha as the Mean of All Possible k-Split Alphas. Adv. Stat. 2014; 2014(1): 1–5. Publisher Full Text\n\nWaxin MF, Panaccio A: Cross-cultural training to facilitate expatriate adjustment: it works!. Pers. Rev. 2005; 34(1): 51–67. Publisher Full Text\n\nWessa P: Free Statistics Software, Office for Research Development and Education. version 1.2.1. 2024. wessa.net\n\nWiener Y, Vardi Y: Relationships between job, organization, and career commitments and work outcomes—An integrative approach. Organ. Behav. Hum. Perform. 1980; 26(1): 81–96. Publisher Full Text\n\nYamane T: Research Methodology/Sample Size. Gainesville, FL, USA: Florida: University of Florida; 1973.\n\nYang JT: Effect of newcomer socialisation on organisational commitment, job satisfaction, and turnover intention in the hotel industry. Serv. Ind. J. 2008; 28(4): 429–443. Publisher Full Text\n\nYing Z: Towards better cross-cultural adjustment: From cultural distance to cultural intelligence. Faculty of Business, Charles Sturt University; 2013.\n\nZakariyaa NH, Othmanb AK, Abdullahb Z: The relationship between expatriate adjustment and expatriate job performance at multinational corporations in Malaysia. National Human Resource Management Conference Proceedings. 2018; pp. 51–58." }	[ { "id": "332572", "date": "06 Nov 2024", "name": "Sadia Anwar", "expertise": [ "Reviewer Expertise Human Resource management" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis report investigates the impact of cross-cultural adjustment on employee work commitment in selected mission hospitals in Kenya. Findings indicate that effective cross-cultural integration positively influences job satisfaction and loyalty. By addressing cultural differences and promoting supportive work factors, these hospitals can enhance employee engagement, leading to improved patient care and a stronger organizational culture overall.\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": "345383", "date": "12 Dec 2024", "name": "Robert Zacca", "expertise": [ "Reviewer Expertise Entrepreneurship and Expatriate 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\nRecommend the following: 1.Citations are very old especially in literature review - update with citations from 2020 onward. 2. Hypotheses should be explained in Theory section and not the methodology section 3. Research design should be expanded upon 4, The very high R-squared and high correlation values: A very high R-squared value (close to 1 or 100%) indicates that the model explains almost all of the variability in the dependent variable. Similarly, a high correlation coefficient (close to 1 or -1) suggests a strong linear relationship between variables. While these results may seem positive, they should be interpreted cautiously:\nOverfitting: An extremely high R-squared could indicate that the model is overfitted, capturing noise in the data rather than true relationships Multicollinearity: High correlations between independent variables can lead to unstable and unreliable coefficient estimates Non-linear relationships: A high R-squared doesn't necessarily mean the model fits the data well. Other functions might better describe the trend Lack of generalizability: The model may perform poorly on new data if it's too closely fitted to the training set. Spurious correlations: Strong correlations can occur by chance, especially with small sample sizes or when comparing trended time series Limited practical significance: In some fields, even low R-squared values can be meaningful, while in others, very high values are expected Add practical implications and limitations.\n\n5. Review similar methodology papers and revise to follow the best practice paper structure design.\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/13-1229
https://f1000research.com/articles/12-815/v1	11 Jul 23	{ "type": "Study Protocol", "title": "Comparative evaulation of condylar guidance obtained by digital panoramic radiographic images with that of obtained during jaw relation and try-in using two different interocclusal record material in completely edentulous patients: an in vivo study", "authors": [ "Khushbu Doshi", "Seema Sathe", "Seema Sathe" ], "abstract": "Background: In completely edentulous patients, maintaining the patient's TMJ health and intraoral components is very important. This can be achieved by an accurate interocclusal record, which can we taken by various materials and also at various stages. Simulation of the temparomandibular joint anatomy and mandibular movements is possible on a semi adjustable articulator which is use widely in prosthodontics. Transferring the record on articulator is a critical step in fabrication of complete dentures so it should be done precisely to reduce chair side time and also to avoid complications for patients. This study examines which material is more accurate and also records which stage gives more precision, by comparing the Condylar guidance on radiographs. This is because it has consistent bony landmarks and is comparable to clinical methods in terms of standardisation. The objective will be to determine the inter occlusal records created during Jaw Relation stage and Try-in using reinforced wax and Polyvinyl siloxane and compare these values to the condylar guidance obtained by OPG. Methods: Recording the Condylar Guidance value on OPG, obtained with tracing Glenoid fossa, Articular eminence and the Frankfurt Horizontal Plane. Followed with conventional steps in making complete dentures, at jaw relation and try-in stage. we will record values of condylar guidance with the two different Interocclusal record materials. Expected result: It will help the clinicians to get knowledge about obtaining precise condylar inclination angle by using right interocclusal record materials. Conclusions: This study will help us to obtain condylar inclination which inturn helps the patients satisfaction as it maintains the patient's TMJ health and intraoral components.", "keywords": [ "Condylar guidance", "Jaw relation", "Try-in", "Interocclusal records", "Semi adjustable articulator", "OPG" ], "content": "Introduction\n\nIn order to achieve a comfortable prosthesis that will last several years and maintain the patient's Temporomandibular joint health and intraoral components, proper interocclusal recording should be followed during the procedure.1 In completely edentulous patients, the slope of articular eminence on a digital panoramic radiographic image will be traced, which will be utilised in the semi-adjustable articulator's programming.2\n\nMandibular movements can be mimicked with the help of a semi-adjustable articulator. Due to their ease of handling and programming, they are frequently used in prosthodontics.3 Mounting of the master casts on an articulator is very important step in treatment of complete edentulous patient.1 In articulator programming, the device is modified to mimick the patient's temporomandibular joint structure and movement patterns of the patient. As a result, it acts as a patient when the patient is not present.3\n\nCondylar guidance is described as mandibular guidance generated by the condyle and articular disc traversing the contour of the articular eminence-GTP-9.4 In the event that condylar guidance the mandibular movements are not accurately recorded, the occlusal interference will occur. The time it takes to adjust dentures might go up as a result. Therefore, it is crucial to accurately capture the maxillomandibular relationship.5\n\nCondylar inclinations are provided by semi-adjustable articulators in two different ways: horizontally and laterally. Hanau's formula can be used to calculate the lateral condylar inclination from the horizontal condylar inclination (HCI), which determined with protrusive interocclusal records, or it can be done with individual lateral records.5\n\nOn semiadjustable articulators, The condylar guidance has been found to be unreliable when recorded and reproduced.5 There was a notable variation amongst the condylar guidance angle recorded successively by different practitioner, among multiple record materials, and amongst various articulator. This can be avoided by taking interocclusal records at various points in an edentulous subject, such as after teeth have been arranged or during jaw relation (Arrow point tracing). It is observed that records taken after teeth arrangement is much accurate. The values for the individual's condylar guidance are calculated using these records.3\n\nRadiographs can also be used to measure condylar guidance. When compared to clinical methods, it is more reliable because it uses consistent bony landmarks and can be standardised. These pictures offer composite skeleton representations in the sagittal plane. In a semi-adjustable articulators, condylar guidance inclination will be set using outline of the eminence.3\n\nTherefore, in the current research comparison of condylar guidance measurements will be made using records intraocclusally and digital orthopantomograph image in edentulous subject. Interocclusal recording medium should be capable of reproducing the details of the occlusal surface, as well as preserving the rigidity and accuracy of the materials for re-use more than once. For the purpose of keeping inter-occlusal records, there are several materials that can be used.1 In this study we will also compare the precision and repeatability of two interocclusal recording materials, that is Reinforced wax and Polyvinylsiloxane (Jet bite) in determining the condylar inclination values in semi-adjustable articulators.\n\n\n\n• To determine condylar guidance values using OPG image.\n\n• To evaluate the condylar guidance values utilize records intraocclusally taken during Jaw Relation stage with Reinforced wax and Polyvinyl siloxane (jet bite).\n\n• To evaluate the condylar guidance values utilize records intraocclusally taken during Try-in with Reinforced wax and Polyvinyl siloxane (jet bite).\n\n• Comparing the condylar guidance obtained using OPG with that determined during the Jaw Relation and Try-In.\n\nStudy design: Analytical observational study.\n\nThe upcoming research work shall be done in Department of Prosthodontics Crown & Bridge at Sharad Pawar Dental college, Sawangi, Wardha.\n\nThe study will be conducted on the patient reporting to the Department of Prosthodontics crown & bridge, with the chief complain of completely edentulous upper and lower archs and who are consider for complete denture prosthesis at Sharad Pawar dental college and hospital, Sawangi (Meghe), Wardha.\n\n\n\n• Participants with no teeth at all and has well-defined ridges\n\n\n\n• People who exhibit symptoms of neuromuscular and temporomandibular joint conditions.\n\n\nMethods\n\nWritten informed consent from the patient will be taken, After taking informed consent, the following procedure will be done.\n\nOrthopantomograph will be taken with the normal exposure and tracings will be done, Marking the Glenoid fossa (Superior curvature), Articular eminence (Inferior curvature) and the Frankfurt Horizontal Plane (FHP). The angle formed by joining the lines will be the horizontal condylar guidance angle, for that patient. The condylar guidance values on both right and left sides is recorded. This will be recorded for all the subject.\n\nPreliminary Impressions will be taken with modelling compound and Impressions will be filled with dental plaster, a positive replica of primary impression known as preliminary cast. On which wax spacer and custom tray will be made. Using the low fusing impression compound, Border moulding will be done and Final impression will be taken by zinc oxided eugenol paste. This impression will also be poured with dental plaster and cast obtained will be the master cast. Temporary record base will be made on it along with the occlusal rims.\n\nThe jaw relation will be recorded using standard techniques. Face bow transfer will be completed and maxillary cast will be orient on the articulator with the centric relation record mandibular cast will be related to maxillary cast and mount on the articulator’s mandibular component. Tracers will be affixed to the rims of the maxilla and mandible. Subject will be seated in upright position and he/she will be trained for mandibular movements. Once the dentist is satisfy with the patients mandibular movements, tracer plate will be ready to document.\n\nThe patient will be asked to retrude the mandible in centric relation once a distinct arrow point tracing with a sharp apex has been made, and the interocclusal recorded using reinforced wax and polyvinyl siloxane (jet bite) will be taken. The rims will be held intraorally till interocclusal material is set. When the mandibular jaw is in the centric relation, the head of the condyle is positioned, anteriorly & superiorly within the mandibular fossa/glenoid fossa as it is possible. And protrusive interocclusal record will also be made by instructing patient to protrude 6mm of distance from the apex of the arrow and it will be marked. This will be programmed on hanu-articulator. Articulator programming simulate tmj anatomy and movements of the subject, thus it serves as subject in the absences of the subject. Horizontal condylar guidance adjustments will be freed by releasing the locknuts.\n\nTeeth arrangement will be done, will proceed for try-in procedure and interocclusal records will be made using two different interocclusal record material namely, Polyvinaly siloxane and Reinforced wax. As it is difficult to maintain jaw stability at 6mm protrusion position, we will make a Wax indentations prior which will help subject to maintain the desired protrusive jaw position. The articulator’s lower member will be moved forward by about 6 mm after the try-in procedure, and it will then be closed in that position. The trial dentures will then be placed on the articulator. The interaction of the upper and lower midlines, as well as the horizontal relationship between the lower and upper anterior teeth, will be closely scrutinised. The locknuts will be fixed in that position. After proper training of the patient, we will register interocclusal record using bite registration paste and reinforced wax, hold the records in the mouth till the material gets hard.\n\nOn the articulator, the trial dentures will be put, and the interocclusal records will be used for programming. The maxillary cast will be constructed in two parts with a horizontal division method to evaluate the condylar guidance angulation. The condylar guidance values will be logged for both the interocclusal material reinforced wax and polyvinylsiloxane for each side, right and left of condyle.\n\nThe condylar guidance values succeeded in getting will be subjected to statistical analysis.\n\nOutcome: Expected outcome of the study is that it will help the clinicians to get knowledge about obtaining precise condylar inclination angle.\n\nBIAS: Bias will be minimized as patients are randomly will be selected from the Outpatient Department of Department Prosthodontics Crown & Bridge, of Sharad Pawar Dental College and Hospital, Wardha.\n\nFormula Using Mean difference\n\nWhere;\n\nZ1-α/2 is level of significance at 5% i.e., 95%\n\nConfidence interval = 1.96\n\nZ1-β is the power of test = 90% = 1.28\n\nPrimary variable:\n\nAs per reference articles.\n\nMinimum Total samples required = 7 per Group.\n\nMinimum Total sample size is 14.\n\nStatistical analysis will be done with the aid of Independent t-test., Analysis of variances (ANOVA) will be applied for analysis. The software that will be used in the analysis will be SPSS 27.0 version.\n\nThe scope of this study is to provide the dental practitioners with a method to effectively and precisely record condylar guidance, which won’t lead to maximum intercuspation interference while doing lower jaw movements. This will contribute to meet needs of the patient in accordance with the operation and durability of the denture in the oral cavity.\n\nStudy status: Study not yet started.\n\n\nDiscussion\n\nIn 2021 s.r keerthana studied a article to evaluate the reproducibility of condylar inclination and conclude that HCI values varied with respect to the record material used.5 R. Venkateshwaran in 2014 The relationship amongst the angle of horizontal condylar inclination measured on a semi-adjustable articulator and the angle marked on a TMJ tomogram in patient presenting with no teeth was investigated. He came to the conclusion that the horizontal condylar inclination, which is represented by the articular eminence marked on a TMJ tomogram image, has a mean difference of 5 degrees.2 Another author in 2013 studied the accuracy of articulator programming using radiographs and interocclusal records captured during the Arrow point tracing and Try-in stages. In that they noticed the easonable condylar guidance values determined at Try-in stage was nearer by average condylar guidance values determined on Radiographs.3 Pragya Shreshta in 2012 wanted to evaluate how the horizontal condylar guidance is measured clinically and radiographically. The CT scan and three clinical techniques—the wax protrusive record, Lucia jig record, and intraoral central bearing device were used to assess the condylar guidance. He came to the conclusion that the left and right HCG values were nearly identical. Particularly in comparison to clinical methods, the CT scan revealed higher HCG values, and all of the analytical methodologic values were comparable.6 In 2003, Jose dos Santos Jr(2003) studied this article to differentiate the condylar inclination angles between the protrusive wax record in semi adjustable Hanau articulator and the quick-set recorder for pantographic tracings. He determined that the protrusive wax record did not precisely reproduce the protrusive condylar inclination & that the pantographic tracer technique could do.7\n\n\n\n• Dentulous patient\n\n• Patient not willing to participate\n\n• Radiographic distortion\n\nEthical approval received by Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha (IEC ref no.-DMIHER (DU)/IEC/2023/849).", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nI want to thank my institute and my coworkers.\n\n\nReferences\n\nEl-Kouedi AY, Omar EA, Hamza T: EFFECT OF DIFFERENT BITE RECORDING MATERIALS ON MOUNTING ACCURACY OF WORKING CAST. Al-Azhar J. Dent. Sci. 2020 Oct 1; 23(4): 347–353. Publisher Full Text\n\nVenkateshwaran R, Karthigeyan S, Manoharan PS, et al.: A newer technique to program a semi adjustable articulator. J. Pharm. Bioallied Sci. 2014 Jul; 6(Suppl 1): S135–S139. PubMed Abstract \| Publisher Full Text\n\nShetty S, Satish Babu CL, Tambake D, et al.: A Comparative Evaluation of Condylar Guidance Value from Radiograph with Interocclusal Records made During Jaw Relation and Try-in: A Pilot Study. J. Indian Prosthodont. Soc. 2013 Sep; 13(3): 321–326. PubMed Abstract \| Publisher Full Text\n\nFerro KJ, Morgano SM, Driscoll CF, et al.: The glossary of prosthodontic terms.\n\nKeerthana SR, Mohammed HS, Hariprasad A, et al.: Comparative evaluation of condylar guidance obtained by three different interocclusal recording materials in a semi-adjustable articulator and digital panoramic radiographic images in dentate patients: An in vivo study. J. Indian Prosthodont. Soc. 2021 Oct 1; 21(4): 397. Publisher Full Text\n\nShreshta P, Jain V, Bhalla A, et al.: A comparative study to measure the condylar guidance by the radiographic and clinical methods. J. Adv. Prosthodont. 2012 Aug 1; 4(3): 153–157. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\ndos Santos JJ , Nelson S, Nowlin T: Comparison of condylar guidance setting obtained from a wax record versus an extraoral tracing: a pilot study. J. Prosthet. Dent. 2003 Jan 1; 89(1): 54–59. PubMed Abstract \| Publisher Full Text" }	[ { "id": "198382", "date": "18 Sep 2023", "name": "Jiefei Shen", "expertise": [ "Reviewer Expertise Prosthodotics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, the core structure and contents of this protocol appear well-developed. The manuscript focuses on comparing the condylar guidance values obtained from reinforced wax and polyvinyl siloxane interocclusal record materials, using panoramic radiographic images as a reference. However, the article requires further proofreading and improvement in terms of editing.\nAbstract:\nThe author mentions that the study will provide clinicians with knowledge about obtaining precise condylar inclination angles using the right interocclusal record materials. Including the results of the horizontal condylar guidance values at the jaw relation and try-in stage in the expected outcomes would also be desirable.\n\nPlease clarify the abbreviation \"OPG\" and explain which word it represents.\nIntroduction:\nRegarding the background and rationale, I disagree with the statement that panoramic radiographic images provide more reliable values for condylar guidance compared to conventional methods. Panoramic radiographic images may exhibit significant deformation and distortion in the anatomic structures.\n\nThe stated objective of \"Determining condylar guidance values using OPG image\" is inappropriate for this study. In the Objectives section, the main purpose of the study should be articulated. It should be noted that the measurement of horizontal condylar guidance values using OPG images introduces bias compared to conventional methods, as the temporomandibular joint consists of hard and soft tissue structures. Therefore, using OPG images as a \"control group\" in this experiment is not valid.\n\nThe inclusion criteria should provide more specificity regarding the width and height of the remaining alveolar ridge for participants with no teeth.\nMethods:\nConsider using CBCT or lateral cephalometrics instead of OPG for the evaluation of the Condylar Guidance value. Additionally, provide a more detailed description of the method used to obtain horizontal condylar guidance values from the OPG image, allowing for replication by others.\n\nNote that the articulator used is different from an actual patient. It is recommended to take the protrusive interocclusal record intraorally, rather than programming it on the articulator.\n\nClarify the material of the wax indentations used to determine the values of condylar guidance with the Interocclusal record material at the try-in stage. Also, correct the sentence: \"The articulator's lower member will be moved forward by about 6 mm after the try-in procedure, and it will then be closed in that position.\" The movement can only be done on the upper part of the articulators.\n\nPlease provide information on where the data for the sample size calculation came from.\nDiscussion:\nEnsure that the references used are up to date by checking and replacing them with more recent articles.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "10375", "date": "20 Nov 2023", "name": "khushbu doshi", "role": "Author Response", "response": "Please clarify the abbreviation \"OPG\" and explain which word it represents. Ans- Orthopantomogram, It represents Digital Panoramic Radiographic Images Regarding the background and rationale, I disagree with the statement that panoramic radiographic images provide more reliable values for condylar guidance compared to conventional methods. Panoramic radiographic images may exhibit significant deformation and distortion in the anatomic structures. Ans. Yes sir, I have consider this as a limitation of my study. The statement that panoramic radiographic images provide more reliable values for condylar guidance compare to conventional is taken from literature. Shetty S, Satish Babu CL, Tambake D, Surendra Kumar GP, Setpal AT. A comparative evaluation of condylar guidance value from radiograph with interocclusal records made during jaw relation and try-in: A pilot study. The Journal of Indian Prosthodontic Society. 2013 Sep;13:321-6. The stated objective of \"Determining condylar guidance values using OPG image\" is inappropriate for this study. In the Objectives section, the main purpose of the study should be articulated. It should be noted that the measurement of horizontal condylar guidance values using OPG images introduces bias compared to conventional methods, as the temporomandibular joint consists of hard and soft tissue structures. Therefore, using OPG images as a \"control group\" in this experiment is not valid. Ans. Yes sir, I will mention. Thank you. Sir, Bias will be eliminated as the same person will be evaluating the conventional method records as well as OPG tracing, patient will be taken from out patient department so bais will be eliminated their also And limitation of OPG image distortion is also consider. The inclusion criteria should provide more specificity regarding the width and height of the remaining alveolar ridge for participants with no teeth. Ans. Yes sir, I will specify in inclusion criteria. Patient should have class I ridge relation and interocclusal space should be minimum 3-4 mm Consider using CBCT or lateral cephalometrics instead of OPG for the evaluation of the Condylar Guidance value. Additionally, provide a more detailed description of the method used to obtain horizontal condylar guidance values from the OPG image, allowing for replication by others. Ans. Keeping economy and availability of machinery in clinic set up in mind OPG is chosen over CBCT and lateral cephalometrics. Method: On OPG we should trace the following points to get horizontal condylar guidance angle - Marking the Glenoid fossa (Superior curvature), Articular eminence (Inferior curvature) and the Frankfurt Horizontal Plane (FHP). The angle formed by joining the lines will be the horizontal condylar guidance angle, for that patient. See image. Tracing of line AB joining height of superior curvature A and inferior curvature B, representing inclination of articular eminence. XY is parallel to FHP. C is angle made by intersection of mean curvature line and horizontal reference line. Note that the articulator used is different from an actual patient. It is recommended to take the protrusive interocclusal record intraorally, rather than programming it on the articulator. Ans. Yes sir, The protrusive interocclusal record will be taken intraorally. Clarify the material of the wax indentations used to determine the values of condylar guidance with the Interocclusal record material at the try-in stage. Also, correct the sentence: \"The articulator's lower member will be moved forward by about 6 mm after the try-in procedure, and it will then be closed in that position.\" The movement can only be done on the upper part of the articulators. Ans. Bite registration aluminum wax will be used. Yes sir, The articulator’s upper member will be moved forward by about 6 mm after the try-in procedure, and it will then be closed in that position. Please provide information on where the data for the sample size calculation came from. Ans. The values for sample size is been taken from the following article- Keerthana SR, Mohammed HS, Hariprasad A, Anand M, Ayesha S. Comparative evaluation of condylar guidance obtained by three different interocclusal recording materials in a semi-adjustable articulator and digital panoramic radiographic images in dentate patients: An in vivo study. The Journal of Indian Prosthodontic Society. 2021 Oct 1;21(4):397. Venkateshwaran R, Karthigeyan S, Manoharan PS, Konchada J, Ramaswamy M, Bhuminathan null. A newer technique to program a semi adjustable articulator. J Pharm Bioallied Sci. 2014 Jul;6(Suppl 1):S135-139." } ] } ]	1	https://f1000research.com/articles/12-815
https://f1000research.com/articles/13-1228/v1	14 Oct 24	{ "type": "Review", "title": "Recycling of collagen from solid tannery waste and prospective utilization as adhesives.", "authors": [ "Nelly Esther Flores Tapia", "Hannibal Brito Moina", "Rodny Peñafiel", "Lander Vinicio Pérez Aldás", "Hannibal Brito Moina", "Rodny Peñafiel", "Lander Vinicio Pérez Aldás" ], "abstract": "Abstract This study explores the innovative potential of recycled collagen derived from tannery waste for use in high-performance adhesive formulations. The leather industry generates significant amounts of solid waste, primarily from chromium-tanned leather, which poses substantial environmental challenges. Recent advancements in recycling techniques have opened new avenues for repurposing this waste, particularly through collagen extraction, which comprises about 30-35% of tannery residues. This research systematically reviews the methods and applications of collagen extraction, highlighting the material’s versatility and environmental benefits when used as a bio-adhesive. The review identifies key challenges such as low water resistance, shear strength, and adhesiveness in collagen-based adhesives compared to synthetic counterparts. However, innovative solutions are emerging, including the incorporation of silane coupling agents and cross-linking technologies that significantly improve the water resistance and mechanical properties of these adhesives. Economic analyses further support the viability of using tannery waste-derived collagen in adhesive production, aligning with global sustainability goals and reducing reliance on petrochemical-based adhesives. Despite these advancements, the transition from laboratory research to commercial applications remains a significant challenge. Current studies primarily focus on small-scale experiments, with limited pilot-scale studies available. Nonetheless, the potential for collagen-based adhesives to replace harmful chemicals in industrial applications is promising, especially in sectors requiring biodegradable and non-toxic materials. This review concludes that while significant progress has been made, further research is necessary to overcome existing limitations and fully realize the commercial potential of collagen-based adhesives derived from tannery waste.", "keywords": [ "collagen", "solid tannery wastes", "animal glue", "collagen adhesives", "bio-adhesive", "recycled" ], "content": "Introduction\n\nThe leather industry, particularly chromium-based tanning, generates substantial solid waste, including chromium sludge, chrome-tanned leather shavings, and trimmings, with only 20% of raw material converted into leather.1–4 This results in significant waste, rich in collagen, which is often discarded in landfills due to the absence of cost-effective recycling programs.5–7 Solid tannery waste, comprising around 25% untreated skin, contains approximately 30% to 35% collagen and 1.5% chromium, underscoring its potential for resource recovery.8 India alone produces 0.02 million tons of chromium shavings annually (0.8 million tons of chromed leather trimmings per year), indicating a large potential resource for recycling into valuable products like renewed leather,9 fertilizers in agriculture, composting,10 formulation of composite materials,11,12 production of biodiesel,13–17 and extraction of raw materials such as keratin,18 chromium,19 and collagen20,21 (see Figure 1).\n\nHowever, synthetic adhesives have largely replaced animal glues due to concerns over cost, availability, and consistency. Despite this, synthetic adhesives are highly polluting, non-biodegradable, and dependent on petroleum, underscoring the need for eco-friendly alternatives. Collagen-modified adhesives, especially those derived from tannery waste, present a promising solution by offering both environmental benefits and effective adhesive properties.\n\nHistorically, collagen sourced from animal tissues like cartilage and tendons has long been used as an adhesive due to its environmentally friendly and non-toxic properties.22 Over time, animal collagen has been applied in various forms, from craftsmanship to industrial processes, for its natural adhesive qualities. Its composition facilitates efficient and reversible adhesion in applications such as paper and cardboard, with low cure temperatures compared to dispersions or hot melts, setting it apart from synthetic counterparts.23,24 Despite these advantages, synthetic chemicals supplanted animal glues at the beginning of the 20th century25 due to drawbacks like cost, availability, animal welfare concerns, and inconsistencies in raw material composition that affect adhesive performance.26 While synthetic adhesives provide several benefits, they are highly polluting, non-biodegradable, and reliant on petroleum, driving the search for eco-friendly alternatives.27–29 Utilizing collagen extracted from tannery waste offers a promising avenue for producing effective adhesives while minimizing waste.30\n\nAlthough animal glues derived from tannery wastes have been explored as renewable alternatives, their viability is limited by the contamination present in tannery waste, rendering them unsuitable for applications like human tissue glues.31–33 This review evaluates the potential of producing adhesives from collagen extracted from tannery wastes. It explores the methods, applications, and advancements in this area, with a particular focus on extraction techniques, adhesive formulation, and the associated environmental and economic benefits. By addressing gaps in current research, this review provides a comprehensive overview of the challenges and opportunities in utilizing tannery waste for sustainable adhesive production.\n\n\nMethods\n\nSeveral online databases were searched to ensure comprehensive topic coverage: PubMed/MEDLINE, MDPI, Web of Science, Scopus, and ScienceDirect. The central theme was sourcing articles discussing adhesives and glues derived from solid tannery waste, focusing on innovations that utilize recycled collagen.\n\n\n\n- Terms Used: ‘collagen’ AND ‘adhesives’ AND NOT ‘dental’ AND NOT ‘human’ AND NOT ‘surgical’ AND NOT ‘skin’ AND NOT ‘healing.’\n\nOutcomes: A total of 426 records were identified, excluding those discussing collagen adhesives for medical applications.\n\n\n\n- Terms Used: ‘tannery’ AND ‘wastes’ AND (‘glues’ OR ‘adhesives’ OR ‘collagen’).\n\nOutcome: 99 records identified.\n\n\n\n- Terms Used: ‘tannery’ AND ‘wastes’ AND ‘collagen-derived.’\n\nOutcome: 93 articles were found.\n\nAlthough numerous documents were retrieved, a limited number genuinely addressed the desired information. After removing the duplicates, 125 pertinent records were selected for the initial search.\n\nTimeline analysis\n\nThe search was confined to the past decade for in-depth scrutiny and to remain current. Of the shortlisted articles, 22 were subjected to qualitative analysis of the innovations in adhesive creation (Figure 2). The data search was conducted from June 1 to August 24, 2023.\n\nLanguage\n\nOnly documents in English.\n\nEconomic, historical, and industrial data were extracted individually from specialized websites to provide a holistic perspective, focusing on the past 20 years.\n\nThe systematic search across multiple databases resulted in the identification of 125 pertinent records, which were further refined through qualitative analysis. These findings lay the foundation for evaluating the current state of research on recycled collagen-based adhesives, highlighting both the advancements and the ongoing challenges in this innovative field.\n\n\nDiscussion\n\nGlobal trade in animal leather accounted for only 0.091% of the total international market in 2021, reaching a substantial value of $242.85 billion in 2022.34 Notable exporters in this trade were Italy ($3.55 billion), the United States ($1.88 billion), Brazil ($1.45 billion), China ($1.07 billion), and Germany ($734 million) in terms of exports. In comparison, China ($3.42 billion) and Italy ($2.3 billion) were significant importers of animal leather.35 Despite being economically significant for many nations, the tanning industry poses significant environmental challenges owing to solid waste and liquid and gaseous effluents, causing detrimental impacts on air, water, and soil quality.\n\nSolid tannery waste can be divided into removed hair, untreated skin residues, waste from tanned skin, leather trimming, and processed sludge. These residues are abundant and rich in fats36 and proteins37 and depending on their chemical composition, these residues can be recycled for diverse purposes, provided they undergo proper treatment and characterization.\n\nMoreover, regarding water usage in the tanning process, an incredible 50,000 kg of water is required to process just one kilogram of cowhide.38 In addition, tannery effluents are hazardous to decontamination because of their chromium, sulfide, heavy metal, and organic matter content.38,39 These effluents also exhibit elevated Chemical Oxygen Demand (COD) and Biochemical Oxygen Demand (BOD),40 and even after undergoing advanced chemical and physical treatments, they show low degradability indices.41 In addition, wastewater can permeate through underground layers, as confirmed by research conducted in India, Iran, and Bangladesh, where groundwater samples near tanneries showed high concentrations of Cu, Cr, Pb, Zn, Ni, Al, and As, with Cr registering the highest concentration, ranging from 0.01 to 2.07 mg/L.42–50 Undoubtedly, this risks ecosystem stability.51\n\nThe environmental impact of tannery waste has been under scrutiny for decades, with substantial evidence highlighting the high toxicity of such residues to plants52 and animals53–55 and bioaccumulation exacerbating this concern. The hazard posed by these residues relies on the presence of contaminating substances, such as sulfides,56 chromium (III), chromium (VI),57,58 lead, and other heavy metals. The immediate and severe effects of tannery waste on the environment and human health are undeniable.59 In recent years, substantial efforts have been made to remediate, recycle, and reuse various tannery wastes. In this context, repurposing solid tannery waste for glue production is a viable strategy for reducing waste and generating environmentally friendly products within a circular economic framework.\n\nAdhesives derived from natural sources have had the oldest known historical use in all civilizations for at least 200000 years.60 Evidence of glue residues dates to 1350 BCE, as observed in wood decorations found in King Tutankhamun’s tombs. Additionally, indications of glue usage have been found in ancient civilizations such as Greece and Rome.61 Furthermore, historical records highlight its presence in Edo period paintings in Japan and artifacts from the Joseon dynasty in Korea.62 Today, natural glues have specific services, such as artistic applications, historical conservation, cardboard, packaging63 and the creation of new adhesives.\n\nHistorically, glue was primarily produced from animal collagen derived from hides, bones, and connective tissues. Industrially, animal glues come from slaughterhouses that provide animal hides, blood,64,65 and other sources of proteins66 that can be extracted by hydrolysis.67 Traditionally, to recover animal glue, animal parts, primarily bones from horses, cattle, other livestock, and fishes, are boiled for extended periods in water to obtain collagen, which solidifies into glue upon cooling.68\n\nOther glue sources include water-resistant rennet casein and acidic casein. Rennet casein is produced by coagulating rennets with skim milk at 30°C and acidic casein.69 In contrast, lactic acid casein is derived from inoculating milk with certain bacteria such as Streptococcus lactis, Streptococcus cremoris, and Lactococcus lactis subspecies cremoris.69,70 Chitosan is another natural glue obtained from ground crab and shrimp shell waste, processed through acid or alkali treatment.71,72 Marine organisms such as mussels, barnacles, and tubeworms secrete protein adhesives that effectively adhere to hydrated underwater surfaces owing to the high proportion of amino acids with phenolic hydroxyl chemical groups.73 These secretions open ample avenues for developing water-resistant adhesives for various purposes.\n\nIn Asian cultures, the isinglass is the purest form of fish glue derived from the swim bladder membranes of sturgeons.74 Bone, fish, and hide adhesives have low moisture resistance, which affects the properties of the bond and notably decreases its elasticity and tensile strength.75\n\nAdhesives have been derived from plant resins, saps, natural rubber,76 starches,77 natural gums, latex, soy, lignin, algae, and cellulose.78 Glues from starches such as wheat and rice are commonly used in paper and woodworking applications. The mixture of corn starch with hydrolyzed acrylic emulsion and uzkhitan serves to glue warp threads79 and some starches serve as cohesive elements to create conductive glue for electrode materials.80 The functionality of these glues from starch can be improved with additives; for example, with polymerized lignosulfonates, the water resistance increases.81\n\nThe adhesive industry has become a specialized field of science, developing numerous innovative adhesive products. To create customized formulas for specific applications, it is crucial to understand the various existing adhesive types. This differentiation forms the basis for the evolution of collagen-modified adhesives. While this review does not delve extensively into the categorization of adhesives, Figure 3 provides a concise overview of the different segments within the adhesive industry, serving as a foundational reference for understanding the different adhesive types.\n\nWith the evolution of industrial processes, there is a need for more efficient and cost-effective adhesives.82 Tanneries, which process animal hides to produce leather, generate significant amounts of waste rich in collagen, particularly trimmings, and shavings, whether tanned or not.83 Rather than discarding these by-products, innovators have realized the potential to utilize this waste for glue production.\n\nCollagen is a complex protein with approximately 28 types.84,85 This protein is characterized by a unique structure consisting of three parallel polypeptide strands with a left-handed, polyproline II-type (PPII) helical conformation that coils together to form a right-handed triple helix. This structure necessitates that every third residue be glycine, leading to a consistent XaaYaaGly sequence throughout all collagen types. Within this sequence, the amino acids at the Xaa and Yaa positions are (2S)-proline (28%) and (2S,4R)-4-hydroxyproline (38%), respectively, making ProHypGly the predominant triplet, occurring at 10.5% in collagen.86 This formation provides strength and flexibility owing to the high proline and hydroxyproline contents, which prevent the protein from assuming a globular shape. Numerous polar groups in collagen enhance the chain interactions.87,88\n\nThe source and preparation method of collagen largely determines its physical, chemical, and mechanical properties. When its chains are shortened, differences originating from various sources diminish, leading to coiled proteins with reduced molecular weight. Native collagen, with a molecular weight of 285–300 KDa, undergoes significant structural changes upon hydrolysis. After denaturation, its triple-helix structure transforms into a random coil form owing to the dissociation of the hydrogen bonds. As a result of this process, hydrolyzed collagen consists of numerous peptides with much lower molecular weights (3–6 KDa).89 The best glues contain collagen Type I because they retain high adherence, ease of gel formation, and an excellent structure to form bonds with other substances compared to simple peptides. Collagen variability is influenced by its origin—whether it comes from skin, connective tissue, cartilage, or bones—as well as by the age and species of the animal, in Figure 4, a schematic representation of five types of collagen is presented. Type I human collagen is predominantly found in the skin, bone, teeth, tendons, ligaments, vascular ligature, and various organs (Figure 4a).90 Type II collagen is primarily located within cartilage (Figure 4b),91 while Type III collagen is commonly sourced from the skin, muscles, and blood vessels (Figure 4c).92 Type IV collagen is present in the epithelial-secreted layer of the basement membrane, as well as the basal lamina (Figure 4d).93 Type V collagen is a principal component of cell surfaces and the placenta (Figure 4e). Additionally, Bos Taurus Type IV collagen is depicted in the schematic (Figure 4e).94\n\nImages are used without modification under the terms of the CC BY 4.0 license—courtesy of PDB-101 (PDB101.rcsb.org)\n\nThe adhesion of the protein glue to wood depends on polar and nonpolar group interactions. Amino acids such as glutamic acid, tyrosine, and proline form hydrogen bonds, but these groups often remain inaccessible owing to internal bonds caused by forces such as van der Waals, hydrogen bonds, and hydrophobic interactions. Consequently, basic proteins have limited adhesion and require chemical changes to expose polar protein molecules.95,96 Furthermore, intramolecular cross-linking is achieved through the oxidative removal of amine groups from specific amino acids within proteins to develop high-strength collagen adhesives. This process leads to the formation of aldehydes, a phenomenon known as the Schiff base protein cross-linking.97\n\nResidues suitable for collagen extraction include untanned skin trimmings and tanned leather shavings.98 Tanneries sell the untanned residues to gelatin factories, which undergo a relatively straightforward transformation.\n\nIn contrast, tanned residues, such as wet blue and leather trimmings, require more intricate extraction processes99 because tanned wastes are intertwined collagen strands with agents like tannins, chromium, and alum100 The extraction processes commonly applied to these residues are acid or base hydrolysis at near boiling temperatures or complex enzymatic hydrolysis.101 However, recent investigations have employed multiple combined techniques to enhance collagen yield recovery while mitigating energy consumption102 Collagen extraction typically involves the pre-treatment, hydrolysis, and purification processes.\n\nPre-treatment tannery waste\n\nThe main goal of pre-treatment is to disrupt covalent cross-links between collagen molecules because they do not break down even in boiling water.103 Additionally, trimmings and untanned skin must be liberated from chemicals and dirt. These materials are then processed to remove all traces of hair, fat, and flesh, ensuring they can absorb more components for further acid or alkaline treatments.104\n\nAcid Pre-treatment: This method immerses washed and chopped skin pieces in dilute acid. The acid causes the skin to swell and hydrolyze the cross-links. Acid pre-treatment suits fragile skin with less fiber intertwinement, such as porcine and fish skin.105\n\nAlkaline Pre-treatment: Dilute alkalis such as sodium hydroxide, calcium hydroxide, and hydrogen peroxide106 are used. Alkalis is effective for extracting collagen from thick and hard materials. Despite being lengthy, sodium hydroxide treatment is preferred because it swells the skin, aiding alkali diffusion into the tissue matrix. Alkalis also hydrolyses unwanted components. Lower hydroxide concentrations at suitable temperatures retain the acid-soluble collagen and its native structure.107\n\nCollagen Extraction processes from tannery wastes\n\nProlonged boiling for collagen recovery is energy-intensive and inefficient, making it unsuitable for contemporary fabric treatment. Consequently, there is a pressing need to refine the process of extracting collagen from tannery wastes. The most prevalent method for such extraction involves hydrolysis using different agents, as shown in Table 1. There is also a growing interest in advancing novel techniques to enhance extraction yields. Moreover, establishing mathematical-physical models is crucial for improving the efficiency of shaving hydrolysis to reduce the need for extensive experimental trials, as emphasized by Vaskova and Vasek108 whose model introduced a parameter simulation aimed at deriving hydrolyzed collagen from tannery shavings using a flow reactor.\n\nPost-extraction purification and characterization\n\nThe purification of chromium-extracted collagen is crucial to ensure its suitability for subsequent applications.120 Chromium (III) is the most used as tanning agent. The chrome tanning reaction predominantly targets the carboxyl groups of collagen, which are assumed to be located at the aspartic and glutamic side chains. Kinetics showed quicker Cr (III) reactions with aspartic acid, whereas thermodynamics revealed a stronger tendency of glutamic acid for stable Cr (III) complexes involving Cr-O-Cr bridges. These bridges contribute to bridging the gaps between the collagen chains in the structure of the hide, thereby enabling tanning.121 Hence, the remarkable stability of leather underscores the necessity of devising methods that can disrupt the Cr-O-Cr complex while preserving collagen integrity.\n\nThe purification of collagen can be achieved by removing chromium through chemical methods122,123 such as alkali hydrolysis using 6% magnesium oxide and 1.0% sodium carbonate at 70°C for 48 h, followed by 1% bate enzyme hydrolysis to eliminate almost 80% of chromium from wet blue samples.124 New technologies include ultrasonic dechroming at a maximum of 200 MHz to reduce Cr by 70.2%.125,126 However, better results were achieved by applying sonication to the waste and adding EDTA at a ratio of 1:3 at 80°C for 30 min to achieve a chromium removal efficiency of 98%.127\n\nThese results show that purification of the extracted collagen is possible and practical. The efficiency and yield of dechroming depends on the nature of the waste and the process applied. This field of investigation offers abundant research opportunities and has considerable potential for prolific research.\n\n\nDevelopment and comparative analysis of eco-friendly adhesives utilizing collagen recycled from tannery wastes\n\nThere are two methods for utilizing natural adhesives. One involves using them directly for their adhesive properties; however, this approach is limited in its applications. Another approach involves blending collagen with other materials to produce copolymers.\n\nNegash et al. fabricated a glue for direct application from a hide-trimming waste.128 through a sequential treatment process involving soaking in a lime solution for four hours, washing, and neutralization with hydrochloric acid. The extraction procedure was conducted under varying conditions from 60 to 70°C for 2.5 to 3.5 hours in a water bath. The optimal conditions were found to be 60°C for three hours. The resulting glue had a viscosity of 90 centipoise, moisture content of 14.6%, ash content of 2.23%, density of 1259 kg/m3, yield of 32%, pH of 5.98, and a shear strength of 260 MN, characteristics that that were superior to the glue used as standard; indicating an optimum extraction process and a standard glue quality for restoration of artistic paintings, sculptures, and other historical artifacts crafted in the past.129 Another advantage is that it is possible to determine the exact composition of these glues. It has become imperative to meticulously analyze the composition of the glues utilized for recreating the original adhesive130 and ensuring meticulous restoration of ancient artworks131,132 without causing significant alterations that could potentially harm these invaluable pieces.\n\nFormaldehyde-based adhesives have been extensively used owing to their adhesive properties; however, formaldehyde gas emissions present significant health and environmental challenges specially when adopting rigorous emission standards, such as the European Emission Standards E1 and E0.133,134 One prospective solution combines collagen enzymatically extracted from chromed tannery waste into formaldehyde-based adhesive formulations. Intriguingly, the introduction of hydrolysate at a mass fraction of 0.05 displayed a two-fold increase in methylene bridges compared to methylene-oxide bridges (–CH2–O–CH2–), as revealed by thermogravimetric analysis. This enhancement implies a potential advantage in mitigating the formation of methylene oxide, a pivotal precursor to formaldehyde emissions, while concurrently enhancing the mechanical attributes of the final product, owing to the augmented molecular mass of the hydrolysate.135 Moreover, the stability of the cross-links observed during condensation in a neutral setting, even when exposed to phthalic acid as a curing agent.136,137\n\nSedlicik et al. worked with condensation adhesives based on urea-formaldehyde (UF) mixed with collagen hydrolysate from chrome-tanned leather. The adhesive mixtures were prepared by adding 5% of different modified collagen hydrolysates to the UF adhesive, which underwent condensation at 100°C for a maximum of 45 min. Shear strength testing, EN 314-1, was conducted on beech three-layer plywood after subjecting it to a water-resistance test. The results indicate that all samples meet the required standard values, with a maximum of 2.07 MPa at 19% humidity, although there is a specific decrease in the shear strength compared to the reference sample. Adding collagen hydrolysate within the 3–8% range reduced formaldehyde emissions compared to the commercial reference; this new mixture belongs to the E1 emission class. Experimental evidence, including FT-IR spectroscopy analysis, supports the existence of chemical reactions between the UF resin and collagen hydrolysate138 which is the reason for the improved characteristics of the mix in comparison with hydrolyzed collagen.\n\nRegarding formaldehyde-free adhesives, Islam et al.139 developed a sustainable binding agent for particleboard. This innovative approach yields three distinct adhesive types: collagen-based (Type A), acid extraction (Type B), and PVA/collagen ratio 4:1 (Type C). Notably, adhesive Type C showed a gel time of 4.2 minutes and an impressively high shear strength of 5.31 MPa. Comparatively, adhesive Type B, which lacks additives, exhibited a shear strength of 3.98 MPa. This discrepancy underscores the positive impact of incorporating a modifying agent, indicating that such agents can significantly enhance protein bonding. However, the Type C adhesive performance falls short of the 9.5 MPa exhibited by commercial urea formaldehyde resin. This suggests refining the formulation by adding PVA to increase shear strength.\n\nIn another scenario, by fortifying gelatin-based glue with a combination of epoxy-terminated hyperbranched polymers (EHPAE) and sodium dodecyl sulfate, the resulting adhesive showed a remarkable enhancement in shear strength, increasing from 0.92 MPa in pure collagen to 2.285 MPa in the EHPAE-III adhesive. However, it is important to note that this improved shear strength still falls short of the shear strength exhibited by commercially available adhesives (2.469 MPa). The increase in shear strength is attributed to the number of epoxy groups, which establish a robust multipoint cross-linking structure between the molecular chains of gelatin. The EHPAE-III meets the quality requirements of the EN standard for footwear applications.140 Formulation refinement is essential for achieving characteristics equal to or superior to commercial adhesives.\n\nYang et al.141 conducted a study to create a wood adhesive by combining waterborne polyurethane (WPU) and gelatin (G) derived from residual chromium tannery waste. Through this process, they generated a graft copolymer called WPUG using a method that avoids solvents and involves emulsion copolymerization. They discovered that the adhesive exhibited specific noteworthy characteristics: a considerable dry bonding strength of 4.21 MPa that was recorded at an R-value of 1.5, a contact angle of 111.5°, tensile strength measuring 32.91 MPa, and a temperature exceeding 350°C at which maximum weight loss occurred.\n\nAnother approach combines acrylic and hydrolyzed collagen through emulsion copolymerization of acrylic acid and butyl acrylate at various concentrations of hydrolyzed collagen. The resulting acrylic-collagen latex films exhibited changes in their characteristics upon neutralization, becoming sticky and highly flexible, especially the formulation A-C 25 N, containing 25% collagen, demonstrating promising probe track adhesion properties, although the maximum force required to separate the sample, and the stress-strain behavior was 0.0115 MPa.142\n\nWhen looking for adhesives for a specific application, such as corrugated cardboard, the collagen adhesive CPP-G is produced without water through an anhydrous condensation process driven by mechanical force. The foundation of adhesive CPP-100-2.2 is a collagen-degrading polypeptide-based polymer (CPP) resulting from the synthesis of tricyanogen chloride (TC) and collagen-degrading polypeptides (CDPs) extracted from leather scraps. The research identified that the prime conditions for optimal condensation were a high solubility rate of 97% with an n (TC)/n (CDP) ratio of 2.2 at 100°C. The developed adhesive adhered to the national standard (GB/T6544-2008) S-1.1 grade. The viscosity of CPP-100-2.2 was 0.256 Pa, and its thermal stability ranged from 220°C to 260°C. Notably, the initial adhesion capacity of CPP-G reached 90%, surpassing that of commercial adhesives, and its 48-hour water resistance was comparable to that of a commercial adhesive.143\n\nIn these studies, collagen-based adhesives were generally vulnerable to water and tended to redissolve upon heating, posing a drawback for adhesive applications in humid environments. Zhou et al.,144 developed a novel adhesive called collagen hydrolysates–silane coupling agent hybrids (CSH). This adhesive uses collagen hydrolysate extracted via the alkali method from leather waste as the base material and three silane coupling agents ((3-glycidyloxypropyl) dimethoxymethylsilane (GPDMS), (3-glycidyloxypropyl) trimethoxysilane (GPTMS), and (3-glycidyloxypropyl) triethoxysilane (GPTES)). The CSH adhesive demonstrated strong adhesive strength and excellent water resistance in tests. Significantly, the water resistance of the adhesive could be increased by modifying the type and quantity of silane coupling agent used. For wood adhesive, the CSH adhesive displayed an impressive dry adhesive strength of 1.57 MPa and a wet adhesive strength of 0.95 MPa, with a maximum cross-linking degree of 43%.144 These results suggest that, given an adequate formulation, collagen hydrolysate derived from tannery waste can potentially serve as a cost-effective and highly efficient adhesive for humid applications.\n\nBiodegradable adhesives can be derived from collagen extracted through alkali hydrolysis combined with magnesium oxide and trypsin from tannery-shaved waste. Extracted collagen was incorporated into biodegradable components, including polyvinyl alcohol and glycerol, at specific concentrations. Using Artificial Neural Network Analysis, the optimal production parameters were determined: working temperature of 65°C, polyvinyl alcohol concentration of 3.2%, and glycerol concentration of 4.2%. The optimal conditions led to an adhesive displaying an experimental peel strength of 12.5 N/mm, higher biodegradability, and similar adhesion power compared to the chemical-based adhesive evaluated in this study.145\n\nAnother example of the biodegradability of an adhesive made from collagen is an adhesive consisting of cross-linked collagen and γ-polyglutamic acid. Although this adhesive has a relatively low shear strength of 0.0429 MPa, it displayed a high degree of biodegradation when applied to skin incisions in rats, this adhesive degraded within two weeks in vivo, highlighting the advantages over non-biodegradable petrochemical adhesives.146\n\nA drawback of collagen-based adhesives is their notably low water resistance compared to commercial adhesives. Various studies have explored the incorporation of suitable enhancers to address the water resistance limitations to counteract this issue. For instance, blending collagen with methacrylate,147 incorporating gallic acid into collagen, and ε-polylysine as a bridge,148 melamine-formaldehyde149 or zein150 to mitigate this drawback, but it is recommended more investigation to improve water resistance in collagen-based adhesives.\n\nThese studies highlight that collagen can produce diverse adhesives with appropriate additives that will enhance strength, adhesiveness, water resistance, and increased biodegradability.\n\nThe opportunity to manufacture collagen-based adhesives arises at an opportune time, with promising data indicating significant market growth in the hydrolyzed collagen sector, projected to nearly double in value from 2023 to 2032, reaching an estimated $2.34 billion by 2032.151,152 This is particularly pronounced in North America and Europe, where diverse industries, including food and cosmetics, are heavily invested. Furthermore, the adhesives market ranked as the 281st most traded global commodity, with a trade value of $14.2 billion in 2021. Additionally, the adhesive sector demonstrated an impressive growth rate of 21.3% within a single year, underscoring its dynamic and expanding nature.153,154 Given the significant growth in the collagen sector, there is potential to establish a sustainable and profitable niche within the global adhesives industry by utilizing tannery waste as a collagen source. This approach could cater to non-edible or medical sectors, although the recovery process costs must be mitigated. The integration could revolutionize the supply chain by aligning waste utilization with market expansion opportunities.\n\nIt is feasible and profitable to produce gelatin from chrome shavings in a pilot plant operating with specific equipment, as demonstrated by Cabeza et al.155 In 24 hours, processing 9072 kg of chrome shavings can yield over 900 kg of gelatin daily at approximately $0.52 to $0.57 per kg. Meanwhile, commercially available low-quality gelatins were $3.20 per kg in the same year.156 These studies also illustrated that recovering collagen from tannery wastes can generate additional revenue from the reclaimed chrome and savings related to landfill disposal. In 2023, animal glue prices range between $1.5 to $4 per kilogram,157 making it cost-effective to recycle collagen at an industrial scale even today.158 The competitive price of collagen extracted from tannery wastes makes the industrial production of adhesives and glues possible, especially given the new technology that today is apt to improve collagen yield recovery from tannery wastes,159 as seen in Table 1.\n\n\nUtilization and innovations: Tannery waste-derived collagen adhesives applications\n\nIn various industries, such as woodwork, textiles, footwear, and packaging, versatile applications of innovative adhesive formulations are making significant strides. These formulations offer promising solutions and advancements for each sector.\n\nAs illustrated in Table 2, recycled collagen has been harnessed to produce adhesives suitable for the wood, paper, and textile industries. However, the potential applications of these adhesives extend well beyond the applications. They also hold promise in different arenas where the demand for effective bonding agents is considerable. As technology progresses, these innovative adhesive solutions are anticipated to find novel and unforeseen applications, thereby influencing industries with distinctive attributes and environmentally conscious qualities.\n\n\nChallenges and Future Directions\n\nThere is significant potential for innovation and improvement in collagen adhesives derived from recycled solid waste from tanneries. Exploration of collagen extraction processes, characterization, and modification is necessary to enhance its utility and sustainability. Research efforts should focus on increasing collagen’s adhesion strength, durability, and biodegradability by adding different polymers while considering its compatibility with various substrates, scalability, and commercial viability.169\n\nIt is crucial to examine the regulatory compliance and safety of collagen-based adhesives, mainly when used in consumer products like textiles and packaging. By exploring these areas, innovative solutions can be discovered, developing more sustainable, efficient, and versatile collagen adhesives sourced from recycled tannery waste. These efforts can potentially revolutionize industries while aligning them with global sustainability goals.\n\n\nConclusion\n\nThis review examines the potential of utilizing collagen extracted from tannery waste for adhesive production and provides a detailed analysis of the extraction methods, formulation techniques, and applications. This study demonstrated the technical feasibility and environmental benefits of this approach.\n\nResearch suggests a high level of versatility in using collagen, including blending it with urea-formaldehyde or combining it with waterborne polyurethane for wood-based applications. These blends demonstrated the desired adhesive properties and, in some cases, surpassed those of commercial adhesives. However, collagen-based adhesives are limited by their water resistance. To address this issue, innovations such as the incorporation of silane coupling agents or the addition of other compounds such as methacrylate, gallic acid, ε-polylysine, melamine-formaldehyde, or zein are being explored, indicating a promising future for this field.\n\nHowever, transitioning from an experimental to a commercial scale remains a challenge. Current investigations are mostly laboratory-level, and comprehensive economic analyses or pilot-scale studies are scarce. Historical data suggests the economic viability of collagen extraction from tannery waste and its subsequent use in adhesive production. However, further consistent and extensive studies are required to confirm this finding.\n\nIn essence, environmentally conscious sourcing and the adaptability of collagen are exciting prospects for future adhesive technologies.\n\n\nAuthor contributions\n\nConceptualization: NEFT; supervision: NEFT and HBM; literature search: NEFT, RDPA and HBM material preparation: NEFT, RDPA and HBM; methodology: NEFT; acquisition of data: NEFT; interpretation of data: NEFT, RDPA; writing—original draft: NEFT, RDPA, HBM; writing—review and final editing: NEFT and HBM; supervision: RDPA, HBM; all authors have read and agreed to the published version of the manuscript.\n\n\nEthical approval\n\nEthical approval and consent were not required.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\n\nReferences\n\nMontalvão M, da Silva Castro A , de Lima Rodrigues A , et al.: Impacts of Tannery Effluent on Development and Morphological Characters in a Neotropical Tadpole. Sci. Total Environ. 2018; 610-611: 1595–1606. PubMed Abstract \| Publisher Full Text\n\nSaxena G, Purchase D, Bharagava R: Environmental Hazards and Toxicity Profile of Organic and Inorganic Pollutants of Tannery Wastewater and Bioremediation Approaches.Saxena G, Bharagava R, editors. Bioremediation of Industrial Waste for Environmental Safety. Singapore: Springer; 2020. Publisher Full Text\n\nHansen É, Monteiro de Aquim P, Hansen AW, et al.: Impact of Post-Tanning Chemicals on the Pollution Load of Tannery Wastewater. J. Environ. Manag. 2020; 269: 110787. Publisher Full Text\n\nHansen É, de Aquim PM , Gutterres M: Environmental Assessment of Water, Chemicals and Effluents in Leather Post-Tanning Process: A Review. Environ. Impact Assess. Rev. 2021; 89: 106597. Publisher Full Text\n\nSaira GC, Shanthakumar S: Zero Waste Discharge in Tannery Industries – An Achievable Reality? A Recent Review. J. Environ. Manag. 2023; 335: 117508. Publisher Full Text\n\nGuo SS, Tian YQ, Wu H, et al.: Spatial Distribution and Morphological Transformation of Chromium with Coexisting Substances in Tannery Landfill. Chemosphere. 2021; 285: 131503. Publisher Full Text\n\nSzuba A, Lorenc-Plucińska G: Field Proteomics of Populus Alba Grown in a Heavily Modified Environment – An Example of a Tannery Waste Landfill. Sci. Total Environ. 2018; 610-611: 1557–1571. PubMed Abstract \| Publisher Full Text\n\nVerma SK, Sharma PC: Current Trends in Solid Tannery Waste Management. Crit. Rev. Biotechnol. 2023; 43(5): 805–822. PubMed Abstract \| Publisher Full Text\n\nDunky M: Introduction to Naturally-Based (Bio-) Adhesives. Biobased Adhesives: Sources, Characteristics, and Applications. 2023; pp. 1–44. 307–319. Publisher Full Text\n\nFerreira S, de Melo W , Araujo F, et al.: Long-Term Effect of Composted Tannery Sludge on Soil Chemical and Biological Parameters. Environ. Sci. Pollut. Res. 2020; 27: 41885–41892. PubMed Abstract \| Publisher Full Text\n\nRigueto CVT, Rosseto M, Nazari MT, et al.: Adsorption of Diclofenac Sodium by Composite Beads Prepared from Tannery Wastes-Derived Gelatin and Carbon Nanotubes. J. Environ. Chem. Eng. 2021; 9: 105030. Publisher Full Text\n\nŁawińska K: Production of Agglomerates, Composite Materials, and Seed Coatings from Tannery Waste as New Methods for Its Management. Materials. 2021; 14: 6695. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTujjohra F, Alam MS, Rahman MM, et al.: An Eco-Friendly Approach of Biodiesel Production from Tannery Fleshing Wastes by Crude Neutral Protease Enzyme. Clean. Eng. Technol. 2023; 14: 100638. Publisher Full Text\n\nOlubunmi B, Alade A, Ebhodaghe S, et al.: Optimization and Kinetic Study of Biodiesel Production from Beef Tallow Using Calcium Oxide as a Heterogeneous and Recyclable Catalyst. Energy Conversion and Management: X. 2022; 14: 100221. Publisher Full Text\n\nNagi M, He M, Li D, et al.: Utilization of Tannery Wastewater for Biofuel Production: New Insights on Microalgae Growth and Biomass Production. Sci. Rep. 2020; 10: 1–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBooramurthy VK, Kasimani R, Pandian S: Biodiesel Production from Tannery Waste Using a Nano Catalyst (Ferric-Manganese Doped Sulphated Zirconia). Energy Sources. 2022; 44: 1092–1104. Publisher Full Text\n\nTujjohra F, Alam MS, Rahman MM, et al.: An Eco-Friendly Approach of Biodiesel Production from Tannery Fleshing Wastes by Crude Neutral Protease Enzyme. Clean. Eng. Technol. 2023; 14: 100638. Publisher Full Text\n\nSanchez-Olivares G, Sanchez-Solis A, Calderas F, et al.: Keratin Fibres Derived from Tannery Industry Wastes for Flame Retarded PLA Composites. Clean. Eng. Technol. 2017; 140: 42–54. Publisher Full Text\n\nJacob JJ, Varalakshmi R, Gargi S, et al.: Removal of Cr (III) and Ni (II) from Tannery Effluent Using Calcium Carbonate Coated Bacterial Magnetosomes. Clean Water. 2018; 1: 1–10. Publisher Full Text\n\nAshokkumar M, Ajayan PM: Materials Science Perspective of Multifunctional Materials Derived from Collagen. Int. Mater. Rev. 2020; 66: 160–187. Publisher Full Text\n\nSinaga MZE, Sihombing YA, Hardiyanti R, et al.: Preparation and Mechanical Properties of Biodegradable Films Based on Seaweed, Chitosan, and Collagen. AIP Conference Procedings. 2021; 2342. Publisher Full Text\n\nBrum IS, Elias CN, de Carvalho JJ , et al.: Properties of a Bovine Collagen Type I Membrane for Guided Bone Regeneration Applications. E-Polymers. 2021; 21: 210–221. Publisher Full Text\n\nNoorzai S, Verbeek CJR: Biomaterials Derived from Agricultural Waste: A Focus on Collagen.Ramawat K, Mérillon JM, Arora J, editors. Agricultural Waste: Environmental Impact, Useful Metabolites and Energy Production. Sustainable Development and Biodiversity. Singapore: Springer; 2023; 31. : 87–107. Publisher Full Text\n\nSierra-Romero A, Novakovic K, Geoghegan M: Adhesive Interfaces toward a Zero-Waste Industry. Langmuir. 2022; 38: 15476–15493. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDunky M: Wood Adhesives Based on Natural Resources: A Critical Review: Part I. Protein-Based Adhesives. Progress in Adhesion and Adhesives. 2021; 6: 203–336. Publisher Full Text\n\nFay P: A History of Adhesive Bonding. Adhesive Bonding: Science, Technology and Applications. 2021; pp. 3–40. Publisher Full Text\n\nPatel K, Munir D, Santos RM: Beneficial Use of Animal Hides for Abattoir and Tannery Waste Management: A Review of Unconventional, Innovative, and Sustainable Approaches. Environ. Sci. Pollut. Res. 2022; 29: 1807–1823. PubMed Abstract \| Publisher Full Text\n\nDeskera: Leathers Manufacturing and Recycling: A Detailed Guide!. (accessed on 17 May 2024). Reference Source\n\nHeinrich LA: Future Opportunities for Bio-Based Adhesives – Advantages beyond Renewability. Green Chem. 2019; 21: 1866–1888. Publisher Full Text\n\nYorgancioglu A, Onem E, Yilmaz O, et al.: Interactions Between Collagen and Alternative Leather Tanning Systems to Chromium Salts by Comparative Thermal Analysis Methods: Thermal Stabilisation of Collagen by Tanning Process. Johns. Matthey Technol. Rev. 2022; 66: 215–226. Publisher Full Text\n\nOcak B: Film-Forming Ability of Collagen Hydrolysate Extracted from Leather Solid Wastes with Chitosan. Environ. Sci. Pollut. Res. Int. 2018; 25: 4643–4655. PubMed Abstract \| Publisher Full Text\n\nLutz TM, Kimna C, Casini A, et al.: Bio-Based and Bio-Inspired Adhesives from Animals and Plants for Biomedical Applications. Materials Today Bio. 2022; 13: 100203. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAssmann A, Vegh A, Ghasemi-Rad M, et al.: A Highly Adhesive and Naturally Derived Sealant. Biomaterials. 2017; 140: 115–127. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrand View Research, Inc: Leather Goods Industry Growth & Analysis, Data Book. (accessed on 22 August 2023). Reference Source\n\nOEC - The Observatory of Economic Complexity: Raw Hides & Skin (Non-Fur). (accessed on 11 August 2023). Reference Source\n\nOnem E, Renner M, Prokein M: Green Separation and Characterization of Fatty Acids from Solid Wastes of Leather Industry in Supercritical Fluid CO2. Environ. Sci. Pollut. Res. Int. 2018; 25: 22213–22223. PubMed Abstract \| Publisher Full Text\n\nPan F, Xiao Y, Zhang L, et al.: Leather Wastes into High-Value Chemicals: Keratin-Based Retanning Agents via UV-Initiated Polymerization. J. Clean. Prod. 2023; 383: 135492. Publisher Full Text\n\nSivaram NM, Barik D: Chapter 5 - Toxic Waste From Leather Industries. Woodhead Publishing Series in Energy, Energy from Toxic Organic Waste for Heat and Power Generation. Woodhead Publishing; 2019; pp. 55–67. Publisher Full Text\n\nSadeghi H, Fazlzadeh M, Zarei A, et al.: Spatial Distribution and Contamination of Heavy Metals in Surface Water, Groundwater and Topsoil Surrounding Moghan’s Tannery Site in Ardabil, Iran. Int. J. Environ. Anal. Chem. 2022; 102(5): 1049–1059. Publisher Full Text\n\nUrbina-Suárez A, Machuca-Martínez N, Barajas-Solano A: Advanced Oxidation Processes and Biotechnological Alternatives for the Treatment of Tannery Wastewater. Molecules. 2021; 26(11): 3222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSivagami K, Sakthivel KP, Nambi IM: Advanced Oxidation Processes for the Treatment of Tannery Wastewater. J. Environ. Chem. Eng. 2018; 6: 3656–3663. Publisher Full Text\n\nVasanthan SV, Murugesan AM, Selvam AS: Study of Seasonal, Spatial Deviation and Pollution Indices of Ground Water by Tannery Activities in Vaniyambadi, Vellore District, Tamilnadu, India. Orient. J. Chem. 2022; 38: 56–64. Publisher Full Text\n\nKanagaraj G, Elango L: Chromium and Fluoride Contamination in Groundwater around Leather Tanning Industries in Southern India: Implications from Stable Isotopic Ratio Δ53Cr/Δ52Cr, Geochemical and Geostatistical Modelling. Chemosphere. 2019; 220: 943–953. PubMed Abstract \| Publisher Full Text\n\nBhattacharya M, Shriwastav A, Bhole S, et al.: Processes Governing Chromium Contamination of Groundwater and Soil from a Chromium Waste Source. ACS Earth Space Chem. 2020; 4: 35–49. Publisher Full Text\n\nKanagaraj G, Mohana P, Muthusamy S, et al.: Geochemical Evaluation of Groundwater around Chromepet Tannery Belt, Southern India. Groundw. Sustain. Dev. 2023; 22: 100963. Publisher Full Text\n\nKarunanidhi D, Aravinthasamy P, Subramani T, et al.: Chromium Contamination in Groundwater and Sobol Sensitivity Model Based Human Health Risk Evaluation from Leather Tanning Industrial Region of South India. Environ. Res. 2021; 199: 111238. PubMed Abstract \| Publisher Full Text\n\nAlam MS, Han B, Al-Mizan; Pichtel, J.: Assessment of Soil and Groundwater Contamination at a Former Tannery District in Dhaka, Bangladesh. Environ. Geochem. Health. 2020; 42: 1905–1920. PubMed Abstract \| Publisher Full Text\n\nTripathi S, Chaurasia SR: Detection of Chromium in Surface and Groundwater and Its Bio-Absorption Using Bio-Wastes and Vermiculite. Engineering Science and Technology, an International Journal. 2020; 23: 1153–1161. Publisher Full Text\n\nKhan A, Michelsen N, Marandi A, et al.: Processes Controlling the Extent of Groundwater Pollution with Chromium from Tanneries in the Hazaribagh Area, Dhaka, Bangladesh. Sci. Total Environ. 2020; 710: 136213. PubMed Abstract \| Publisher Full Text\n\nKistan A, Kanchana V, Geetha NK: Seasonable Variation of Trace Metals, Statistical Values of Groundwater in and around Tannery Areas of Vellore District. Orient. J. Chem. 2021; 37: 735–745. Publisher Full Text\n\nAhmed F, Fakhruddin ANM, Fardous Z, et al.: Investigation of Human Health Risks Influenced by Trace Metals (TMs) in Chili Plant (Capsicum Annuum L.) Grown on Tannery Effluents Contaminated Soil. Toxicol. Int. 2021; 28: 67–80. Publisher Full Text\n\nNirola R, Megharaj M, Subramanian A, et al.: Analysis of Chromium Status in the Revegetated Flora of a Tannery Waste Site and Microcosm Studies Using Earthworm E. Fetida. Environ. Sci. Pollut. Res. Int. 2018; 25: 5063–5070. PubMed Abstract \| Publisher Full Text\n\nBaratzadeh-Poustchi F, Tabatabaei-Yazdi F, Heidari A, et al.: Evaluation of Chromium Accumulation and Resulting Histopathological Changes in Libyan Jirds (Mammals, Rodentia), Affected by Effluent from Ghazghan Leather Industrial Town, Iran. Environ. Sci. Pollut. Res. 2020; 27: 39343–39353. PubMed Abstract \| Publisher Full Text\n\ndos Reis Sampaio D , Estrela F, Mendes B, et al.: Ingestion of tannery effluent as a risk factor to the health of birds: A toxicological study using Coturnix coturnix japonica as a model system. Sci. Total Environ. 2019; 681: 275–291. PubMed Abstract \| Publisher Full Text\n\nBakshi A, Panigrahi AK: A Comprehensive Review on Chromium Induced Alterations in Fresh Water Fishes. Toxicol. Rep. 2018; 5: 440–447. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHorn E, Oyekola O, Welz P, et al.: Biological Desulfurization of Tannery Effluent Using Hybrid Linear Flow Channel Reactors. Water. 2022; 14(1): 32. Publisher Full Text\n\nPrasad S, Yadav K, Kumar S, et al.: Chromium Contamination and Effect on Environmental Health and Its Remediation: A Sustainable Approaches. J. Environ. Manag. 2021; 285: 112174. PubMed Abstract \| Publisher Full Text\n\nThangam T, Kumar V, Vasline Y: Decontamination of Hexavalent Chromium by Geo Chemical Fixation Method in a Hazardous Dump Site, Ranipet, Tamil Nadu, India. J. Eng. Appl. Sci. 2018; 13: 208–212. Publisher Full Text\n\nArti, Mehra R: Analysis of Heavy Metals and Toxicity Level in the Tannery Effluent and the Environs. Environ. Monit. Assess. 2023; 195: 554. PubMed Abstract \| Publisher Full Text\n\nLangejans G, Aleo A, Fajardo S, et al.: Archaeological Adhesives. Oxford Research Encyclopedia of Anthropology. 2022. Publisher Full Text\n\nFay P: A History of Adhesive Bonding. Adhesive Bonding. In Woodhead Publishing Series in Welding and Other Joining Technologies. Woodhead Publishing; 2021; pp. 3–40. Publisher Full Text\n\nYu J, Chung YJ: Analysis of Cow Hide Glue Binder in Traditional Dancheong by Enzyme-Linked Immunosorbent Assay. JCS. 2019; 35: 363–372. Publisher Full Text\n\nFan C, Tang Q: Allyl Glycidyl Ether-Modified Animal Glue Binder for Improved Water Resistance and Bonding Strength in Sand Casting. Organic Polymer Material Research. 2021; 2: 1–7. Publisher Full Text\n\nLi X, Li J, Luo J, et al.: A Novel Eco-Friendly Blood Meal-Based Bio-Adhesive: Preparation and Performance. J. Polym. Environ. 2018; 26: 607–615. Publisher Full Text\n\nWusigale, Liang L, Luo Y: Casein and Pectin: Structures, Interactions, and Applications. Trends Food Sci. Technol. 2020; 97: 391–403. Publisher Full Text\n\nAdhikari B, Chae M, Bressler DC: Utilization of Slaughterhouse Waste in Value-Added Applications: Recent Advances in the Development of Wood Adhesives. Polymers. 2018; 10: 176. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeón-López A, Morales-Peñaloza A, Martínez-Juárez V, et al.: Hydrolyzed Collagen-Sources and Applications. Molecules. 2019; 24(22): 4031. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWan Y, Gao Y, Shao J, et al.: Effects of Ultrasound and Thermal Treatment on the Ultrastructure of Collagen Fibers from Bovine Tendon Using Atomic Force Microscopy. Food Chem. 2021; 347: 128985. PubMed Abstract \| Publisher Full Text\n\nBadem A, Ucar G, Gupta P: Production of Caseins and Their Usages. Int. J. Food Sci. Nutr. 2017; 2(1): 2455–4898. Reference Source\n\nGalante R, Cunha F, Fangueiro R: Extraction and Properties of Casein Biopolymer from Milk. Handbook of Natural Polymers. 2023; Vol. 1: pp. 471–487. Publisher Full Text\n\nSilvestre J, Delattre C, Michaud P, et al.: Optimization of Chitosan Properties with the Aim of a Water-Resistant Adhesive Development. Polymers. 2021; 13: 4031. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPakizeh M, Moradi A, Ghassemi T: Chemical Extraction and Modification of Chitin and Chitosan from Shrimp Shells. Eur. Polym. J. 2021; 159: 110709. Publisher Full Text\n\nFan H: Getting Glued in the Sea. Polym. J. 2023; 55: 653–664. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOlden J, Vitule J, Cucherousset J, et al.: There’s More to Fish than Just Food: Exploring the Diverse Ways That Fish Contribute to Human Society. Fisheries (Bethesda). 2020; 45: 453–464. Publisher Full Text\n\nBachtiar EV, Niemz P, Sandberg D: Properties of Adhesive Films Used in Cultural Assets. Wood Mater. Sci. Eng. 2022; 17: 147–150. Publisher Full Text\n\nLv S, Tan L, Peng X, et al.: Experimental Investigation on the Performance of Bone Glue and Crumb Rubber Compound Modified Asphalt. Constr. Build. Mater. 2021; 305: 124734. Publisher Full Text\n\nDunky M: Wood Adhesives Based on Natural Resources: A Critical Review: Part II. Carbohydrate-Based Adhesives. Progress in Adhesion and Adhesives. 2021; 6: 337–382. Publisher Full Text\n\nNasiri A, Wearing J, Dubé MA: Using Lignin to Modify Starch-Based Adhesive Performance. ChemEngineering. 2020; 4(1): 3. Publisher Full Text\n\nMardonov S, Shokirov L, Rakhimov K: Development of Technology for Obtaining Starch Gluing Modified with Uzkhitan and Hydrolyzed Emulsion. J. Phys. Conf. Ser. 2021; 2094: 042070. Publisher Full Text\n\nJezowski P, Kowalczewski PŁ: Starch as a Green Binder for the Formulation of Conducting Glue in Supercapacitors. Polymers (Basel). 2019; 11: 1648. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJimenez M, Schwaiger N, Flicker R, et al.: Enzymatic Synthesis of Wet-Resistant Lignosulfonate-Starch Adhesives. New Biotechnol. 2022; 69: 49–54. PubMed Abstract \| Publisher Full Text\n\nParvin S, Mazumder LT, Hasan S, et al.: What Should We Do With Our Solid Tannery Waste. IOSR Journal of Environmental Science, Toxicology and Food Technology. 2017; 11: 82–89. Publisher Full Text\n\nRaguraman R, Sailo L: Efficient Chromium Recovery from Tannery Sludge for Sustainable Management. Int. J. Environ. Sci. Technol. 2017; 14: 1473–1480. Publisher Full Text\n\nLeón-López A, Morales-Peñaloza A, Martínez-Juárez VM, et al.: Hydrolyzed Collagen—Sources and Applications. Molecules. 2019; 24(22): 4031. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRevell CK, Jensen OE, Shearer T, et al.: Collagen Fibril Assembly: New Approaches to Unanswered Questions. Matrix Biology Plus. 2021; 12: 100079. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShoulders MD, Raines RT: Collagen Structure and Stability. Annu. Rev. Biochem. 2009; 78: 929–958. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoldberga I, Li R, Duer MJ: Collagen Structure−Function Relationships from Solid-State NMR Spectroscopy. Acc. Chem. Res. 2018; 51(7): 1621–1629. PubMed Abstract \| Publisher Full Text\n\nAvila-Rodríguez MI, Rodríguez-Barroso L, Sánchez ML: Collagen: A Review on Its Sources and Potential Cosmetic Applications. J. Cosmet. Dermatol. 2017; 17: 20–26. PubMed Abstract \| Publisher Full Text\n\nLeón-López A, Morales-Peñaloza A, Manuel Martínez-Juárez V, et al.: Hydrolyzed Collagen-Sources and Applications. Molecules. 2019; 24(22): 4031. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu Y, Yang X, Sun F: RCSB PDB - 7CWK: Structure of a Triple-Helix Region of Human Collagen Type I. (accessed on 24 August 2023). Reference Source\n\nYang X, Zhu Y, Ye S, et al.: RCSB PDB - 6JEC: Structure of a Triple-Helix Region of Human Collagen Type II. (accessed on 24 August 2023). Reference Source\n\nHua C, Zhu Y, Xu W, et al.: Characterization by High-Resolution Crystal Structure Analysis of a Triple-Helix Region of Human Collagen Type III with Potent Cell Adhesion Activity. Biochem. Biophys. Res. Commun. 2019; 508: 1018–1023. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCasino P, Gozalbo-Rovira R, Rodríguez-Díaz J, et al.: Structures of Collagen IV Globular Domains: Insight into Associated Pathologies, Folding and Network Assembly. IUCrJ International Union of Cristallography Journal. 2018; 5: 765–779. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSundaramoorthy M, Meiyappan M, Todd P, et al.: Structure of Type IV Collagen NC1 Domains. J. Biol. Chem. 2002; 277(34): 31142–31153. PubMed Abstract \| Publisher Full Text\n\nPizzi A, Mittal K, Bhatnagar N: Theories and Mechanisms of Adhesion. Theories and Mechanisms of Adhesion. CRC Press; 2017; pp. 3–18. 9781315120942.\n\nRathi S, Saka R, Domb AJ, et al.: Protein-Based Bioadhesives and Bioglues. Polym. Adv. Technol. 2019; 30: 217–234. Publisher Full Text\n\nRamesh M, Kumar L: Bioadhesives. Green Adhesives: Preparation, Properties and Applications. John Wiley & Sons, Ltd; 2020; pp. 145–164. 9781119655053. Publisher Full Text\n\nYang J, Shan Z, Zhang Y, et al.: Stabilization and Cyclic Utilization of Chrome Leather Shavings. Environ. Sci. Pollut. Res. 2019; 26: 4680–4689. PubMed Abstract \| Publisher Full Text\n\nBaggio E, Scopel BS, Krein DDC, et al.: Transglutaminase Crosslinked Gelatin Films Extracted from Tanned Leather Waste. J. Am. Leather Chem. Assoc. 2021; 116: 3–10. Publisher Full Text\n\nGao D, Wang P, Shi J, et al.: A Green Chemistry Approach to Leather Tanning Process: Cage-like Octa (Aminosilsesquioxane) Combined with Tetrakis (Hydroxymethyl) Phosphonium Sulfate. J. Clean. Prod. 2019; 229: 1102–1111. Publisher Full Text\n\nGargano M, Florio C, Sannia G, et al.: From Leather Wastes to Leather: Enhancement of Low Quality Leather Using Collagen Recovered from Leather Tanned Wastes. Clean Techn. Environ. Policy. 2023; 25: 3065–3074. Publisher Full Text\n\nParisi M, Nanni A, Colonna M: Recycling of Chrome-Tanned Leather and Its Utilization as Polymeric Materials and in Polymer-Based Composites: A Review. Polymers (Basel). 2021; 13: 1–23. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOstadi A, Arshee M, Lin Z, et al.: Orientation-Dependent Indentation Reveals the Crosslink-Mediated Deformation Mechanisms of Collagen Fibrils. Acta Biomater. 2023; 158: 347–357. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYoseph Z, Gladstone J, Assefa B, et al.: Extraction of Elastin from Tannery Wastes: A Cleaner Technology for Tannery Waste Management. J. Clean. Prod. 2020; 243: 118471. Publisher Full Text\n\nVenupriya V, Krishnaveni V, Ramya M: Effect of Acidic and Alkaline Pretreatment on Functional, Structural and Thermal Properties of Gelatin from Waste Fish Scales. Polym. Bull. 2022; 80: 10533–10567. Publisher Full Text\n\nSathish M, Madhan B, Raghava Rao J: Leather Solid Waste: An Eco-Benign Raw Material for Leather Chemical Preparation – A Circular Economy Example. Waste Manag. 2019; 87: 357–367. PubMed Abstract \| Publisher Full Text\n\nMatinong A, Chisti Y, Pickering K, et al.: Collagen Extraction from Animal Skin. Biology. 2022; 11: 905. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVaskova H, Vasek V: Mathematical model of Hydrolysis Reaction for the Collagen Hydrolyzate Production from Leather Shavings. Annals of DAAAM and Proceedings of the International DAAAM Symposium. 2016; 1: 271–274. Publisher Full Text\n\nNiculescu M, Epure D, Lasoń-Rydel M, et al.: Biocomposites Based on Collagen and Keratin with Properties for Agriculture and Industrie Applications. Eurobiotech Journal. 2019; 3: 160–166. Publisher Full Text\n\nKumar N, Strachowski P, Undeland I, et al.: Structural and Functional Properties of Collagen Isolated from Lumpfish and Starfish Using Isoelectric Precipitation vs Salting Out. Food Chemistry: X. 2023; 18: 100646. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDang X, Yang M, Zhang B, et al.: Recovery and Utilization of Collagen Protein Powder Extracted from Chromium Leather Scrap Waste. Environ. Sci. Pollut. Res. 2019; 26: 7277–7283. PubMed Abstract \| Publisher Full Text\n\nTian Z, Wang Y, Wang H, et al.: Regeneration of Native Collagen from Hazardous Waste: Chrome-Tanned Leather Shavings by Acid Method. Environ. Sci. Pollut. Res. 2020; 27: 31300–31310. PubMed Abstract \| Publisher Full Text\n\nNoorzai S, Verbeek C, Lay M, et al.: Collagen Extraction from Various Waste Bovine Hide Sources. Waste Biomass Valorization. 2020; 11: 5687–5698. Publisher Full Text\n\nPurba F, Suparno O, Rusli M, et al.: Novel Method of Hydrolysed Collagen Extraction from Hide Trimming Waste. Int. Food Res. J. 2023; 30: 365–374. Publisher Full Text\n\nPecha J, Barinova M, Kolomaznik K, et al.: Technological-Economic Optimization of Enzymatic Hydrolysis Used for the Processing of Chrome-Tanned Leather Waste. Process Saf. Environ. Prot. 2021; 152: 220–229. Publisher Full Text\n\nDuan Y, Cheng H: Preparation of Immobilized Pepsin for Extraction of Collagen from Bovine Hide. RCS Advances. 2022; 12: 34548–34556. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi L, Zhang J, Wang M, et al.: Electrospun Hydrolyzed Collagen from Tanned Leather Shavings for Bio-Triboelectric Nanogenerators. Materials Advances. 2022; 3: 5080–5086. Publisher Full Text\n\nJian S, Wenyi T, Wuyong C: Ultrasound-Accelerated Enzymatic Hydrolysis of Solid Leather Waste. J. Clean. Prod. 2008; 16: 591–597. Publisher Full Text\n\nScopel BS, Restelatto D, Baldasso C, et al.: Steam Explosion in Alkaline Medium for Gelatine Extraction from Chromium-Tanned Leather Wastes: Time Reduction and Process Optimization. Environ. Technol. 2018; 41: 1857–1866. PubMed Abstract \| Publisher Full Text\n\nWang L, Li J, Jin Y, et al.: Study on the Removal of Chromium (III) from Leather Waste by a Two-Step Method. J. Ind. Eng. Chem. 2019; 79: 172–180. Publisher Full Text\n\nHan W, Zeng Y, Zhang W: View of A Further Investigation on Collagen-Cr (III) Interaction at Molecular Level. J. Am. Leather Chem. Assoc. 2016; 111: 101–106. Reference Source\n\nLiu J, Luo L, Zhang Z, et al.: A Combined Kinetic Study on the Pyrolysis of Chrome Shavings by Thermogravimetry. Carbon Resources Conversion. 2020; 3: 156–163. Publisher Full Text\n\nZhao L, Mu S, Wang W, et al.: Toxicity Evaluation of Collagen Hydrolysates from Chrome Shavings and Their Potential Use in the Preparation of Amino Acid Fertilizer for Crop Growth Open Access Journal of Leather Science and Engineering. J. Leather Sci. Eng. 2022; 4: 2. Publisher Full Text\n\nAsava A, Sasia A, Sang P, et al.: Recovery of Collagen Hydrolysate from Chrome Leather Shaving Tannery Waste through Two-Step Hydrolysis Using Magnesium Oxide and Bating Enzyme Hydrolysis Dechroming of Chrome Shaving Tannery Waste. Journal of the Society of Leather Technologists and Chemists. 2019; 103(02): 80–84. Reference Source\n\nBizzi C, Zanatta RC, Santos D, et al.: Ultrasound-Assisted Extraction of Chromium from Residual Tanned Leather: An Innovative Strategy for the Reuse of Waste in Tanning Industry. Ultrason. Sonochem. 2020; 64: 104682. PubMed Abstract \| Publisher Full Text\n\nPedrotti M, Santos D, Cauduro V, et al.: Ultrasound-Assisted Extraction of Chromium from Tanned Leather Shavings: A Promising Continuous Flow Technology for the Treatment of Solid Waste. Ultra Ultrasonics Sonochemistry. 2022; 89: 106124. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPopiolski A, Dallago R, Steffens J, et al.: Ultrasound-Assisted Extraction of Cr from Residual Tannery Leather: Feasibility of Ethylenediaminetetraacetic Acid as the Extraction Solution. ACS Omega. 2018; 3: 16074–16080. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNegash T, Emiru A, Amare D, et al.: Production and Characterization of Glue from Tannery Hide Trimming Waste. Lecture Notes of the Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering LNICST. 2020; 308: 59–70. Publisher Full Text\n\nZhang Y, Chen Z, Liu X, et al.: SEM, FTIR and DSC Investigation of Collagen Hydrolysate Treated Degraded Leather. J. Cult. Herit. 2021; 48: 205–210. Publisher Full Text\n\nMosleh Y, Van Die M, Gard W, et al.: Gelatine Adhesives from Mammalian and Fish Origins for Historical Art Objects Conservation: How Do Microstructural Features Determine Physical and Mechanical Properties?. J. Cult. Herit. 2023; 63: 52–60. Publisher Full Text\n\nNtasi G, Sbriglia S, Pitocchi R, et al.: Proteomic Characterization of Collagen-Based Animal Glues for Restoration. J. Proteome Res. 2022; 21: 2173–2184. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDai C, Li C: Characterization of Two Kinds of Animal Glues Used for the Restoration of Murals. Sciences of Conservation and Archaeology. 2022; 34: 101–107. Publisher Full Text\n\nEuropean Parliament Parliamentary Question: Mandatory E1 Standard in Europe. E-004321/2017. European Parliament; (accessed on 1 August 2024). Reference Source\n\nEuropean Chemicals Agency Substance Obligatory Regulations: Formaldehyde. (accessed on 1 August 2024). Reference Source\n\nLangmaier F, Šivarová J, Mládek M, et al.: Curing Adhesives of Urea-Formaldehyde Type with Collagen Hydrolysates of Chrome-Tanned Leather Waste. J. Therm. Anal. Calorim. 2004; 75: 205–19. Publisher Full Text\n\nLangmaier F, Šivarová J, Kolomazník K, et al.: Curing of Urea-Formaldehyde Adhesives with Collagen Type Hydrolysates under Acid Condition. J. Therm. Anal. Calorim. 2004; 76: 1015–1023. Publisher Full Text\n\nLangmaier F, Kolomazník K, Mládek M, et al.: Curing Urea–Formaldehyde Adhesives with Hydrolysates of Chrome-Tanned Leather Waste from Leather Production. Int. J. Adhes. Adhes. 2005; 25: 101–108. Publisher Full Text\n\nSedlicik J, Matyasovsky J, Smidriakova M, et al.: Application of Collagen Extracted from Chrome Shavings for Innovative Polycondensation Adhesives. J. Am. Leather Chem. Assoc. 2011; 106(11): 332–340. (accessed on 21 April 2024). Reference Source\n\nIslam N, Liza A, Khatun M, et al.: Formulation and Characterization of Formaldehyde-Free Chemically Modified Bone-Based Adhesive for Lignocellulosic Composite Products. Global Chall. 2021; 5: 2100002. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang X, Zhu J, Liu X, et al.: Novel Gelatin-Based Eco-Friendly Adhesive with a Hyperbranched Cross-Linked Structure. Ind. Eng. Chem. Res. 2020; 59: 5500–5511. Publisher Full Text\n\nYang M, Li Y, Dang X: An Eco-Friendly Wood Adhesive Based on Waterborne Polyurethane Grafted with Gelatin Derived from Chromium Shavings Waste. Environ. Res. 2022; 206: 112266. PubMed Abstract \| Publisher Full Text\n\nLuque GC, Stürtz R, Passeggi MCG, et al.: New Hybrid Acrylic/Collagen Nanocomposites and Their Potential Use as Bio-Adhesives. Int. J. Adhes. Adhes. 2020; 100: 102624. Publisher Full Text\n\nLiu D, Zhang J, You C, et al.: Study on the Anhydrous Condensation of Collagen Polypeptide and Tricyanogen Chloride. RSC Adv. 2022; 12: 20403–20411. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou J, Xu T, Wang X, et al.: A Low-Cost and Water Resistant Biomass Adhesive Derived from the Hydrolysate of Leather Waste. RSC Adv. 2017; 7: 4024–4029. Publisher Full Text\n\nGebremariam E, Malede Y, Prabhu S, et al.: Development of Bio-Based Adhesive Using Tannery Shaving Dust: Process Optimization Using Statistical and Artificial Intelligence Techniques. Bioresource Technology Reports. 2023; 22: 101413. Publisher Full Text\n\nHsu FY, Cheng YY, Tsai SW, et al.: Fabrication and Evaluation of a Biodegradable Cohesive Plug Based on Reconstituted Collagen/γ-Polyglutamic Acid. J. Biomed. Mater. Res. B Appl. Biomater. 2010; 95B: 29–35. PubMed Abstract \| Publisher Full Text\n\nLiu B, Wang Y, Miao Y, et al.: Hydrogen Bonds Autonomously Powered Gelatin Methacrylate Hydrogels with Super-Elasticity, Self-Heal and Underwater Self-Adhesion for Sutureless Skin and Stomach Surgery and E-Skin. Biomaterials. 2018; 171: 83–96. PubMed Abstract \| Publisher Full Text\n\nYang Q, Tang L, Guo C, et al.: A Bioinspired Gallol-Functionalized Collagen as Wet-Tissue Adhesive for Biomedical Applications. Chem. Eng. J. 2021; 417: 127962. Publisher Full Text\n\nMatyšovskỳ J, Jurkovič P, Duchovič P, et al.: Collagen Modified Hardener for Melamine-Formaldehyde Adhesive for Increasing Water Resistance of Plywood. In Current State of the Art on Novel Materials; Balkose, D., Horak, D., Soltes, L., CRC Press and Taylor Francis Group: Boca Raton, FL, USA. Key Eng. Mater. 2014; 1(2): 7–14. Publisher Full Text\n\nAhammed S, Liu F, Khin M, et al.: Improvement of the Water Resistance and Ductility of Gelatin Film by Zein. Food Hydrocoll. 2020; 105: 105804. Publisher Full Text\n\nFact.MR: Hydrolyzed Collagen Market Size, Share & Trends 2032. (accessed on 10 April 2024). Reference Source\n\nAlipal J, Mohd Pu’ad N, Lee T, et al.: A Review of Gelatin: Properties, Sources, Process, Applications, and Commercialisation. Materials Today: Proceedings. 2021; 42: 240–250. Publisher Full Text\n\nOEC - The Observatory of Economic Complexity. Gelatina y Derivados, ISINGLASS, PLACES (ANIMAL) NES. (accessed on 10 April 2024). Reference Source\n\nOEC - The Observatory of Economic Complexity Dextrins, Gelatins and Glues. (accessed on 10 April 2024). Reference Source\n\nCabeza L, McAloon A, Yee W, et al.: Process Simulation and Cost Estimation of Treatment of Chromium-Containing Leather Waste. J. Am. Leather Chem. Assoc. 1998; 98: 299–315.\n\nCabeza L, Taylor M, Dimaio G, et al.: Processing of Leather Waste: Pilot Scale Studies on Chrome Shavings. Isolation of Potentially Valuable Protein Products and Chromium. Waste Manag. 1998; 18: 211–218. Publisher Full Text\n\nInterMESH Ltda: Animal Glue - Jelly Glue Latest Price, Manufacturers & Suppliers. (accessed on 21 April 2024). Reference Source\n\nBosques J, Sánchez J, Mendoza-Novelo B, et al.: Profitability of Chemically Cross-Linked Collagen Scaffold Production Using Bovine Pericardium: Revaluing Waste from the Meat Industry for Biomedical Applications. Polymers (Basel). 2023; 15: 2797. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOEC.World: Observatory of Economic Complexity. Glues; (accessed on 21 April 2024). Reference Source\n\nZhihua S, Mao Y, Yuzeng W, et al.: CN106753159B-Degradable Collagen-Polyurethane Water-Based Wood Adhesive and Preparation Method Thereof.2016. Reference Source\n\nFenglang L: CN106800907A-A Kind of Environment-Friendly Water-Based Wood Adhesive Based on Degraded Collagen Solution and Preparation Method Thereof.2016. Reference Source\n\nShan Z, Yang M, Wang Y, et al.: CN106753159A-One kind degraded polyurethane aqueous wood adhesive of collagen and preparation method thereof 2016.Reference Source\n\nQuanjie W, Lijie H, Baorong D, et al.: CN109554153A -A Kind of Preparation Method and Application of Collagen Base Adhesive.2018. Reference Source\n\nMao Y, Chun LY, Jun GR, et al.: CN110256651A-A Kind of Preparation Method of Collagen-Base Papermaking Function Sizing Agent.2019. Reference Source\n\nXiaoqun S, Hua YW, Wensheng C, et al.: CN111704879A-Air-Permeable Leather Adhesive and Preparation Method Thereof.2020. Reference Source\n\nFenglang L: CN106800907-A Kind of Environment-Friendly Water-Based Wood Adhesive Based on Degraded Collagen Solution and Preparation Method Thereof.2016. Reference Source\n\nJie WQ, Jie HL, Baorong D, et al.: CN109554153A-A Kind of Preparation Method and Application of Collagen Base Adhesive.2018. Reference Source\n\nChuan WX, Xiaoli H, Taotao Q: CN103669109B-A Kind of Preparation Method of Glue Used in Paper-Making.2013. Reference Source\n\nKanagaraj JK, Panda RC, Vinodh Kumar MVK: Trends and Advancements in Sustainable Leather Processing: Future Directions and Challenges—A Review. J. Environ. Chem. Eng. 2020; 8: 104379. Publisher Full Text" }	[ { "id": "336497", "date": "14 Nov 2024", "name": "Ali Yorgancioglu", "expertise": [ "Reviewer Expertise Leather" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 as ‘‘\"Recycling of collagen from solid tannery waste and prospective utilization as adhesives\" for F1000Research” was reviewed. I have evaluated the paper in light of the F1000Research scope. The submission was made as Review Paper. The manuscript discusses the extraction and application of collagen from solid tannery waste as an adhesive. This topic aligns well with current sustainability objectives, particularly within the leather industry. The authors provide a comprehensive review of collagen extraction methods, adhesive formulation, and potential applications, supported by recent advancements in the field. However, while the paper is informative, it faces several scientific and structural limitations. Key aspects require refinement to ensure clarity and to meet the publication standards of F1000Research. The study addresses an important topic in the circular economy and sustainable waste management. Converting tannery waste into adhesives could reduce landfill waste and minimize reliance on petroleum-based adhesives. This aligns with the increasing need for sustainable materials and methods in various industrial applications. While the study is comprehensive in discussing various collagen extraction and adhesive production techniques, it lacks specific experimental data or case studies to support some of its claims. The paper would benefit from quantitative data that compares the performance of collagen-based adhesives with traditional adhesives in specific applications. The authors briefly mention the limitations of collagen adhesives, particularly in water resistance and durability. However, more detailed discussion and proposed solutions for overcoming these limitations are necessary to make the paper more practical and applicable to real-world scenarios. The manuscript is structured logically, yet certain sections (e.g., Background, Methods) could be more concise. In some parts, especially the discussion on different adhesive applications, the information appears repetitive. A clearer distinction between current findings and future directions could improve readability. Moreover, methods section should be removed. Review papers rarely include a method section since they do not report on original research. Author needs to send this manuscript for English proofread as I found some grammatical errors while reviewing the article. In the Abstract: \"This research systematically reviews the methods and applications of collagen extraction, highlighting the material’s versatility and environmental benefits when used as a bio-adhesive.\" The phrase “when used as a bio-adhesive” could be simplified to “as a bio-adhesive.” In the Methods: \"Only documents in English,\" which should be “Only English-language documents were included.” Further editing for grammatical accuracy and flow would enhance the manuscript’s clarity and professionalism. After these revision, the paper can be considered publication\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": "359783", "date": "29 Jan 2025", "name": "Anke Mondschein", "expertise": [ "Reviewer Expertise Leather" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 fully agree with the issues raised by the first reviewer Ali Yorgancioglu from Ege Üniversitesi, Bornova, Turkey. The topic of the review is very important, but the paper has its scientific limitations. I will not repeat here the topics that have already been addressed and precisely outlined by reviewer 1. Additional topics are:\nLiterature source missing for the statement that Typ I Col is the best Col type for glueing (p. 7) The intended uses of adhesives, technical and medical, should not be mixed and should be clearly separated, ideally with their respective specific challenges for the use of collagen or gelatine as an adhesive. If possible, the market data should also refer to these two very different applications. Practical data is lacking, especially for the technical application. Gelatine as an adhesive is already used industrially. It would be instructive to discuss where the actual limits to increased use are (price?, properties?, and how the respective deficits can be overcome) Captions should be more precise (e.g. Fig. 4: Explain a - d)\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": [] } ]	1	https://f1000research.com/articles/13-1228
https://f1000research.com/articles/13-1226/v1	14 Oct 24	{ "type": "Research Article", "title": "Podiatry risk in diabetic pilgrims: a prospective study in Tunisia", "authors": [ "Yosra HASNI", "Hamza ELFEKIH", "Ameni SALAH", "Zomorda KAMMOUN", "Safa AMARA", "Nour AMARA", "Sawssen MRAD", "Wiem SAAFI", "Molka CHADLI-CHAIEB", "Yosra HASNI", "Ameni SALAH", "Zomorda KAMMOUN", "Safa AMARA", "Nour AMARA", "Sawssen MRAD", "Wiem SAAFI", "Molka CHADLI-CHAIEB" ], "abstract": "Background Each year, over 340,000 diabetic patients across the world travel to Saudi Arabia for the Hajj pilgrimage. As they carried out important rituals, several complications might be encountered, particularly foot lesions. We’ve been therefore interested, through this study, in the assessment of podiatric risk in diabetic pilgrims.\n\nMethods A prospective longitudinal study was conducted in the region of Sousse, Tunisia. The evaluation of diabetic patients preparing for the pilgrimage was conducted in two phases, before and after the pilgrimage.\n\nResults Forty-three diabetic patients planning to perform pilgrimage were included in the study. Post-pilgrimage clinical exams revealed hyperkeratosis (96.8%) and superficial fungal infections (61.3%) as the most common podiatric lesions. Foot ulcers attributed to trauma from walking were found in 7% of patients. Our data showed a significant association between foot ulcer risk and lower total cholesterol (p=0.02), HDL cholesterol (p=0.02), LDL cholesterol (p=0.01), as well as higher triglyceride levels (p=0.04) only in univariate analysis. Other diabetes-related risk factors did not show significant correlations.\n\nConclusion Given the increased risk of foot lesions in diabetic pilgrims, a thorough assessment and tailored management based on individual risk levels are essential before, during, and after the pilgrimage.", "keywords": [ "Diabetes mellitus", "Education", "Foot Injuries", "Pilgrimage", "Risk Factors" ], "content": "Introduction\n\nThe Hajj pilgrimage is one of the five pillars of Islam. Every practicing Muslim is bound by faith to do it at least once in his life if he is physically and financially capable. During the journey to Mecca for Hajj, pilgrims perform a series of religious rituals, including barefoot circuits around the holy mosque - Tawaf - and walk between two hills, Safa and Marwah, for long hours. They are also required to spend five days in tents in the Mina Valley where sanitation is very basic, in a hot climate, where the average temperatures can reach 45 °C in the summer.1\n\nThe global prevalence of diabetes mellitus is estimated at 10.5% and this prevalence increases with age.2 Given that approximately 2 million Muslims perform the pilgrimage each year, many of them are aged 60 and above, it was projected that the number of pilgrims with diabetes could surpass 340,000 annually.3,4\n\nDiabetes mellitus is characterized by various complications, including retinopathy, neuropathy, nephropathy, and an increased risk of cardiovascular diseases. Diabetes complications affecting the lower limbs are common, complex, and costly.5 People with diabetes are exposed to a range of complications during the pilgrimage, with diabetic foot reported once to be one of the most common causes of admissions in two pilgrimage site hospitals.6 However, few studies have studied the podiatry risk in pilgrims with diabetes. The purpose of this study was to evaluate the risk of foot lesions in diabetic pilgrims and to assess the degree of knowledge of diabetic subjects regarding podiatric risk.\n\n\nMethods\n\nA prospective longitudinal cross-sectional study was conducted on diabetic individuals from Sousse, Tunisia, and consisted of two phases, before and after the pilgrimage. It included patients who planned to undertake the pilgrimage in 2019 and consulted the Endocrinology-Diabetology department of Farhat Hached University Hospital of Sousse. All participants gave informed consent to participate in the research and for publication.\n\nThe exclusion criteria were patients with a major amputation such as mid-leg or mid-thigh, non-autonomous patients using a wheelchair, or those with a severe deformation of the feet as clubfoot or Charcot’s foot.\n\nThe evaluation was made before and after the pilgrimage. It was based on an anamnesis, a general somatic examination, and a foot examination. The evaluation of peripheral neuropathy was made using the Semmes-Weinstein 10g monofilament test and the DN4 score.\n\nPeripheral arteriopathy was assessed by calculating the arm-ankle index using a pocket Doppler ultrasound machine. A blood test was also requested, including fasting blood sugar, glycated hemoglobin (A1C), renal and lipid blood tests. The grade of podiatric risk was specified for each patient, based on the classification of “The International Working Group on The Diabetic Foot (IWGDF)”.7\n\nKnowledge of diabetic foot risks and its preventive measures were evaluated through a survey consisting of 16 questions. Each question was noted 1 if the answer was “Yes”, and 0 if the answer was “No”. A score from 0 to 16 was then determined for each patient which helped to avoid information biases (Figure 1).\n\nStatistical analysis was performed using GNU PSPP V2.0.0 software, a free statistical analysis package (https://www.gnu.org/software/pspp/). Patients who were lost to follow up were not included in the analysis. Data between groups were compared using χ2-Test (2-sided), and Mann-Whitney U test. The level of significance was set at p < 0.05.\n\n\nResults\n\nThe study involved 43 patients with a sex ratio (male:female) of 0.72 (Table 1). The average age of patients was 62.5±5.4 years. Most patients (65.15%) had high education levels, while 11.6% were illiterate. Associated comorbidities were dominated by hypertension in 55.8% of cases and 18.6% of patients received treatment with statins.\n\nAll patients in the study had type 2 diabetes mellitus. The average course of diabetes was 12.5±9.3 years (Table 2). Thirty patients (69.75%) were on oral antidiabetic drugs and 25.65% were on insulin. Most patients (74.4%) had good therapeutic compliance with treatments and the diabetes was controlled in 61.5% of cases with an average A1C of 7.9±1.3%.\n\nOnly 20.9% of patients reported that they had received at least one podiatry risk education session from their attending physician. When assessing practical knowledge, the average level of knowledge was 8.3±3.4 out of 16 (Figure 2).\n\nThe clinical exam before the pilgrimage showed that the most frequent podiatric lesions were hyperkeratosis (88.1%), heel cracks (34.9%) as well as superficial fungal infections (60.4%). The most frequent foot deformities were flat feet (30.2%), hallux valgus (23%), and claw toes (16.2%).\n\nIschemia and neuropathy were noted in 30.2% and 18.6% of patients respectively.\n\nMost patients (48.8%) had grade 0 podiatry risk according to the classification of the IWGDF and only one patient had a grade 3 due to a history of a foot ulcer (Table 3).\n\nThe evaluation after the pilgrimage concerned 31 patients. The remaining 12 patients were lost to follow-up. The clinical exam showed that hyperkeratosis was the most common form of podiatric lesions (96.8%) as well as fungal infections of the nails and inter-toe spaces (61.3%).\n\nThe occurrence of superficial fungal infection of the foot was significantly correlated with the history of inter-toe fungal infection or onychomycosis (p=0.03). However, it wasn’t correlated with glycemic control or with anti-diabetic treatment.\n\nThree patients had foot ulcers which were mainly due to walking injuries and unsuitable shoes (Figure 3). Hospitalization was indicated in only one case of foot ulcer with infection signs, but he refused so that he could perform the rituals and he was given oral antibiotics.\n\nNote: Patient 1 (A) presented an ulceration in the big toe (purple arrow), second toe (green arrow), and next to the first metatarsal (orange arrow). Patient 2 (B) had dry gangrene in the second toe. Foot ulcer before (C) and after (D) debridement in patient 3.\n\nThe study of the risk of developing a foot ulcer showed that it was significantly associated with lower total cholesterol, HDL cholesterol, and LDL cholesterol and a higher triglyceride level (p respectively 0.02, 0.02, 0.01, and 0.04) (Table 4).\n\na Analyzed using Mann-Whitney U test.\n\nb Analyzed using χ2-Test (2-sided).\n\n* Statistically significant at p=0.05.\n\nFurthermore, the risk of developing a foot ulcer was not correlated with age, tobacco, or body mass index (Table 4). The study of other risk factors linked to diabetes (length of diabetes, insulin treatment, A1C, existence of neuropathy or ischemia, grade of podiatric risk, and level of knowledge) did not show significant correlations.\n\nA binary logistic regression was performed to define independent predictors of the occurrence of a foot ulcer (variables with p < 0.2 were included). In multivariate analysis, no factor was significantly correlated to a higher risk of foot ulcer.\n\nHowever, there was a significant increase in the systolic pressure index in the left as well as the right foot after the pilgrimage (1.03±0.19 vs 1.11±0.19 and 1.03±0.28 vs 1.11±0.18, p <0.05).\n\n\nDiscussion\n\nDuring the Hajj pilgrimage, Muslims are required to perform physically strenuous rituals in crowded and hot environments, which can present significant challenges, especially for individuals with pre-existing health conditions such as diabetes mellitus. The combination of these factors increases the risk of foot lesions, particularly among those with diabetic neuropathy.8\n\nFoot injuries represented an important part of the reasons for admissions among diabetic patients.9 A study carried out in tertiary care facilities in Saudi Arabia, to assess the causes of admissions, showed that 31.9% of a total 689 emergency patients had diabetes.10 In our study, hospitalization was indicated in only one case.\n\nDiabetic foot ulcers are commonly caused by repetitive stress on areas that are susceptible to strong vertical or shear stress in patients with diabetic neuropathy. The addition of peripheral arterial disease further contributes to the development of foot ulcers.11 Our study revealed that ischemia and neuropathy were present in 30.2% and 18.6% of patients, respectively. Plantar hyperkeratosis was observed in 88.1% of the population. These findings underscore the importance of addressing both neuropathy and arterial disease in the prevention and treatment of diabetic foot ulcers.\n\nIt has been demonstrated that education on the autonomous management of diabetes and its complications is effective in achieving therapeutic goals. Patients who have not received this education are four times more likely to develop complications compared to those who have.12 Moreover, educational interventions can reduce the risk of amputation by up to 85% and decrease the associated cost of care.13\n\nOnly 20.9% of our patients have received therapeutic education regarding podiatric risks. This percentage varied greatly between countries. In developed countries, most patients receive information and practical advice for preventing diabetic foot complications, with rates as high as 71.3% in the United Kingdom.14 In developing countries, the therapeutic education rate was lower, with only 48% of patients in Tanzania for example.15\n\nThis lack of education was also reported by Alfelali et al.16 in a study that included 197 subjects and where only 30% of diabetic patients benefited from at least one education session before the pilgrimage. It was suggested that a health education strategy is effective in improving knowledge and practice, as well as in reducing the incidence of health problems among pilgrims.17\n\nOur study revealed also that the most common foot lesions among diabetic patients after returning from pilgrimage were hyperkeratosis (96.8%) and superficial fungal infections (61.3%). A foot ulcer was noted in three cases. In the study of Alfelali et al.,16 blisters and erythema were the most common lesions in diabetic as well as non-diabetic patients. In addition, hyperkeratosis was comparatively more frequent in diabetic pilgrims and more likely to be complicated by a foot ulcer. The absence of blisters and erythema lesions in our study group may be attributed to the timing of the clinical examination, which occurred 15 days to one month after the return of pilgrims from Hajj.\n\nRegarding infections, fungal and bacterial ones are reported to be more prevalent, particularly in pilgrims with unbalanced diabetes and unhealthy lifestyles.18 Fungal foot infections were found to be more common in patients taking anti-diabetic medications compared to those using insulin.19 However, in our research, fungal infections were found to be only linked to a history of inter-toe infection or onychomycosis. There was no correlation between these infections and diabetes control, or treatment used.\n\nThe conducted survey did not reveal any significant correlations between the occurrence of foot ulcers and the duration of diabetes, gender, insulin intake, body mass index, average A1C levels, or a history of foot ulcers. This aligns with findings from several studies showing the absence of a correlation between the duration of diabetes, insulin treatment, weight excess, and foot ulcer development.20,21 Other studies reported that men and history of foot ulcers did raise the risk of developing foot lesions and that risk was tripled in case of A1C level beyond 9%.22–24\n\nHowever, our study has shown an association between the occurrence of a foot ulcer and lipid profile abnormalities. In fact, patients, who had a foot ulcer, had significantly lower total cholesterol and LDL cholesterol levels, this could be explained by the fact that these patients were at high cardiovascular risk and were already on statin therapy. They also had a higher triglyceride level and a lower HDL cholesterol rate. Even so, in multivariate analysis, no factor was significantly correlated with a higher risk of foot ulcer. The correlation between the occurrence of a foot ulcer and total cholesterol level was reported in the study by Porciúncula et al.25 Nevertheless, a correlation with other abnormalities in the lipid profile has not been demonstrated.25,26\n\nThe small sample size and the loss to follow-up after returning from pilgrimage were the main limitations of our study. The assessment of microvascular diabetes complications among pilgrims was not conducted due to time constraints.\n\nIn summary, the Hajj pilgrimage poses a potential risk of foot injuries for diabetic pilgrims, which could significantly impact their health and well-being. Therefore, an assessment of all patients before the pilgrimage is necessary, not only to ensure glycemic control but also to prevent diabetes-related complications. Prioritizing education on podiatric care is essential for diabetic patients who are considering the pilgrimage to mitigate the risk of foot-related complications and guarantee a successful pilgrimage experience.\n\nThe study has been approved by the Ethics Committee of the Faculty of Medicine of Sousse (Ref: CEFMS 24/2019) with date of approval 17/07/2019. Consent to participate and to publish: Written informed consent was obtained from all participants in this study.", "appendix": "Data and software availability\n\nThe project contains the following underlying data:\n\nDATA Hajj.sav (study dataset). Figshare. HASNI Y, ELFEKIH H, SALAH A, KAMMOUN Z, AMARA S, AMARA N, et al. Podiatry risk in diabetic pilgrims: a prospective study in Tunisia 2024. https://doi.org/10.6084/m9.figshare.26965915.v3. 27\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe project contains the following extended data:\n\n- Knowledge and preventive measures score for diabetic foot.xlsx. (Questionnaire). Figshare. HASNI Y, ELFEKIH H, SALAH A, KAMMOUN Z, AMARA S, AMARA N, et al. Knowledge and preventive measures score for diabetic foot 2024. https://doi.org/10.6084/m9.figshare.27079123.v1. 28\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n- STROBE Podiatry risk in diabetic pilgrims.docx. (adherence to STROBE guidelines). Figshare. HASNI Y, ELFEKIH H, SALAH A, KAMMOUN Z, AMARA S, AMARA N, et al. STROBE Podiatry risk in diabetic pilgrims 2024. https://doi.org/10.6084/m9.figshare.27068518.v1. 29\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n- ar consent form.docx. (Informed consent for participation and publication). Figshare. HASNI Y, ELFEKIH H, SALAH A, KAMMOUN Z, AMARA S, AMARA N, et al. Consent form: Podiatry risk in diabetic pilgrims: a prospective study in Tunisia 2024. https://doi.org/10.6084/m9.figshare.27068368.v1. 30\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nNone.\n\n\nReferences\n\nSalmon-Rousseau A, Piednoir E, Cattoir V, et al.: Hajj-associated infections. Med. Mal. Infect. 2016; 46(7): 346–354. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMagliano DJ, Boyko EJ: IDF DIABETES ATLAS. IDF Diabetes Atlas. 10th ed.Brussels; 2021.\n\nIbrahim M, Ba-Essa E, Alarouj M, et al.: Recommendations for management of diabetes and its complications during Hajj (Muslim Pilgrimage) - 2024 update. Diabetes Res. Clin. Pract. 2024; 212: 111647. PubMed Abstract \| Publisher Full Text\n\nSiavash M, Haghighi S: Recommendations for patients with diabetes mellitus during hajj pilgrimage. J. Res. Med. Sci. 2012; 17(10): 988–989. PubMed Abstract\n\nArmstrong DG, Boulton AJM, Bus SA: Diabetic Foot Ulcers and Their Recurrence. N. Engl. J. Med. 2017; 376(24): 2367–2375. Publisher Full Text\n\nAl-Salamah SM: General surgical problems encountered in the Hajj pilgrims. Saudi Med. J. 2005; 26(7): 1055–1057. PubMed Abstract\n\nSchaper NC, van Netten JJ , Apelqvist J, et al.: Practical Guidelines on the prevention and management of diabetic foot disease (IWGDF 2019 update). Diabetes Metab. Res. Rev. 2020; 36: e3266. Publisher Full Text\n\nYezli S, Mushi A, Almuzaini Y, et al.: Prevalence of Diabetes and Hypertension among Hajj Pilgrims: A Systematic Review. Int. J. Environ. Res. Public Health. 2021; 18(3). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlsafadi H, Goodwin W, Syed A: Diabetes care during Hajj. Clin. Med. (Lond.). 2011; 11(3): 218–221. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIbrahim M, Abdelaziz SI, Abu Almagd M, et al.: Recommendations for management of diabetes and its complications during Hajj (Muslim pilgrimage). BMJ Open Diabetes Res. Care. 2018; 6(1): e000574. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMonteiro-Soares M, Boyko EJ, Ribeiro J, et al.: Predictive factors for diabetic foot ulceration: a systematic review. Diabetes Metab. Res. Rev. 2012; 28(7): 574–600. Publisher Full Text\n\nSuhl E, Bonsignore P: Diabetes Self-Management Education for Older Adults: General Principles and Practical Application. Diabetes Spectr. 2006; 19(4): 234–240. Publisher Full Text\n\nSwain J, Sahoo AK, Jadhao PA, et al.: Addressing the Inertia: A Holistic Approach to Diabetic Foot Evaluation. Cureus. 2023; 15(4): e37186. PubMed Abstract \| Publisher Full Text\n\nPollock RD, Unwin NC, Connolly V: Knowledge and practice of foot care in people with diabetes. Diabetes Res. Clin. Pract. 2004; 64(2): 117–122. Publisher Full Text\n\nChiwanga FS, Njelekela MA: Diabetic foot: prevalence, knowledge, and foot self-care practices among diabetic patients in Dar es Salaam, Tanzania - a cross-sectional study. J. Foot Ankle Res. 2015; 8: 20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlfelali M, Barasheed O, Alshehri J, et al.: Foot Injuries Among Hajj Pilgrims with and Without Diabetes Mellitus: Implications for Infection Management. Infect. Disord. Drug Targets. 2014; 14(2): 140–147. PubMed Abstract \| Publisher Full Text\n\nAlamri FA, Amer SA: Knowledge and Practice after Health Education Program among Hajj 1438 H (2017) Pilgrims. Saudi Arabia: 2018.\n\nBeshyah S, Sherif I: Care for People with Diabetes during The Moslem Pilgrimage (Haj) An Overview. Libyan J. Med. 2008; 3(1): 39–41. PubMed Abstract \| Publisher Full Text\n\nMlinaric-Missoni E, Kalenic S, Vazic-Babic V: Species distribution and frequency of isolation of yeasts and dermatophytes from toe webs of diabetic patients. Acta Dermatovenerol. Croat. 2005; 13(2): 85–92. PubMed Abstract\n\nBoyko EJ, Ahroni JH, Stensel V, et al.: A prospective study of risk factors for diabetic foot ulcer. The Seattle Diabetic Foot Study. Diabetes Care. 1999; 22(7): 1036–1042. PubMed Abstract \| Publisher Full Text\n\nPeters EJ, Lavery LA, Armstrong DG: Diabetic lower extremity infection: influence of physical, psychological, and social factors. J. Diabetes Complicat. 2005; 19(2): 107–112. Publisher Full Text\n\nHokkam EN: Assessment of risk factors in diabetic foot ulceration and their impact on the outcome of the disease. Prim. Care Diabetes. 2009; 3(4): 219–224. PubMed Abstract \| Publisher Full Text\n\nKiziltan ME, Gunduz A, Kiziltan G, et al.: Peripheral neuropathy in patients with diabetic foot ulcers: clinical and nerve conduction study. J. Neurol. Sci. 2007; 258(1-2): 75–79. Publisher Full Text\n\nResnick HE, Carter EA, Sosenko JM, et al.: Incidence of lower-extremity amputation in American Indians: the Strong Heart Study. Diabetes Care. 2004; 27(8): 1885–1891. PubMed Abstract \| Publisher Full Text\n\nPorciúncula MVP, Rolim LCP, Garofolo L, et al.: Análise de fatores associados à ulceração de extremidades em indivíduos diabéticos com neuropatia periférica. Arq. Bras. Endocrinol. Metabol. 2007; 51(7): 1134–1142. PubMed Abstract \| Publisher Full Text\n\nLitzelman DK, Marriott DJ, Vinicor F: Independent physiological predictors of foot lesions in patients with NIDDM. Diabetes Care. 1997; 20(8): 1273–1278. PubMed Abstract \| Publisher Full Text\n\nYosra H, Elfekih H, Salah A, et al.: Podiatry risk in diabetic pilgrims: a prospective study in Tunisia. figshare. [Dataset]. 2024. Publisher Full Text\n\nYosra H, Elfekih H, Salah A, et al.: Knowledge and preventive measures score for diabetic foot. figshare. Online resource. 2024. Publisher Full Text\n\nYosra H, Elfekih H, Salah A, et al.: STROBE Podiatry risk in diabetic pilgrims. figshare. Online resource. 2024. Publisher Full Text\n\nYosra H, Elfekih H, Salah A, et al.: Consent form : Podiatry risk in diabetic pilgrims: a prospective study in Tunisia. figshare. Online resource. 2024. Publisher Full Text" }	[ { "id": "331985", "date": "25 Nov 2024", "name": "Yaasirah Mohomed Choonara", "expertise": [ "Reviewer Expertise diabetes", "podiatry education", "podiatric pharmacology." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. Relevance: The study addresses an important public health issue for diabetic patients participating in Hajj, a unique and understudied population. 2. Structured Methodology: The prospective longitudinal design and the evaluation of patients both before and after the pilgrimage provide valuable insights into the progression of foot health risks during the pilgrimage. 3. Clinical Implications: The study highlights actionable recommendations, including pre-pilgrimage assessments, education, and tailored interventions, which are crucial for reducing complications. 4. Comprehensive Analysis: A variety of factors were analysed, such as lipid profiles, neuropathy, and education levels, offering a well-rounded exploration of potential risk factors for foot ulcers.\n\nAreas for Improvement 1. Study Design and Sample Size - Small Sample Size: The study includes only 43 participants, of whom 31 completed the post-pilgrimage assessment. The small sample size limits the generalizability of the findings. - Loss to Follow-Up: Nearly 28% of participants were lost to follow-up, which could introduce bias. Strategies to minimize attrition, such as remote follow-up or incentives, should be discussed. - Control Group: The absence of a non-diabetic control group makes it difficult to isolate the risks specific to diabetic pilgrims.\n2. Statistical Analysis - Univariate vs. Multivariate Analysis: While some associations were significant in univariate analysis, none were retained in multivariate analysis. This limitation should be discussed further to clarify the clinical significance of findings like lipid abnormalities and foot ulcer risk. - Missing Data on Correlations: The discussion could benefit from exploring why some expected correlations (e.g., with A1C or diabetes duration) were absent and whether these might be due to the small sample size or confounding factors.\n3. Educational Interventions - Limited Insights into Education Impact: Only 20.9% of participants received podiatry risk education, yet the role of education in preventing complications is highlighted. Exploring why education uptake was low and how it could be improved would strengthen the article. - Lack of Details on Education Programs: What specific education content or strategies were provided (if any) to participants? This information could be crucial for practical application.\n4. Methodological Limitations - Timing of Post-Pilgrimage Assessment: Conducting post-pilgrimage exams 15 days to a month after the pilgrimage may have missed transient or acute lesions (e.g., blisters, erythema). Earlier assessments could provide a more comprehensive picture. - Assessment of Microvascular Complications: The exclusion of microvascular complication assessments (e.g., retinopathy, nephropathy) limits the understanding of systemic diabetic risks during Hajj. - Use of Tools: While the study uses established tools (e.g., IWGDF classification), the reliability or calibration of instruments like the monofilament or Doppler device is not mentioned. Ensuring standardization of methods would bolster credibility.\n5. Presentation and Structure - Clarity in Reporting:\n\n- The tables and figures need clearer labels and descriptions. For example, Figure 3 lacks adequate explanation for readers unfamiliar with podiatric pathology.\n\n- The Results section is dense and could benefit from breaking into subsections with clearer headings to guide the reader. - Redundancy: Some points, such as the significance of education, are repeated without adding new insights. This space could be used for discussing additional findings or limitations.\n\nSuggestions for Improvement 1. Expand Sample Size: Future studies should aim for larger, more diverse cohorts to improve generalizability. 2. Include a Control Group: Comparing diabetic and non-diabetic pilgrims would help isolate the impact of diabetes on podiatric risks. 3. Focus on Education: Evaluate and describe the effectiveness of tailored educational interventions, perhaps by piloting them in a subset of participants. 4. Improve Post-Pilgrimage Follow-Up: Implement earlier and more frequent assessments to capture acute complications and their resolution. 5. Refine Statistical Analysis: Consider larger multivariate models with interaction terms or use advanced methods like propensity score matching to strengthen causal inferences.\n\nConclusion The article makes an important contribution to understanding diabetic risks during Hajj but could benefit from addressing the above methodological, analytical, and reporting limitations. Enhanced sample size, better follow-up strategies, and greater focus on educational interventions could make future studies more impactful.\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": [] }, { "id": "338749", "date": "27 Nov 2024", "name": "Salim Parker", "expertise": [ "Reviewer Expertise Mass Gatherings", "Religious Mass Gatherings", "Hajj", "Umrah" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 concept and design is good. The major drawbacks are the small sample size, the significant post Hajj loss of follow up (it may affect the results significantly) and some inconsistency in reporting. It needs some significant revisions as detailed below. It is still of value as a study and should be considered after some revision even if there is no statistically significant trends.\n\n1.The abstract is needs to indicate that the post Hajj results are similar to the pre-Hajj ones. 2. Hyperkeratosis presence is already high in pre-Hajj data and with 12 out of 43 pilgrims not followed up, the significance of the post Hajj numbers are questionable. I would suggest to also compare the pre and post Hajj prevalence of the 31 for who all details are available. 3. The description (and number) of pre and post superficial fungal infections should be the same.\nThere are other minor grammatical issues (use gender neutral or he/she instead of he only). I have attached the comments on a PDF.\nPlease refer the link for further comments: https://f1000research.s3.amazonaws.com/supplementary/156345/c6186ce5-a89e-4eb4-9765-6aad68a5f0a9.pdf\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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1226
https://f1000research.com/articles/13-324/v1	23 Apr 24	{ "type": "Systematic Review", "title": "A scoping review on what constitutes a good research culture", "authors": [ "Amanda Jane Blatch-Jones", "Kay Lakin", "Sarah Thomas", "Kay Lakin", "Sarah Thomas" ], "abstract": "Background The crisis in research culture is well documented, covering issues such as a tendency for quantity over quality, unhealthy competitive environments, and assessment based on publications, journal prestige and funding. In response, research institutions need to assess their own practices to promote and advocate for change in the current research ecosystem. The purpose of the scoping review was to explore ‘What does the evidence say about the ‘problem’ with ‘poor’ research culture, what are the benefits of ‘good’ research culture, and what does ‘good’ look like?’\n\nAims To examine the peer-reviewed and grey literature to explore the interplay between research culture, open research, career paths, recognition and rewards, and equality, diversity, and inclusion, as part of a larger programme of activity for a research institution.\n\nMethods A scoping review was undertaken. Six databases were searched along with grey literature. Eligible literature had relevance to academic research institutions, addressed research culture, and were published between January 2017 to May 2022. Evidence was mapped and themed to specific categories. The search strategy, screening and analysis took place between April-May 2022.\n\nResults 1666 titles and abstracts, and 924 full text articles were assessed for eligibility. Of these, 253 articles met the eligibility criteria for inclusion. A purposive sampling of relevant websites was drawn from to complement the review, resulting in 102 records included in the review. Key areas for consideration were identified across the four themes of job security, wellbeing and equality of opportunity, teamwork and interdisciplinary, and research quality and accountability.\n\nConclusions There are opportunities for research institutions to improve their own practice, however institutional solutions cannot act in isolation. Research institutions and research funders need to work together to build a more sustainable and inclusive research culture that is diverse in nature and supports individuals’ well-being, career progression and performance.", "keywords": [ "research culture", "research institutions", "funding organisations", "academia", "open research", "early career researchers", "transparency", "research integrity" ], "content": "Background\n\nConcerns about the pressures of working in research and the potential negative impact of a poor research culture are well documented in academic literature across diverse disciplines.1,2 There is a strong connection between concerns about research culture and the inappropriate use of metrics and indicators that drive both institutional and individual researcher behavior, assessment and reward.3–5 In response to these concerns, a number of actions have emerged to enable and encourage the adoption of a healthier research culture.6–8 International action to address the underlying drivers of poor research culture include INORMS SCOPE framework for responsible research evaluation9; Declaration on Research Assessment (DORA)10; development of 10 principles for the measurement of research performance: the Leiden Manifesto for Research Metrics11; establishment of the International School on Research Impact Assessment (ISRIA)12; and the HuMetricsHSS Initiative.13\n\nIn response to concerns about the experience of working in research, the Wellcome Trust undertook work in the UK to better understand research culture, which has enabled initiatives from the Russell Group and the Royal Society to actively work towards enabling researchers to ‘flourish’.14 A survey conducted by the Wellcome Trust, focused on the experience of researchers, revealed that poor research culture is leading to unhealthy competition, bullying and harassment, mental health issues, and a system that favours quantity over quality.15 Unfortunately, these experiences mirror previous findings, and show the longevity of the issues as the research environment continues to be pressured, competitive and uncertain for many researchers.16\n\nThe consequences of poor research culture does not only impact researchers, it also effects research support staff (e.g., technicians, research managers and administrative staff), the production and quality of research, reduces innovation in research and affects public trust in research.17–21 Funding organisations such as UK Research and Innovation (UKRI) enhanced its 2021-2022 allocation of research culture funding to Higher Education Providers (HEPs) to further explore research processes and experiences of working in research, through piloting new initiatives or enhancing existing activities.22\n\nStriving for excellence and changing research culture is a collective responsibility, requiring action from research institutions, funding organisations and researchers.14 Higher Education Institutions (HEIs) need to assess their own practices to promote and advocate for change in the current research ecosystem. As highlighted by the Wellcome Trust and others, there remains a tendency for quantity over quality, assessment based on publications, journal prestige and funding.5,15,23,24 Any attempts on reform requires commitment from everyone (e.g., publishers, research institutions, funders, researchers etc.) so that diversity, impact, teamwork, open research, and assessment systems are valued. In turn, we may begin to see enhancements for the promotion of transparency, open access, knowledge mobilisation and collaborative networking practices.\n\nThe consequences and challenges associated to an inadequate research culture is well evidenced across the research ecosystem and several reports, from funding organisations to independent providers, demonstrating the extent of the problem (for whom and in what context) and the need for a cultural change in research.14,15,25,26 However, the evidence very much focuses on the challenges and barriers, with limited evidence on solutions or how to implement change, initiate opportunities, or what works for whom and in what context that is fit for purpose for all individuals (inclusive of all research and non-research staff in an academic environment).27–29\n\nThe purpose of this scoping review was to explore the evidence on what constitutes a good research culture and how open research, career research paths (recognition and awards) and equality, diversity, and inclusion interplay to enhance and promote a more sustainable research culture environment. The scoping review was intended to inform future practice within a specific research organisation (the University of Southampton, UK), recognising the broader interest in and application of the findings. The scoping review was conducted to address the following question: What does the evidence say about the ‘problem’ (barriers, challenges, consequences etc.) with ‘poor’ research culture, and what are the benefits of ‘good’ research culture, and what does it look like?\n\n\nMethods\n\nScoping reviews are relevant to addressing research questions that seek to identify priorities for research, clarification on concepts and definitions, identifying research frameworks, or locating background information in preparation for a systematic review. Scoping reviews aim to understand ‘What has been done previously?’ and ‘What does the literature say?’ compared to systematic reviews that ask the question ‘Does this intervention work for this group of individuals?’ The purpose of this scoping review was to identify the current evidence and body of relevant literature using the Joanna Briggs Institute (JBI) guidance/approach to guide the development, analysis and write up of the scoping review.30–32 Using this approach enabled the reviewers to map the evidence to four key areas highlighted from existing published work from the Wellcome Trust, to ensure consistency and continuity to predefined areas already established by the research environment.15\n\nContext: The context included UK and international settings within the academic environment (research ecosystem).\n\nParticipants: Academic, administrative, and technical staff and students of all levels, grades, disciplines, and professions. To be inclusive of academic and non-academic staff to ensure an inclusive approach and incorporating the principles of ‘team science’ and organisational culture.\n\nInclusion criteria: Evidence from research institutions only (considering Education, Enterprise and Research, the triple helix approach33,34) for both academic and grey literature were included. All disciplines within the academic environment were included.\n\nExclusion criteria: Anyone undertaking or supporting research outside of a research institution/Higher Education Institutes environment (for example in the health and social care field the National Health Service (NHS) Trusts, hospital settings, primary health care settings, allied health professional settings). Industry and non-academic businesses (including consultancies) were not included as they were not considered to have an academic focus. Non-English articles were excluded if no translation was available for the full article.\n\nThe database searches and grey literature did not have any limitations on country of origin, apart from news items that were restricted to the UK, Europe, North America, and Australasia.\n\nThe scoping review considered all types of study designs for inclusion (e.g., randomised controlled trials, non-randomised controlled trials, before and after studies and interrupted time-series studies, analytical observational studies including prospective and retrospective cohort studies, case-control studies, analytical cross-sectional studies, descriptive observational study designs including case series, individual case reports and descriptive cross-sectional studies).\n\nQualitative studies were also considered that focused on qualitative data including, but not limited to, designs such as phenomenology, grounded theory, ethnography, qualitative description, action research and feminist research. In addition, systematic reviews that met the inclusion criteria were considered, depending on the research question. Editorials and opinion papers were also considered for inclusion in the scoping review.\n\nA range of data were required to be as inclusive as possible due to the diverse nature of how research culture is reported and discussed in the public domain (and its associated parts in Open Access (OA), Equality, Diversity, and Inclusion (EDI) and career paths). Therefore, the review included published material from academic outputs (e.g., Journal articles, commentaries, editorials, perspectives, opinion letters) and from grey literature (e.g., reports, blogs, web-based articles, and newsletters including associated webpages of relevance).\n\nThe search strategy aimed to locate both published and unpublished citations. An initial limited search of Medline and Web of Science (WoS) was undertaken to identify articles on the topic, to develop and pilot the search strategy. The text words contained in the titles and abstracts of relevant articles and reports, and the index terms used to describe the articles were used to develop a full search strategy.15,35–38 The search strategy, including all identified keywords and index terms, were adapted for each included database and/or information source.\n\nThere were no study or language limits applied in the information retrieval process. The search strategy was limited from 2017 to 2022 but a preliminary search of citations during 2015-2022 was initially screened for relevance. Preliminary scoping and piloting of the search terms and strategies suggested that five years was sufficient for literature to be relevant, current, and broad (including relevant citations on the reporting of initiatives such as DORA, and any changes due to the COVID-19 pandemic). The review included UK and international literature (including grey literature, although see below for pragmatic restrictions for news items).\n\nDatabases: Six databases were searched (Medline, Engineering village, Scopus, JSTOR, ProQuest and WoS) during the period 29 April to 18 May 2022. A range of databases enabled the reviewers to capture several disciplines and to be as inclusive as possible.\n\nGrey literature searches: A pragmatic systematic search was undertaken of the Lexis-Nexis Academic database concentrating on newspapers and news items. The scoping and piloting of the search terms in the database suggested that geographical exclusions were needed due to the scale of results from the searches. As part of discussions with team members as well as an experienced librarian, the results were filtered to only include news outlets and organisations based in UK, Europe, North America, and Australasia. To augment the news searches, purposive sampling of relevant research websites was documented in an Excel spreadsheet to record all platforms and webpages visited. The sampling of websites was drawn from discussions with team members as well as an experienced librarian. Examples of research websites explored include: The Conversation, Nature, Science, UK Research and Innovation (UKRI) and Research on Research Institute (RoRi). Relevant citations were identified from Wellcome Trust14,15 as well as snowballing. The key references of the included articles and/or reports were screened for additional citations to be included as part of the overall screening process (including grey literature).\n\nFollowing the searches, all identified articles were collated and uploaded into Endnote version 20 (Clarivate Analytics, PA, USA, https://endnote.com/) (a free alternative is Mendeley: https://www.mendeley.com/) and duplicates were removed. Following a pilot test, all titles and abstracts were screened, by two independent reviewers for assessment against the inclusion criteria for the review using Rayyan. Potentially relevant articles were then retrieved for full extraction. At the full citation screening stage, reasons for exclusion were noted independently by both reviewers. Where the independent reviewer was unsure, the article was discussed, and a decision was made by consensus. Screening at both stages (title and abstract and full extraction) was piloted using Rayyan and labels were applied to categorise the focus of the articles based on four areas:\n\n- Security (including career paths, career progression, stability contracts/careers, issues affecting early career researchers etc.)\n\n- Wellbeing and equality of opportunity (including equality, diversity and inclusion, mental health, and wellbeing, bullying and harassment)\n\n- Teamwork (including team science, recognition of broad contribution to research, incentives)\n\n- Research quality and accountability (including research integrity, reproducibility, policy, and governance).\n\nThese focus areas were reported in the Wellcome Trust report and formed the basis of the current scoping review, to enable the University of Southampton to build on activity already undertaken, activity underway and enable alignment for future consideration.14,15\n\nThe list of included articles for full extraction were then exported to a Microsoft Excel spreadsheet using the labelling of articles from Rayyan (these categories were grouped together under the four focused areas). The results of the search and the study inclusion process are reported in full using the Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for scoping reviews (PRISMA-ScR), including the flow diagram reported in Figure 1.\n\nBoth reviewers extracted data from the full text articles using a data extraction tool developed by the reviewers to address the research question. This included the focus of the article, issues and/or problems reported in the article, solutions and/or recommendations provided in the article and details about whether the article related to more than one topic area.\n\nNo risk of bias or assessment on quality was conducted due to using a scoping review methodological approach. All the evidence was mapped and categorised into the four areas, which were discussed and agreed between team members at various stages of data extraction and during the write-up of the findings.\n\n\nResults\n\nA total of 3,042 articles were retrieved from the six databases. With 1,376 duplications that were removed, 1666 titles and abstracts and 924 full text articles were assessed for eligibility. Of these 924 full text articles, 253 articles met the eligibility criteria for inclusion.\n\nA total of 341 documents were retrieved (Lexis-Nexis) or identified across all the sources based on the titles. These were assessed for eligibility of which 102 met the criteria for inclusion.\n\nFigure 1 provides a full account of the records of identification flow diagram, including the reasons for the excluded articles.\n\nFrom the evidence there was a steady rise in the number of published articles over the last five years, with a notable increase from 2019. Table 1 shows that from the 253 included articles, there were 135 original research articles (this included qualitative and quantitative studies), 20 review articles (using a range of methodological review approaches), 86 perspective articles and 10 conference proceedings.\n\n* Note that some articles reported under more than one area of focus. The total number does not equal to the number of articles included in the scoping review.\n\n Jan-April inclusive, searches were conducted during April-May 2022.\n\n* Includes, editorial, commentaries, news features, correspondence, and perspective articles in journals.\n\nThe location of the study generation was captured for the included articles (based on location of the research and/or authors location). The included articles covered a global perspective with 71 articles from USA and Canada, 73 from international locations such as Africa (n=13), China (n=7), Australia (n=7) and Pakistan (n=4), 36 from Europe and 17 from the UK.\n\nThe grey literature provided 102 additional materials, 40 perspective articles reported in journals, 29 newspaper articles, 17 webpages (including educational webpages such as The Conversation: https://theconversation.com/uk) and including 10 reports. The remaining six were either a podcast, blog or case study. A majority of the grey literature material could not be grouped by location due to the nature of the material (76.5%, 78/102).\n\nThe evidence found in the database searches and grey literature was grouped according to the four focused areas, based on the key concepts developed during the full screening of the articles (based on the Wellcome Trust report).15 Several included articles were relevant to more than one focus area, which showed the breadth of the topic but also how these areas are overlapping and mutually reinforcing. For example, evidence reported under security was also closely linked to wellbeing and equality of opportunity (especially for early career researchers (ECRs) and Science, Technology, Engineering, Mathematics and Medicine (STEMM)).\n\nThe sections below provide a summary of the evidence based on the four focused areas, with particular attention on security, wellbeing, equality of opportunity and teamwork, and research quality and accountability.14,15 (see Figure 2) The quality or assessment of these initiatives were not explored as part of this scoping review and the key considerations arising from the evidence are not presented in order of priority.\n\nFrom the evidence it was clear that there is a global drive to expose the challenges and barriers in academic research culture. It was evident that these factors were not exclusive to specific countries, disciplines, or research institutions and the challenge is at a system level. Concerns over job security, career progression and sustainability were particularly experienced by PhD students, ECRs and junior researchers from a range of academic environments.39–42 The evidence reflects the range of research careers, roles, skills and expertise that are involved in research activity. Research Institutions often separate staff into job families such as research, education, technical, clinical, and managerial and professional roles titles reflecting different career pathways.17,43–45\n\nThe evidence suggests there are concerns that research institutions are not managing career progression expectations or providing ways to develop and train staff, which can result in inequality between career types.17,43–45 This can accumulate in feelings of failure by staff, or staff feeling pressured to be successful, which ultimately could promote unhealthy working practices such as excessive workloads and working long hours to meet expectations.46–48 These issues affect all research institution staff but the evidence suggests they are particularly acute for several groups such as ECRs, STEMM, people on Fixed Term Contracts (FTC), people with caring responsibilities, and people with disabilities46–48 (see Table 2 for a summary of the key considerations associated to security and career progression).\n\nThe review suggests that the problem is reinforced by a culture where researchers are incentivized to produce many funding applications and academic publications where high rejection rates.47 A related issue identified was the risk of evaluating academic performance based on the use of inadequate proxies (e.g., publication productivity, impact factor and citations).3,49 Evidence suggests that this can result in a lack of workload oversight, a culture discouraging of appreciation, that in turn makes researchers feel pressured to be successful, often resulting in a significant amount of time in pursuit of success at the cost of their wellbeing.42,46,47,49–51\n\nThe concept of research culture and job security was broad and included (but is not limited to) career paths; stability of contracts and careers; and issues affecting ECRs and students.57,141,145 A wide range of initiatives were explored in the literature covering a broad spectrum of factors (as detailed in Table 2). The evidence showed how, where, and why changes are needed to establish a global cultural change to the research ecosystem to enable fair and transparent progression for all research staff99,104,161; cultivate a culture that fosters diversity across career pathways17,55 and; initiate deeper integration of knowledge to ensure institutional stability.57,153\n\nThe evidence suggests that offering potential solutions or supportive actions for academic institutions and the research community may enhance and stabilise career paths, particularly those in the early career stage, including those in technical and managerial roles. Although these solutions and supportive actions are by no way exhaustive, they do provide a summary of the range of factors that could go some way in promoting a better research culture.54,138,154,162\n\nA key consideration from the evidence suggests that there are disparities across the research ecosystem, which are in turn influencing individuals’ wellbeing.39,40,43,70,92,96,99,118,163–166 The impact of these disparities are preventing or slowing down initiatives to seek for a cultural change in the academic environment. Although there has been some progress, the evidence suggests progress is slow and continues to be a challenge, especially for under-represented groups.166–169 The disparities highlighted in the literature suggests that under-represented groups are less likely to be promoted or receive funding, and have a higher risk of decreased well-being.18,64,83,89,170–179 However, as Lee (2022) pointed out, although underrepresented groups and junior staff are more likely to experience these challenges, including microaggression (and being victimised regardless of their role or position), anyone can, at some point in their academic career experience some form of microaggression (e.g., bullying, patronage power, exploitation, discrimination).20 This also extends to the notion of imposter syndrome as noted by Hagan (2020).169 Moreover, the way disciplines are taught at university means that curricula focusing on traditional perspectives may not be inclusive to everyone.123,176\n\nThe review revealed that the risks associated with a lack of diversity and inclusion often result in individuals leaving academia, low job satisfaction, increased stress, burnout and mental health problems, and decreased productivity.18,44,74 The evidence suggests that these issues have an impact not only at the institutional level such as having a lack of diversity in organisational leaderships,73,97,180 but also for individuals, leading to a lack of role models and peer mentors163 skills shortages in particular disciplines, sectors and roles,44,92,181 and drives off talent.8 Moreover, the increasing demands of heavy workloads and the risk of perpetuating a culture of academic rejection can impact an individual’s wellbeing.18,46,47,106,182 Table 3 provides a summary of the key considerations associated to wellbeing and equality of opportunity.\n\nThe review illustrates that over the last three years, the COVID-19 pandemic has highlighted some important challenges to this already highly pressured working environment, with mixed effects.18,44,74 Although, the pandemic has brought about challenges to the research workforce, there is also emerging evidence over the last two years showing the potential benefits and opportunities as a result of COVID-19.18,44,64,73,74,97,177,194 For example, use of online platforms for training and teaching purposes has opened up opportunities to bring together specific communities and countries. The pandemic also initiated ‘kindness in research’ where empathy replaced the usual expectations on work-life balance.73,97,180 The review also identified clear efforts to improve and raise awareness of the need for academia to embrace the EDI agenda through several initiatives, movements, and policy implementations (as detailed in Table 3). Most prominently, focusing on efforts to improve individuals’ opportunities through networking, collaborations, mentoring and peer-to-peer support, balancing career, and family aspirations can help to guide inclusivity and strengthen infrastructure and local capacity.171,177,183,205\n\nCollaboration, openness, and transparency were highlighted in the evidence as key indicators of success for driving forward a positive cultural change. However, the emerging evidence suggested that perverse incentives within the research ecosystem, a lack of training, opportunity, support, and infrastructure can undermine ambitions for change, which is further hampered by researcher perceptions.4,24,60,154,181,218,219\n\nThe evidence pointed to a range of barriers that have repercussions on the notion of teamwork, such as the ongoing tradition of first and last authors taking most or all of the credit for the work,220 the use of ‘gift authorship’ to enhance research publication of academics with poor research performance,5 and the pressures to have global impact on the scientific community through high-quality scientific writing.164 Researchers are incentivized to attain research excellence, which can often result in hyper-competitiveness and unfair working practices.4,19,24,50,59,88,89,206 The evidence further suggested that the Research Excellence Framework (REF) in the UK has been criticised as promoting competition between departmental colleagues rather than collaboration due to criteria on contributors and the increased demand on publications.49,89\n\nThese practices can have a detrimental impact for the promotion of research integrity and team science, especially for ECRs. Research careers encompass a range of roles, skills, and expertise but as the evidence suggests this is not universal, with some universities separating research active staff from colleagues such as research managers, technicians, administrators, and librarians, some of whom have research-level qualifications and experience.41,99,158 Separation in this way could lead to inequality of how staff are included (or not), trained, mentored and perceived by fellow colleagues (see Table 4 for a summary of the key considerations associated to teamwork and supportive working relationships).\n\nAs the evidence has shown, working relationship challenges in research culture require structural changes by transforming people, places, and practices.247 Any steps to reform will require accessibility to opportunities and resources that collectively bring research staff together in a unified and cohesive way to promote and create trust (rather than having intensive competitive pressures to achieve based on individual merit).51,164,247\n\nThe evidence reveals multiple layers of complexity around the notion of ‘teamwork’ and the interrelated social and environmental factors that unfortunately reinforce a status quo. For change to occur there needs to be synergy for collaboration to ensure individuals, Research Performing Organisations (RPOs), Research Funding Organisations (RFOs) and society share a unified approach to move beyond solitary, isolated teams to a deeper integration of multi-disciplinary/inter-disciplinary culture.7,57 An inclusive, representative, and collaborative research environment contributes to improvement in researchers’ sense of belonging and to positive cultural change.206\n\nThe identified evidence suggests that there is a need to take a holistic and integrated view of the intrinsic (those within disciplines) and extrinsic factors (those outside of disciplines) that affect the research environment to come up with novel ways to tackle the challenges with teamwork and collaboration to ensure openness and a cultural shift in the right direction.7 Given the growing evidence that success in research and innovation requires diversity in roles, knowledge, and skills, an inclusive, representative, and collaborative research environment contributes to improvement in researchers’ sense of belonging and to positive cultural change is required.206\n\nFrom the existing evidence it was clear that transparency, open research, and integrity requires collaboration from RPOs, RFOs, researchers, publishers, and other sectoral organisations such as industry.27,260,261 A large proportion of the evidence (more than a quarter of articles (133/253) included from the database searches and half of the grey literature (52/102)) highlighted several issues inhibiting open research practices, which some have termed as a ‘replication or reproducibility crisis’.24,86,216,235,237,257,262 These increasing pressures on researchers suggest that it is causing a ‘publish or perish’ practice, and has meant that researchers are prioritising ‘getting it published’ rather than ‘getting it right’.24,86,235,237,254,255,257\n\nHowever, as noted by Munafo (2022), the replication crisis could be regarded as an opportunity to promote motivation for improvements. Determining where effort is most needed and what changes are required, not only provides opportunity for the research ecosystem but also how RPOs and RFOs can mandate open research practices, and therefore coordinate change at both research integrity and researcher integrity level261 (see Table 5 for a summary of the key considerations associated to teamwork and supportive working relationships)\n\nThe existing evidence demonstrated that open research practices (e.g., research integrity, researcher integrity, open data, open access and transparency) requires a global effort, as well as involvement from all sectors of the research ecosystem (e.g., institutions, researchers, funding organisations, publishers, industry). However, more evidence is needed to demonstrate where and in what circumstances the change is having tangible benefit.43,260,261,282,329\n\nAs the evidence suggests, practices should be evaluated to assess whether change has been of value, enhancing the research pathway and algin to be evidence informed, therefore avoiding any unintended consequences.5,7,135,261,272 Meta research (e.g., research on research, meta science) is one way to evaluate and evidence any innovation taking place, and therefore determine the impact and tangible benefit of these changes to promote and enhance the research ecosystem.7,24,36,247,261,281,329,341\n\nThe evidence found several initiatives such as the UK Reproducibility Network (UKRN), Declaration on Research Assessment (DORA), and the European Network of Research Integrity (ENRI) to promote, encourage and prioritise the facilitation and creation of open research practices.7,22,281,285,325 Adopting such initiatives enhances innovation across all aspects of the research ecosystem but there is variation on how far they have been implemented (including what stage of the development) and the acceptance level from researchers, RPOs and RFOs.303,322,325,330\n\n\nDiscussion\n\nFrom the evidence, it was clear that there were several initiatives to seek a cultural change across the research institutions/Higher Education Institutions. Although this was promising to see, the commitment is complex considering the multifaceted structures and processes governing the research ecosystem. Adding to the complexity, is the acknowledgement from research institutions that they too have a role to play in not only supporting research staff, at all levels, but also recognise the role and function of research management staff.76,85,114,137,156,229 As noted in the recent Research and Development report on people and culture strategy, high quality research and innovation requires an acknowledgment of the full range of people needed.8 An inclusive, representative and collaborative research environment contributes to improvement in researchers’ sense of belonging and to positive cultural change.206\n\nThe increasing competitiveness within the research environment, with research funding organisations (RFOs) placing greater focus on impact rather than creativity and innovation, is causing a global initiative for cultural change. The health of the research group and those that lead them has been identified as an area that universities need to pay more attention to, rather than centering on individual researchers, particularly in the context of preventing research misconduct.43 Team leaders play an important role in creating trustful environments, which support knowledge exchange processes and open research164 and crucially they act as mentors and role models for research integrity and working practices.43,92\n\nThere was a strong sense and recognition of the value and importance of research capacity building, and the evidence clearly provided a wealth of initiatives to embark on. Interestingly, models, approaches and initiatives for capacity building have been reported by several countries.57,70,90,103,130,133,159,223,310,352 Initiatives taking place in many countries, emphasising the benefits of learning from experiences in other countries was encouraging to report from the literature. Factoring some of these initiatives, it is evident that academia is confronting the challenges ‘head on’ to build a more sustainable and credible research environment.20,162,216 Although this is promising, the evidence suggests that research institutions must not assume that ‘one size fits all’. There is diversity across disciplines, research staff (research, education, enterprise, and professional services) and several types of research institutions. To enhance research culture, different solutions will require different approaches at individual, institutional and systemic levels.\n\nOver the last five years, and particularly the last two years (i.e., post the COVID-19 pandemic), there is a surge of evidence to capture the effects of these challenges and barriers and how these failings in our research ecosystem can be mitigated. Much of the literature focusing on career stability, job security and career progression suggested the need to build research capacity that spans across research, education, enterprise, and professional services. However, with this comes new challenges and pressures for teaching staff to also mentor, support and educate, whilst also having committed time to conduct their own research.7,24,44,50,73,74,97,177,194,337\n\nGuidance on how to create a global long-term sustainable model that has representation at all levels is going to take time, and the COVID-19 pandemic has aggravated this already challenging and highly pressured working environment.18,44,73,74 The COVID 19 pandemic may have perhaps initiated more transparency on obtaining a work/life balance, particularly at a time when many parents across the world were not only managing increasing work demands but also having to manage home life and home schooling simultaneously. The effect of the COVID-19 pandemic has started to emerge in the literature, particularly how additional burden placed on women reduced their productivity far more than men with women having ‘borne the brunt of the pandemic in academic settings.’177 There has been a steady increase in mental health distress arising from COVID-19 pandemic reported, which added to the existing strain in academia can often feel detrimental to an individual’s career.18\n\nHowever, despite the pandemic causing global disruption and concern, it has initiated new opportunities to bring communities and countries together using digital tools.194,241,245,257,264,332,342,344 Research, training and teaching took place online, and the evidence seemed to suggest that offering greater accessibility through virtual platforms goes some way to reform the connectivity and diversity of the research environment. A good example of this is virtual conferences, as those with accessibility issues, family commitments, funding limitations and research communities from Low- and Middle-Income Countries (LMIC) now can attend, where they could not before.208,245 Any changes will inevitably take time, but small improvements over time can have an impact, affecting both research institutions and funding organisations.180 In addition, the pandemic provided the impetus to embed kindness in research where empathy replaced the usual expectations on work-life balance,97 and researchers who felt supported during the pandemic tended to have better indicators of well-being.73,74\n\nGiven the growing evidence that success in research and innovation requires diversity in roles, knowledge, and skills, embedding a research culture of inequality between career types within the same research team discourages a culture of collaboration and appreciation of a diversity of roles, specialisations and contributions.41,164 With increasing demands to incentivise and promote change it is necessary to acknowledge that both funding organisations and research institutions have responsibility to transform and shape best practice in research. Providing opportunities for research staff to combine their academic research with work in other sectors could bring more value to academia and strengthen the synergies for cultural change in the long-term.153\n\nThe main strength of the review was using several systematic database literature searches, which was complemented with additional grey literature searches of known online education articles and websites. However, a limitation is that scoping reviews only map the evidence and do not assess the quality of the articles or risk of bias. Most of the database articles had an international focus, with most of them from USA, Canada (28.0%) and other international countries (27.2%). For a large proportion of the grey literature, it was not possible to ascertain the articles countries region. Moreover, on a pragmatic basis, news items from news organisations based outside of UK, Europe, Norther America, and Australia were excluded, which along with the exclusion of non-English language documents means that other initiatives being used to improve research culture may well have been missed. On this basis, there could have been international and regional biases, but it could also be that there is a lack of evidence from these regions rather than missing articles from the systematic searches.\n\nThe review found more than 200 articles from the systematic database searches (n=253) and more than 100 from the grey literature searches (n=102) which suggested that there is growing literature around what constitutes a ‘good’ research culture and what this could look like. However, as the literature has shown, progress has been slow and although the evidence provided several examples of established initiatives and networking opportunities, the evidence was more anecdotal, and opinion focused.\n\n\nConclusions\n\nThe review has shown that there is a wealth of evidence suggesting how and where changes are needed to establish a global cultural change to the research ecosystem. However, research organisations cannot act in isolation. Individuals, research organisation and funding organisations need to be responsible and work together; to uphold and ensure fair and transparent policies and governance. Change will not happen overnight, but by working together in a collaborative and diverse way to ensure all views, opinions and expectations are fully inclusive that strengthen and enhance research culture for the better.\n\nThe barriers to a sustainable research culture are complex and underneath linger more multi-faceted challenges, such as the impact on the wellbeing of research staff, resistance to innovation, equity for research institution staff and career progression.28,62,64,85,195,260,336 Adding to the complexity is the increasing pressure for academic institutions, research groups, disciplines, and researchers to demonstrate impact. The growing focus on performance measures has undoubtedly caused unintended consequences for the whole research ecosystem. This model is not sustainable, not only for the quality of research and trust in research, but also for the next generation of talented researchers. Researchers are leaving academia, leaving behind a career that should be fostering innovation and building research capacity at its core. Removing such barriers and adopting best research practice and enhancing the diversity of opportunities for all is ultimately down to everyone working within the research environment.\n\n\nEthics and consent\n\nEthical approval and written consent statement were not required.\n\n\nAuthors’ contributions\n\nConceptualization: Amanda Blatch-Jones, Kay Lakin, Sarah Thomas\n\nData curation: Amanda Blatch-Jones, Kay Lakin\n\nFormal analysis: Amanda Blatch-Jones, Kay Lakin\n\nInvestigation: Amanda Blatch-Jones, Kay Lakin\n\nMethodology: Amanda Blatch-Jones, Kay Lakin\n\nValidation: Amanda Blatch-Jones, Kay Lakin\n\nProject administration: Amanda Blatch-Jones\n\nSupervision: Amanda Blatch-Jones\n\nWriting – original draft: Amanda Blatch-Jones\n\nWriting – review and editing: Amanda Blatch-Jones, Kay Lakin, Sarah Thomas", "appendix": "Data availability statement\n\nAll underlying data are available as part of the article and no additional source data are required.\n\nOSF: A scoping review on what constitutes a good research culture. https://osf.io/wjhcf/. 353\n\nThis project contains the following underlying data:\n\n• Fig 1 PRISMA flow diagram (PRISMA)\n\n• Fig 2 themed areas diagram (four areas of statements diagram)\n\n• S1 Appendix search terms and key words (search terms and key words)\n\n• S2 Appendix PRISMA ScR checklist (completed checklist)\n\n• S1 Table database searches examples (search strategies used)\n\n• S2 Table database lit articles (complete list of included articles in the review)\n\n• S3 Table grey lit articles (complete list of included articles from the grey literature in the review)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nReporting guidelines\n\nOSF repository: PRISMA ScR checklist and flow chart for “A scoping review on what constitutes a good research culture.” https://osf.io/wjhcf/. 353\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to thank John Holloway and Rebecca Hoyle for their contribution to the development of the scoping review and Beverly Sherbon for her contribution during the early stages of the planning of the scoping review. We would also like to thank Becky Clarke-Harris for her contribution to screening and full extraction, Jennifer McHugh for her involvement in the wider collaboration across the University of Southampton, and support from the University of Southampton Library during the scoping and piloting phase for grey literature searches using Lexis-Nexis.\n\n\nReferences\n\nHunter J, McKernan R, Rankin S, et al.: Seven principles to change the UK’s research culture. Times Higher Education. 2020.\n\nJong L, Franssen T, Pinfield S: ‘Excellence’ in the Research Ecosystem: A Literature Review. Research on Research Institute; 2021.\n\nElse H: Impact factors are still widely used in academic evaluations. Nature. 2019. PubMed Abstract \| Publisher Full Text\n\nXu X, Oancea A, Rose H: The Impacts of Incentives for International Publications on Research Cultures in Chinese Humanities and Social Sciences. Minerva. 2021; 59(4): 469–492. Publisher Full Text\n\nBuckle RA, Creedy J: Methods to evaluate institutional responses to performance-based research funding systems. Aust. Econ. Pap. 2022; 61: 615–634. Publisher Full Text\n\nGadd E: Metistalk.2022. Reference Source\n\nBeck S, Bergenholtz C, Bogers M, et al.: The Open Innovation in Science research field: a collaborative conceptualisation approach. Ind. Innov. 2022; 29(2): 136–185. Publisher Full Text\n\nBEIS: Research and development (R&D) people and culture strategy. In: Industry DfBE, editor.2021.\n\nInorms: SCOPE Framework for Research Evaluation. Last accessed 22/02/2023. Reference Source\n\nDORA: The Declaration on Research Assessment. Last accessed 22/02/2023. Reference Source\n\nHicks D, Wouters P, Waltman L, et al.: Bibliometrics: The Leiden Manifesto for research metrics. Nature. 2015; 520(7548): 429–431. PubMed Abstract \| Publisher Full Text\n\nISRIA: The International School on Research Impact Assessment. Last Accessed 22/02/2023. Reference Source\n\nAgate N, Long CP, Russell B, et al.: Walking the Talk: Toward a Values-Aligned Academy. HuMetricsHSS; 2022. Publisher Full Text\n\nWellcome: Research culture: let’s reimagine how we work together. Last accessed 22/02/2023. Reference Source\n\nWellcome: What researchers think about the culture they work in. Last accessed 22/02/2023. Reference Source\n\nJo Billings: Research culture: what researchers think of the culture they work in. Last accessed 22/02/2023. Reference Source\n\nUllrich LE, Ogawa JR, Jones-London MD: Factors that influence career choice among different populations of neuroscience trainees. eNeuro. 2021; 8(3): ENEURO.0163–ENEU21.2021. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLimas JC, Corcoran LC, Baker AN, et al.: The Impact of Research Culture on Mental Health & Diversity in STEM. Eur. J. Chem. 2022; 28(9). Publisher Full Text\n\nGrant S, Wendt KE, Leadbeater BJ, et al.: Transparent, Open, and Reproducible Prevention Science. Prev. Sci. 2022; 23: 701–722. Publisher Full Text\n\nErickson M, Walker C, Hanna P: Survey of academics finds widespread feelings of stress and overwork. The Conversation. 2020. Reference Source\n\nMarinetto M: How can we tackle the thorny problem of fraudulent research? The Guardian. 2017.\n\nUK Research and Innovation: Enhancing research culture funding allocations 2021 to 2022. Last accessed 22/02/2023. Reference Source\n\nHorn L, Bouter L: Researchers should be assessed on quality not quantity: here’s how. The Conversation. 2022. Reference Source\n\nKowalczyk OS, Lautarescu A, Blok E, et al.: What senior academics can do to support reproducible and open research: a short, three-step guide. BMC. Res. Notes. 2022; 15(1): 116. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nManville C, d’Angelo C, Culora A, et al.: Understanding perceptions of the Research Excellence Framework among UK researchers.2021.\n\nThe Royal Society: Research culture embedding inclusive excellence: Insights on the future culture of research.2017.\n\nStewart SLK, Pennington CR, da Silva GR , et al.: Reforms to improve reproducibility and quality must be coordinated across the research ecosystem: the view from the UKRN Local Network Leads. BMC. Res. Notes. 2022; 15(1): 58. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoss-Hellauer T, Reichmann S, Cole NL, et al.: Dynamics of cumulative advantage and threats to equity in open science: a scoping review. R. Soc. Open Sci. 2022; 9(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSørensen MP, Ravn T, Marušić A, et al.: Strengthening research integrity: which topic areas should organisations focus on? Hum. Soc. Sci. Comm. 2021; 8(1). Publisher Full Text\n\nJBI: Scoping Review Network. Last accessed 17/02/2023. Reference Source\n\nPeters MDJ, Marnie C, Tricco AC, et al.: Updated methodological guidance for the conduct of scoping reviews. JBI Evid. Implement. 2021; 19(1): 3–10. PubMed Abstract \| Publisher Full Text\n\nKhalil H, Peters MD, Tricco AC, et al.: Conducting high quality scoping reviews-challenges and solutions. J. Clin. Epidemiol. 2021; 130: 156–160. PubMed Abstract \| Publisher Full Text\n\nCai Y, Amaral M: The triple helix model and the future of innovation: a reflection on the triple helix research agenda. Triple Helix. 2021; 8(2): 217–229.\n\nHalilem N: Inside the Triple Helix: An Integrative Conceptual Framework of the Academic Researcher’s Activities, a Systematic Review. J. Res. Adm. 2010; 41(3): 23–50.\n\nBorkowski D, McKinstry C, Cotchett M, et al.: Research culture in allied health: a systematic review. Aust. J. Prim. Health. 2016; 22(4): 294–303. PubMed Abstract \| Publisher Full Text\n\nMunafo MR, Chambers CD, Collins AM, et al.: Research Culture and Reproducibility. Trends Cogn. Sci. 2020; 24(2): 91–93. Publisher Full Text\n\nStentiford L, Koutsouris G, Boyle C, et al.: The structures and processes governing education research in the UK from 1990–2020: A systematic scoping review. Rev. Educ. 2021; 9(3). Publisher Full Text\n\nSlade SC, Philip K, Morris ME: Frameworks for embedding a research culture in allied health practice: a rapid review. Health Res. Policy Syst. 2018; 16(1): 29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAllen J, Smith JL, Ransdell LB: Missing or seizing the opportunity? The effect of an opportunity hire on job offers to science faculty candidates. Equal Diversity Incl. 2019b; 38(2): 160–177. Publisher Full Text\n\nBlackburn H: The Status of Women in STEM in Higher Education: A Review of the Literature 2007–2017. Sci. Technol. Libr. 2017; 36(3): 235–273. Publisher Full Text\n\nTeperek M, Cruz M, Kingsley D: Time to re-think the divide between academic and support staff. Nature. 2022. PubMed Abstract \| Publisher Full Text\n\nHall R: Are PhDs just cheap labour for universities?; PhD grads complain that there are too few academic jobs. Should universities support their postgrads into alternative careers? The Guardian (London). 2019 01/04/2019.\n\nAnon: Integrity starts with the health of research groups. Nature. 2017; 545(7652): 5–6. Publisher Full Text\n\nAnon: COVID is disrupting scientific careers around the world. Nature. 2021; 599: 179. Publisher Full Text\n\nChristian K, Johnstone C, Larkins JA, et al.: A survey of early-career researchers in Australia. elife. 2021; 10(01): 11. Publisher Full Text\n\nCreaton J: Addressing the mental health crisis. Nat. Rev. Cancer. 2021; 21(1): 1–2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAllen K, Donoghue G, Hattie J, et al.: Journal papers, grants, jobs … as rejections pile up, it’s not enough to tell academics to ‘suck it up’. The Conversation. 2021. Reference Source\n\nGrove J: Research intelligence: big ideas to improve research culture. The Times Higher Education Supplement. 2021.\n\nGrove J: Do national research assessment exercises still pass peer review? The Times Higher Education Supplement. 2021. 02/09/2021.\n\nMrva-Montoya A, Luca E: Book publishing sidelined in the game of university measurement and rankings. The Conversation. 2021. Reference Source\n\nCassuto L: The Grief of the Ex-Academic. Chron. High. Educ. 2018 25/02/2018.\n\nAfonja S, Salmon DG, Quailey SI, et al.: Postdocs’ advice on pursuing a research career in academia: A qualitative analysis of free-text survey responses. PLoS One. 2021; 16(5 May): e0250662. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhmed T, Johnson J, Latif Z, et al.: MyNRMN: A national mentoring and networking platform to enhance connectivity and diversity in the biomedical sciences. Faseb Bioadvances. 2021; 3(7): 497–509. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarnes N, du Plessis M , Frantz J: Institutional culture and academic career progression: Perceptions and experiences of academic staff. SA J. Ind. Psychol. 2021; 47: 47. Publisher Full Text\n\nde Herde V , Björnmalm M, Susi T: Game over: Empower early career researchers to improve research quality. Insights UKSG J. 2021; 34: 1–6. Publisher Full Text\n\nFinkel A: To move research from quantity to quality, go beyond good intentions. Nature. 2019; 566(297): 297. PubMed Abstract \| Publisher Full Text\n\nGibson C, Stutchbury T, Ikutegbe V, et al.: Challenge-Led Interdisciplinary Research in Practice: Program Design, Early Career Research, and a Dialogic Approach to Building Unlikely Collaborations. Res. Eval. 2019; 28(1): 51–62. Publisher Full Text\n\nGriffith EE, Dasgupta N: How the demographic composition of academic science and engineering departments influences workplace culture, faculty experience, and retention risk. Soc. Sci. 2018; 7(5). Publisher Full Text\n\nJung J, Horta H, Zhang LF, et al.: Factors fostering and hindering research collaboration with doctoral students among academics in Hong Kong. High. Educ. 2021; 82: 519–540. Publisher Full Text\n\nMaxwell TW, Chophel D: The impact and outcomes of (non-education) doctorates: the case of an emerging Bhutan. High. Educ. 2020; 80(6): 1081–1102. Publisher Full Text\n\nMendez S, Tygret JA, Conley VM, et al.: Exploring the mentoring needs of early- And mid-career URM engineering faculty: A phenomenological study. Qual. Rep. 2020; 25(4): 891–908.\n\nOwusu F, Kalipeni E, Awortwi N, et al.: Building research capacity for African institutions: confronting the research leadership gap and lessons from African research leaders. Int. J. Leadersh. Educ. 2017; 20(2): 220–245. Publisher Full Text\n\nPanina SV, Arkhipova SN, Parnikova TA, et al.: Student Career Choices before and during Quarantine Measures. Propositos Y Representaciones. 2020; 8: 8. Publisher Full Text\n\nRansdell LB, Lane TS, Schwartz AL, et al.: Mentoring new and early-stage investigators and underrepresented minority faculty for research success in health-related fields: An integrative literature review (2010-2020). Int. J. Environ. Res. Public Health. 2021; 18(2): 1–35.\n\nSantos P, Patrício MT: Academic culture in doctoral education: Are companies making a difference in the experiences and practices of doctoral students in Portugal? Int J Doctoral Studies. 2020; 15: 685–704. Publisher Full Text\n\nShelton DS, Delgado MM, Greenway EVG, et al.: Expanding the Landscape of Opportunity: Professional Societies Support Early-Career Researchers Through Community Programming and Peer Coaching. J. Comp. Psychol. 2021; 135(4): 439–449. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTermini CM, Hinton AO Jr, Garza-López E, et al.: Building Diverse Mentoring Networks that Transcend Boundaries in Cancer Research. Trends Cancer. 2021; 7(5): 385–388. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUllah S, Arabia DHA, Mansoor SN, et al.: Beyond publish or perish: Promoting quality and increasing standards in medical research and writing. J. Pak. Med. Assoc. 2018; 68(5): 823–824. PubMed Abstract\n\nAldercotte A, Guyan K, Lawson J, et al.: ASSET 2016: Experiences of gender equality in STEMM academia and their intersections with ethnicity, sexual orientation, disability and age.2017.\n\nAnon: Workshop on ‘Perspective of Manipuri Culture’ to promote quality research. India: Imphal Free Press; 2021c 21/01/2021.\n\nClynes M, Corbett A, Overbaugh J: Why we need good mentoring. Nat. Rev. Cancer. 2019; 19(9): 489–493. PubMed Abstract \| Publisher Full Text\n\nGopalakrishna G: Preprint advocates must also fight for research integrity. Nature. 2021. PubMed Abstract \| Publisher Full Text\n\nGould J: Kindness alone won’t improve the research culture. Nature. 2020. Podcast. Publisher Full Text\n\nGould J: The career costs of COVID-19: how postdocs and PhD students are paying the price. Nature. 2020. Podcast. Publisher Full Text Reference Source\n\nGuccione K: Aren’t they all leaving anyway? What’s the value of mentoring early career research staff?2018.\n\nGunsalus CK, Robinson AD: Nine pitfalls of research misconduct. Nature. 2018; 557(7705): 297–299. PubMed Abstract \| Publisher Full Text\n\nMejlgaard N, Bouter LM, Gaskell G, et al.: Research integrity: nine ways to move from talk to walk. Nature. 2020; 586(7829): 358–360. PubMed Abstract \| Publisher Full Text\n\nMcKinsey & Company: Bridging the challenge gap in Denmark.2018.\n\nMoreau M, Bernard T: Carers and Careers in Higher Education: What works? AdvanceHE. 2018. Reference Source\n\nSample I: Researchers facing ‘shocking’ levels of stress, survey reveals; Nearly two thirds of those who took part had witnessed bullying or harassment. The Guardian (London). 2020 15/01/2020.\n\nThomson R: How we can turn the tide for women in science. The Conversation. 2018. Reference Source\n\nWells B: University holds special academic meeting. The Marquette tribune. Marquette University; 2021 04/05/2021.\n\nYelken Y: The Aditi Leadership Programme: Developing the potential of Black, Asian and Minority Ethnic Leaders. Advance HE; 2018.\n\nJones R, Wilsdon J: The Biomedical Bubble: Why UK research and innovation needs a greater diversity of priorities, politics, places and people.2018.\n\nMejilgaard N, Bouter LM, Gaskell G, et al.: Research integrity: nine ways to move from talk to walk. Nature. 2020; 586: 358–360. PubMed Abstract \| Publisher Full Text\n\nNeff EP: On the past, present, and future of in vivo science. Lab Anim. 2021; 50(10): 273–276. Publisher Full Text\n\nNorris D, Dirnagl U, Zigmond MJ, et al.: Health tips for research groups. Nature Publishing Group; 2018.\n\nPowell K: Should we steer clear of the winner-takes-all approach? Nature. 2018; 553(7688): 367–369. PubMed Abstract \| Publisher Full Text\n\nSibai O, Figueirdo B, Ferreira MC: Overworked and isolated: the rising epidemic of loneliness in academia. The Conversation. 2019. Reference Source\n\nVan Noorden R: Some hard numbers on science’s leadership problems. Nature. 2018; 557: 294–296. PubMed Abstract \| Publisher Full Text\n\nWoolston C: Feeling overwhelmed by academia? You are not alone. Nature. 2018; 557: 129–131. Publisher Full Text\n\nAnon: Research institutions must put the health of labs first. Nature. 2018; 557: 279–280. Publisher Full Text\n\nHan X, Appelbaum RP: China’s science, technology, engineering, and mathematics (STEM) research environment: A snapshot. PLoS One. 2018; 13(4). Publisher Full Text\n\nHartvigson L, Heshmati A: Sustainability of Cooperation in the International Development of African Higher Education. Scan. J. Educ. Res. 2022; 67: 489–503. Publisher Full Text\n\nSheikh A, Malik A, Mahmood K: Research practices of LIS professionals in Pakistan: A study of attitudes, involvement and competencies. J. Inf. Sci. 2020; 48: 587–599. Publisher Full Text\n\nBurton MFZ, Cao XE: Navigating mental health challenges in graduate school. Nat. Rev. Mater. 2022; 7(6): 421–423. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDerrick G: How COVID-19 lockdowns could lead to a kinder research culture. Nature. 2020; 581: 107–108. PubMed Abstract \| Publisher Full Text\n\nGottlieb G, Smith S, Cole J, et al.: Realising Our Potential Backing Talent and Strengthening UK Research Culture and Environment. Russell Group; 2021.\n\nAnon.: Research managers are essential to a healthy research culture. Nature. 2021; 595(150): 150. Publisher Full Text\n\nAzeem M, Mataruna L: Identifying factor measuring collective leadership at academic workplaces. Int. J. Educ. Manag. 2019; 33(6): 1316–1335.\n\nChaplin K, Price D: 7 ways to promote better research culture.2018.\n\nHalpern JB, Huber TE, Sinex SA, et al.: Building a Dynamic University-Community College Partnership: The Second Decade of a Broad, Mutually Beneficial Materials Science Collaboration. Materials Research Society; 2018.\n\nHammad W, Al-Ani W: Building Educational Research Capacity: Challenges and Opportunities From the Perspectives of Faculty Members at a National University in Oman. SAGE Open. 2021; 11(3): 215824402110326. Publisher Full Text\n\nMalotky MKH, Mayes KM, Price KM, et al.: Fostering Inclusion through an Interinstitutional, Community-Engaged, Course-Based Undergraduate Research Experience. J. Microbiol. Biol. Educ. 2020; 21(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcAllister M, Donna LB: ‘Pre-Run, Re-Run’: An innovative research capacity building exercise. Nurse Educ. Pract. 2017; 27: 144–150. PubMed Abstract \| Publisher Full Text\n\nMarín-Spiotta E: Harassment should count as scientific misconduct. Nature. 2018; 557(7704): 141. PubMed Abstract \| Publisher Full Text\n\nRussell S, Foulkes I: Embedding a positive research culture that fosters innovation. Nat. Rev. Cancer. 2019; 19(5): 241–242. PubMed Abstract \| Publisher Full Text\n\nSchiermeier Q: Data management made simple. Nature. 2018; 555: 403–405. Publisher Full Text\n\nWellcome: esponsible conduct of research.2022. Reference Source\n\nWinchester C: Give every paper a read for reproducibility. Nature. 2018; 557(7706): 281–282. PubMed Abstract \| Publisher Full Text\n\nWoolston C: PhDs: the tortuous truth. Nature. 2019; 575: 403–406. PubMed Abstract \| Publisher Full Text\n\nDevi G, Sudan R, Freel S, et al.: 2305: Advancement of translational sciences: developement of an INTL! - erprofessional program and outcome measures for foundational, clinical, and health care researchers. J. Clin. Transl. Res. 2017; 1: 47. Publisher Full Text\n\nJuvonen S, Nurkka P, Vakevainen K, editors. Experiences of cooperation between a higher education institution and industry and its impact on working culture 11th International Conference on Technology, Education and Development (INTED); 2017 2017 Mar 06-08; Valencia, SPAIN.2017.\n\nLanghaug LF, Jack H, Hanlon C, et al.: “We need more big trees as well as the grass roots”: going beyond research capacity building to develop sustainable careers in mental health research in African countries. Int. J. Ment. Heal. Syst. 2020; 14: 1–14.\n\nAbe I, Mugobo V: Low research productivity: Transformation, institutional and leadership concern at a South African University. Perspect. Educ. 2021; 39(2): 113–127. Publisher Full Text\n\nLorenz-Meyer D: The Academic Productivist Regime: Affective Dynamics in the Moral-Political Economy of Publishing. Sci. Cult. 2018; 27(2): 151–174. Publisher Full Text\n\nMadia Lourenco LH, Baker BL, Dias Junior AG, et al.: Engaging local health research communities to enhance long-term capacity building in Brazil. BMJ Glob. Health. 2021; 6(10): 10.\n\nAngelini D: Swindon consultant creates uni course to improve women’s confidence in male-dominated jobs. Swindon Advertiser. 2020 03/08/2020.\n\nAnon: How to grow a healthy lab. Nature. 2018; 557: 293. Publisher Full Text\n\nDougherty S, Ecton W: How better funding can increase the number and diversity of doctoral students. The Conversation. 2021. Reference Source\n\nGrove J: India to train researchers in how to spot predatory journals. The Times Higher Education Supplement. 2020 23/01/2020.\n\nChristian K, Johnstone C, Larkins JA, et al.: Why have eight researcher women in STEMM left academic research, and where did they go? Int. J. Acad. Dev. 2021; 28: 31–44. Publisher Full Text\n\nDowey N, Barclay J, Fernando B, et al.: A UK perspective on tackling the geoscience racial diversity crisis in the Global North. Nat. Geosci. 2021; 14(5): 256–259. Publisher Full Text\n\nHeng K, Hamid MO, Khan A: Research engagement of academics in the Global South: the case of Cambodian academics. Glob. Soc. Educ. 2022; 21: 322–337. Publisher Full Text\n\nHishan SS, Ramakrishnan S, Mansor NNBA: Research engagement of foreign language teachers among select higher education institutions in Malaysia. Rupkatha J. Interdiscip. Stud. Humanit. 2020; 12(1). Publisher Full Text\n\nJessani NS, Valmeekanathan A, Babcock CM, et al.: Academic incentives for enhancing faculty engagement with decision-makers-considerations and recommendations from one School of Public Health. Humanit. Soc. Sci. Commun. 2020; 7(1). Publisher Full Text\n\nPauliuk S: Making sustainability science a cumulative effort. Nat. Sustain. 2020; 3(1): 2–4. Publisher Full Text\n\nPownall M, Talbot CV, Henschel A, et al.: Navigating Open Science as Early Career Feminist Researchers. Psychol. Women Q. 2021; 45(4): 526–539. Publisher Full Text\n\nUniversities New Zealand: Tauira Māori Initiatives – Sharing good practice in New Zealand universities.2018.\n\nMcGinn MK, Niemczyk EK: Team dynamics and learning opportunities in social science research teams. Alta. J. Educ. Res. 2020; 66(4): 364–386.\n\nFaure C, Munung NS, Ntusi NAB, et al.: Considering equity in global health collaborations: A qualitative study on experiences of equity. PLoS One. 2021; 16(10 October): e0258286. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGong Y, MacPhail A, Young AM: Chinese higher education-based physical education teacher educators’ professional learning needs for involvement in research activities. Prof. Dev. Educ. 2021; 1–17. Publisher Full Text\n\nHaja W: OC 8586 Institutional research capacity building for multi-disciplinary health research to support the health system rebuilding phase in sierra leone. BMJ Glob. Health. 2019; 4(Suppl 3): A15.1–A1A15. Publisher Full Text\n\nMalekzadeh A, Michels K, Wolfman C, et al.: Strengthening research capacity in LMICs to address the global NCD burden. Glob. Health Action. 2020; 13(1): 1846904. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuthama E, McKenna S: The unintended consequences of using direct incentives to drive the complex task of research dissemination. Educ. Change. 2020; 24: 1–23.\n\nNorman MK, Mayowski CA, Fine MJ: Authorship stories panel discussion: Fostering ethical authorship by cultivating a growth mindset. Account. Res. 2021; 28(2): 115–124. PubMed Abstract \| Publisher Full Text\n\nOancea A, Fancourt N, Robson J, et al.: Research capacity-building in teacher education. Oxf. Rev. Educ. 2021; 47(1): 98–119. Publisher Full Text\n\nUhlmann EL, Ebersole CR, Chartier CR, et al.: Scientific Utopia III: Crowdsourcing Science. Perspect. Psychol. Sci. 2019; 14(5): 711–733. PubMed Abstract \| Publisher Full Text\n\nTregoning J: Will my popular science book bring any career benefits? The Times Higher Education Supplement. 2021 14/10/2021.\n\nde Jager P , Lubbe I, Papageorgiou E: The South African chartered accountant academic: Motivations and challenges when pursuing a doctoral degree. Meditari. Account. Res. 2018; 26(2): 263–283. Publisher Full Text\n\nGaikwad P: Balancing research productivity and teaching by faculty in higher education: A case study in the philippines. J. High Educ. Theory Pract. 2021; 21(7): 181–192.\n\nInga E, Inga J, Cárdenas J, et al.: Planning and strategic management of higher education considering the vision of latin america. Educ. Sci. 2021; 11(4). Publisher Full Text\n\nNhem D: Quality in higher education: what do students in Cambodia perceive? Tert. Educ. Manag. 2022; 28(1): 43–59. Publisher Full Text\n\nWilson C, Hirtz M, Levkin PA, et al.: Facilitating an International Research Experience Focused on Applied Nanotechnology and Surface Chemistry for American Undergraduate Students Collaborating with Mentors at a German Educational and Research Institution. J. Chem. Educ. 2019; 96(11): 2441–2449. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDelbari S, Rajaipour S, Abedini Y: Investigating the relationship between career development and productivity with the mediating role of self-regulation among university staff. J. Appl. Res. High Edu. 2020; 13(3): 759–781. Publisher Full Text\n\nBabalola OO, du Plessis Y , Babalola SS: Insight into the Organizational Culture and Challenges Faced by Women STEM Leaders in Africa. Soc. Sci. (Basel). 2021; 10(3). Publisher Full Text\n\nWolter I, Ehrtmann L, Seidel T, et al.: Social or Economic Goals? The Professional Goal Orientation of Students Enrolled in STEM and Non-STEM Majors in University. Front. Psychol. 2019; 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDavis D, Garbarino J, Bahia P, et al.: Recommendations for the Continued Professionalization of Science Outreach within the Scientific Enterprise (SciOut18). Figshare. 2020.\n\nSlovacek S, Miu V, Soto K, et al.: Supporting STEM in Higher Education. J. Int. Educ. Pract. 2019; 7(4): 438–449. Publisher Full Text\n\nBond M, Marín VI, Bedenlier S: International Collaboration in the Field of Educational Research: A Delphi Study. J. New Approaches Educ. Res. 2021; 10(2): 190–213. Publisher Full Text\n\nBishop DVM, Bates T, Loryman C, et al.: What can be done to improve research integrity?. The Times Higher Education Supplement. 2022 20/01/2022.\n\nKwok R: How lab heads can learn to lead. Nature. 2018; 557(7706): 457–459. PubMed Abstract \| Publisher Full Text\n\nSaric J, Käser F, Lys JA, et al.: Synergising research and service activities at swiss research institutions to accelerate sustainable development. Sustainability. 2021; 13(17). Publisher Full Text\n\nWay GP, Greene CS, Carninci P, et al.: A field guide to cultivating computational biology. PLoS Biol. 2021; 19(10): e3001419. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrinzel M, Brown J, Kaltenbrunner W, et al.: Ten ways to improve academic CVs for fairer research assessment. Hum. Soc. Sci. Comm. 2021; 8(1): 251. Publisher Full Text\n\nStroobants K: You can help to create a new researcher-reward system. Nature. 2021. PubMed Abstract \| Publisher Full Text\n\nGrove J: Retirement planning: Do compulsory retirement ages benefit the academy? The Times Higher Education Supplement. 2018 13/12/2018.\n\nHanson A, Bullers K, Howard AM, et al.: Using a Reflexive Process to Investigate Organizational Change: The Use of the Research Spider Matrix. Med. Ref. Serv. Q. 2019; 38(4): 312–325. PubMed Abstract \| Publisher Full Text\n\nAchmad S, Badu SQ, editors. Cultural Quality Revitalization Model in Strengthening The Higher Education Capacity Building ‘Good Learning Culture’. 1st Yogyakarta International Conference on Educational Management/Administration and Pedagogy (YICEMAP); 2017 2017 May 13; Yogyakarta, INDONESIA. 2017.\n\nRowtho V, Gopee S, Hingun A: Doctoral boot camps: from military concept to andragogy. Educ. Train. 2020; 62(4): 379–392. Publisher Full Text\n\nRussell S, Foulkes I: Embedding a positive research culture that fosters innovation. Nat. Rev. Cancer. 2019; 19(5): 241–242. PubMed Abstract \| Publisher Full Text\n\nAllen C, Mehler DMA: Open science challenges, benefits and tips in early career and beyond. PLoS Biol. 2019; 17(5). Publisher Full Text\n\nAnon.: Not all scientists are raised equal. Nature. Astronomy. 2017; 1(6): 0167. Publisher Full Text\n\nBallesteros-Rodríguez JL, De Saá-Pérez P, García-Carbonell N, et al.: The influence of team members’ motivation and leaders’ behaviour on scientific knowledge sharing in universities. Int. Rev. Adm. Sci. 2022; 88(2): 320–336. Publisher Full Text\n\nFusulier B, Barbier P, Dubois-Shaik F: “Navigating” through a scientific career: A question of private and professional configurational supports. Eur. Educ. Res. J. 2017; 16(2-3): 352–372. Publisher Full Text\n\nHinton A Jr, Lambert WM: Moving diversity, equity, and inclusion from opinion to evidence. Cell Rep Med. 2022; 3(4): 100619. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhalid S, Tadesse E: Faculty research productivity at women’s universities through the lens of preference theory. High. Educ. 2022; 83(5): 949–968. Publisher Full Text\n\nHernandez R, Hoffmann-Longtin K, Patrick S, et al.: The Conscientious Use of Images Illustrating Diversity in Medical Education Marketing. Acad. Med. 2020; 95(12): 1807–1810. PubMed Abstract \| Publisher Full Text\n\nHagan AK, Topçuoğlu BD, Gregory ME, et al.: Women are underrepresented and receive differential outcomes at asm journals: A six-year retrospective analysis. MBio. 2020; 11(6): 1–21. Publisher Full Text\n\nMadzima TF, MacIntosh GC: Equity, diversity, and inclusion efforts in professional societies: intention versus reaction. Plant Cell. 2021; 33(10): 3189–3193. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarshall A, Pack AD, Owusu SA, et al.: Responding and navigating racialized microaggressions in STEM. Pathog Dis. 2021; 79(5). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartinez LR, Boucaud DW, Casadevall A, et al.: Factors contributing to the success of NIH-designated underrepresented minorities in academic and nonacademic research positions. CBE Life Sci. Educ. 2018; 17(2): ar32. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcGill BM, Foster MJ, Pruitt AN, et al.: You are welcome here: A practical guide to diversity, equity, and inclusion for undergraduates embarking on an ecological research experience. Ecol. Evol. 2021; 11(8): 3636–3645. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMousa M: Academia is racist: Barriers women faculty face in academic public contexts. Higer Educ Q. 2021; 76: 741–758. Publisher Full Text\n\nPrasad A: Why are there still so few black scientists in the UK? The Observer (London). 2021 10/04/2021.\n\nSimpson JS, Giwa S, Denis VS: In times of racial injustice, university education should not be ‘neutral’. The Conversation. 2021. Reference Source\n\nSmith-Carrier TA, Benbow S, Lawlor A, et al.: “My only solution is to work later and sleep less”: exploring the perspectives of parenting in academia in Ontario, Canada. Equal Diversity Incl. 2021; 40(8): 930–946. Publisher Full Text\n\nZambas SI, Dutch S, Gerrard D: Factors influencing Maori student nurse retention and success: An integrative literature review. Nurse Educ. Today. 2020; 91: 104477. Publisher Full Text\n\nZhuwao S, Ngirande H, Ndlovu W, et al.: Gender diversity, ethnic diversity and employee performance in a South African higher education institution. SA J. Hum. Resour. Manag. 2019; 17: 17. Publisher Full Text\n\nFoxx AJ, Meléndez KPF, Hariharan J, et al.: Advancing equity and inclusion in microbiome research and training. mSystems. 2021; 6(5): e0115121. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEtzkorn KB, Braddock A: Are you my mentor? A study of faculty mentoring relationships in US higher education and the implications for tenure. Int. J. Mentor. Coach. Educ. 2020; 9(3): 221–237. Publisher Full Text\n\nMathieson C: 2017. Reference Source\n\nCallwood KAA, Weiss M, Hendricks R, et al.: Acknowledging and Supplanting White Supremacy Culture in Science Communication and STEM: The Role of Science Communication Trainers. Front. commun. 2022; 7: 7. Publisher Full Text\n\nCulpepper D, Reed AM, Enekwe B, et al.: A New Effort to Diversify Faculty: Postdoc-to-Tenure Track Conversion Models. Front. Psychol. 2021; 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrahe JE, Cuccolo K, Leighton DC, et al.: Open Science Promotes Diverse, Just, and Sustainable Research and Educational Outcomes. Psychol. Learn. Teach. 2020; 19(1): 5–20. Publisher Full Text\n\nGutierrez-Wu J, Lawrence C, Jamison S, et al.: An evaluation of programs designed to increase representation of diverse faculty at academic medical centers. J. Natl. Med. Assoc. 2022; 114: 278–289. PubMed Abstract \| Publisher Full Text\n\nHagan AK, Pollet RM, Libertucci J: Suggestions for improving invited speaker diversity to reflect trainee diversity. J Microbiol Biol Educ. 2020; 21(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoy KE, Fitzgibbon BM, Brem AK: Lessons from an initiative to address gender bias. elife. 2021; 10(12): 15. Publisher Full Text\n\nAnon: Slate that disputes command of USP proposes body to take care of inclusion and diversity. CE Noticias Financieras English. 2021. 06/10/2021.\n\nBatty D, Davis N: Why science breeds a culture of sexism. The Guardian.2018. Reference Source\n\nBinns C: How to make universities more inclusive? Hire more working-class academics. The Conversation. 2020. Reference Source\n\nLambert WM, Wells MT, Cipriano MF, et al.: Research culture: Career choices of underrepresented and female postdocs in the biomedical sciences. elife. 2020; 9: 9. Publisher Full Text\n\nLee A: Toward a conceptual model of hierarchical microaggression in higher education settings: a literature review. Educ. Rev. 2022; 74(2): 321–352. Publisher Full Text\n\nLeišytė L, Deem R, Tzanakou C: Inclusive universities in a globalized world. Soc. Incl. 2021; 9(3): 1–5. Publisher Full Text\n\nMehta D, Bediako Y, de Winde CM , et al.: Ways to increase equity, diversity and inclusion. elife. 2020; 9(07): 07. Publisher Full Text\n\nO’Meara K, Nyunt G, Templeton L, et al.: Meeting to transgress The role of faculty learning communities in shaping more inclusive organizational cultures. Equal. Divers. Incl. 2019; 38(3): 286–304. Publisher Full Text\n\nPicardi I: The glass door of academia: Unveiling new gendered bias in academic recruitment. Soc. Sci. 2019; 8(5). Publisher Full Text\n\nFrketich J: McMaster vows to increase diversity among researchers. The Hamilton Spectator (Ontario, Canada). 2019 31/05/2019.\n\nLaw SF, Croucher G: Most of Australia’s uni leaders are white, male and grey. This lack of diversity could be a handicap. The Conversation. 2020. Reference Source\n\nMcIntyre A: Vice-chancellor marks one year at Leeds Trinity. Ilkley Gazette. 2021 02/11/2021.\n\nStack M: Why I’m not surprised Nobel Laureate Donna Strickland isn’t a full professor. The Conversation. 2018. Reference Source\n\nWoolston: Satisfaction in science Nature.2018; 562(7728): 611–614.\n\nFarrugia G, Zorn CK, Williams AW, et al.: A Qualitative Analysis of Career Advice Given to Women Leaders in an Academic Medical Center. JAMA Netw. Open. 2020; 3(7): e2011292. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLinková M: Academic excellence and gender bias in the practices and perceptions of scientists in leadership and decision-making positions. Gend Vyzk/Gend Res. 2017; 18(1): 42–66. Publisher Full Text\n\nNoble CE, Amey MJ, Colon LA, et al.: Building a Networked Improvement Community: Lessons in Organizing to Promote Diversity, Equity, and Inclusion in Science, Technology, Engineering, and Mathematics. Front. Psychol. 2021; 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchipull EM, Quichocho XR, Close EW, editors. “Success Together”: Physics departmental practices supporting LGBTQ plus women and women of color. Physics Education Research (PER) Conference; 2019 2019 Jul 24-25; Provo, UT. 2019.\n\nVega BE: “What Is the Real Belief on Campus?” Perceptions of Racial Conflict at a Minority-Serving Institution and a Historically White Institution. Teach. Coll. Rec. 2021; 123(9): 144–170. Publisher Full Text\n\nHuang CKK, Wilson K, Neylon C, et al.: Mapping open knowledge institutions: an exploratory analysis of Australian universities. PeerJ. 2021; 9: e11391. Publisher Full Text\n\nSusi T, Shalvi S, Srinivas M: ‘I’ll work on it over the weekend’: high workload and other pressures faced by early-career researchers. Nature. 2019. Publisher Full Text\n\nAkbar A, Picard M: Academic integrity in the Muslim world: a conceptual map of challenges of culture. Int. J. Educ. Integr. 2020; 16(1). Publisher Full Text\n\nPage T, Bull A, Chapman E: Making Power Visible: “Slow Activism” to Address Staff Sexual Misconduct in Higher Education. Violence Against Women. 2019; 25(11): 1309–1330. PubMed Abstract \| Publisher Full Text\n\nCresiski RH, Ghent CA, Rutledge JC, et al.: Developing a State University System Model to Diversify Faculty in the Biomedical Sciences. Front. Psychol. 2022; 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCorrea Vera YE, Montoya Monsalve JN, editors. Women’s Access to Research: Mexico. International Conference on Gender Research (ICGR); 2018 2018 Apr 12-13; ISCAP, P Porto, Porto, PORTUGAL. 2018.\n\nChapman A: Using the assessment process to overcome Imposter Syndrome in mature students. J. Furth. High. Educ. 2017; 41(2): 112–119. Publisher Full Text\n\nLee JE, Sung JH, Sarpong D, et al.: Knowledge Management for Fostering Biostatistical Collaboration within a Research Network: The RTRN Case Study. Int. J. Environ. Res. Public Health. 2018; 15(11): 12.\n\nFox N: 142 Open Science: Improving Access and Reducing Bias in Science. J. Anim. Sci. 2021; 99: 75–76. Publisher Full Text\n\nCampbell-Whatley G, O’Brien C, Reddig K, et al.: Non-majority student perceptions of diversity and inclusion at a PWI and an HBCU. J. Multicult. Educ. 2021; 15(3): 253–269. Publisher Full Text\n\nLundwall RA: Changing institutional incentives to foster sound scientific practices: One department. Infant Behav. Dev. 2019; 55: 69–76. PubMed Abstract \| Publisher Full Text\n\nSotomayor-Beltran C, Zarate Segura GW: Peruvian Scientific Production Affected by Predatory Journals. Int. Inf. Libr. Rev. 2022; 54(1): 32–38. Publisher Full Text\n\nBothwell E: US research culture stuck in past, says cancer expert. The Times Higher Education Supplement. 2017 08/07/2017.\n\nAbeysiriwardana PC, Jayasinghe-Mudalige UK: Role of key performance indicators on agile transformation of performance management in research institutes towards innovative commercial agriculture. J. Sci. Technol. Policy Manage. 2021; 13: 213–243. Publisher Full Text\n\nAdefuye AO, Coetzee L, Janse van Vuuren C, et al.: Medical Educators’ Perceptions of Research Culture in a Faculty of Health Sciences: A South African Study. Teach. Learn. Med. 2021; 33(5): 509–524. PubMed Abstract \| Publisher Full Text\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(1): e012332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoffmann K, Berg S, Koufogiannakis D: Understanding factors that encourage research productivity for academic librarians. Evid. Based Libr. Inf. Pract. 2017; 12(4): 102–128. Publisher Full Text\n\nKöse MF, Korkmaz M: Why are some universities better? An evaluation in terms of organizational culture and academic performance. High. Educ. Res. Dev. 2019; 38(6): 1213–1226. Publisher Full Text\n\nLuqman MS, Rehman JU, Islam ZU, et al.: Effect of organizational climate upon the job performance of instructors’ physical education. Pedagogy Phys. Cult. Sports. 2020; 24(2): 72–76. Publisher Full Text\n\nMbeo MA, Rambe P, editors. Managing academic resistance to research of academics at a university of technology. 15th International Conference on Intellectual Capital, Knowledge Management and Organisational Learning, ICICKM 2018; Academic Conferences and Publishing International Limited. 2018.\n\nOlesen AP, Amin L, Mahadi Z: Malaysian researchers talk about the influence of culture on research misconduct in higher learning institutions. Accountability in Research-Policies and Quality Assurance. 2017; 24(8): 469–482. Publisher Full Text\n\nPapatsiba V, Cohen E: Institutional hierarchies and research impact: new academic currencies, capital and position-taking in UK higher education. Br. J. Sociol. Educ. 2020; 41(2): 178–196. Publisher Full Text\n\nSaplan DMM: An innovation to heighten research culture in selected colleges of nursing in Region IX, Philippines. Int. J. Innov. Creat Change. 2020; 12(6): 307–322.\n\nShen W, Jiang J: Institutional prestige, academic supervision and research productivity of international PhD students: Evidence from Chinese returnees. J. Sociol. 2021; 59: 552–579. Publisher Full Text\n\nSuson RL, Capuno R, Manalastas R, et al.: Educational research productivity road map: Conclusions from the identified research barriers and variables. Cypriot J. Educ. Sci. 2020; 15(5): 1160–1175. Publisher Full Text\n\nVachon B, Curran JA, Karunananthan S, et al.: Changing research culture toward more use of replication research: a narrative review of barriers and strategies. J. Clin. Epidemiol. 2021; 129: 21–30. PubMed Abstract \| Publisher Full Text\n\nVuong QH, Napier NK, Ho TM, et al.: Effects of work environment and collaboration on research productivity in Vietnamese social sciences: evidence from 2008 to 2017 scopus data. Stud. High. Educ. 2019; 44(12): 2132–2147. Publisher Full Text\n\nMatthews D: Research funders urge caution over demanding ‘excellence’. The Times Higher Education Supplement. 2020 23/07/2020.\n\nWarren C: ‘Professors eat their own young’: how competition can stifle good science. The Guardian. 2018.\n\nBishop DVM: The psychology of experimental psychologists: Overcoming cognitive constraints to improve research: The 47th Sir Frederic Bartlett Lecture. Q. J. Exp. Psychol. 2020; 73(1): 1–19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChandler N, Heidrich B, Kasa R: Everything changes? A repeated cross-sectional study of organisational culture in the public sector. Evidence-Based Hrm-a Global Forum for Empirical Scholarship. 2017; 5(3): 283–296. Publisher Full Text\n\nHenry C, Md Ghani NA, Hamid UMA, et al.: Factors contributing towards research productivity in higher education. Int. J. Eval. Res. Educ. 2020; 9(1): 203–211. Publisher Full Text\n\nWaters AM, LeBeau RT, Young KS, et al.: Towards the enhancement of quality publication practices in clinical psychological science. Behav. Res. Ther. 2020; 124: 103499. PubMed Abstract \| Publisher Full Text\n\nHeuritsch J: Towards a democratic university: A call for reflexive evaluation and a participative culture.2021b.\n\nKouper I, Raymond AH, Giroux S: An Exploratory Study of Research Data Governance in the U.S. Open Inf. Sci. 2020; 4(1): 122–142.\n\nAjjawi R, Crampton PES, Rees CE: What really matters for successful research environments? A realist synthesis. Med. Educ. 2018; 52(9): 936–950. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChuanfu C, Qiushi L: Library Development in an Open Society. J. Lib. Sci. China. 2020; 46(1): 16–37.\n\nSarabipour S: Virtual conferences raise standards for accessibility and interactions. elife. 2020; 9(11): 04. Publisher Full Text\n\nAdetayo AJ: The Nexus of Social Media Use and Research Productivity of Lecturers in Private Universities in Ogun State, Nigeria. Libr. Philos. Pract. 2021; 2021: 1–14.\n\nCausadias JM, Korous KM, Cahill KM, et al.: The Importance of Research About Research on Culture: A Call for Meta-research on Culture. Cult. Divers. Ethn. Minor. Psychol. 2021.\n\nPalotie P, Nurkka P, Juvonen S, editors. The quality matters - the experiences of a project manager training 10th Annual International Conference of Education, Research and Innovation (ICERI); 2017 2017 Nov 16-18; Seville, SPAIN.2017.\n\nVarma S: Why learn business ethics?-Students’ conceptions of the use and exchange value of applied business ethics. Asian J. Bus. Ethics. 2019; 8(1): 107–125. Publisher Full Text\n\nCrewe R, Gevers W: How to approach the revolution in scholarly publishing. The Conversation. 2019. Reference Source\n\nCurry S: It’s time for academics to take back control of research journals. The Guardian. 2017.\n\nFyfe A, Coate K, Curry S: Untangling academic publishing: A history of the relationship between commercial interests, academic prestige and the circulation of research. Zendo. 2017.\n\nHeuritsch J: Reflexive Behaviour: How publication pressure affects research quality in Astronomy.2021.\n\nKirchherr J: Why we can’t trust academic journals to tell the scientific truth. The Guardian. 2017.\n\nLeyser O, Kingsley D, Grange J: The science ‘reproducibility crisis’ – and what can be done about it. The Conversation. 2017. Reference Source\n\nHeng K, Hamid MO, Khan A: Factors influencing academics’ research engagement and productivity: A developing countries perspective. Issues Educ. Res. 2020; 30(3): 965–987.\n\nGonzalez-Diaz R, Acevedo-Duque Á, Martin-Fiorino V, et al.: Latin American professors’ research culture in the digital age. Comunicar. 2022; 30(70): 71–83. Publisher Full Text\n\nLourdes ESL, Frontera WR, Huertas A: 4143 HiREC Endowment: Building Models in Research Capacity for Infrastructure Sustainability and Productivity. J. Clin. Transl. Sci. 2020; 4(s1): 62–63. Publisher Full Text\n\nRoesdiono E, Saptandari PEP, Suminar DR: Employee retention at ‘Precious’ English language course in Surabaya. Masyarakat Kebudayaan Dan Politik. 2019; 32(1): 95–104. Publisher Full Text\n\nRobson SG, Baum MA, Beaudry JL, et al.: Promoting open science: A holistic approach to changing behaviour. Collabra Phychol. 2021; 7(1). Publisher Full Text\n\nMunafò MR, Chambers C, Collins A, et al.: The reproducibility debate is an opportunity, not a crisis. BMC. Res. Notes. 2022; 15(1): 43. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnon.: Psychology accused of ‘collective self-deception’ over results. The Times Higher Educations Supplement. 2019 12/12/2019.\n\nDominik M, Nzweundji JG, Ahmed N, et al.: Open Science-For Whom? Data Sci. J. 2022; 21(1). Publisher Full Text\n\nEdelmann N, Schoßböck J: Open access perceptions, strategies, and digital literacies: A case study of a scholarly-led journal. Publ. 2020; 8(3). Publisher Full Text\n\nGarcia-Guerrero M, Ramirez-Montoya MS, Garcia-Penalvo FJ, editors. Towards an Open Science technological ecosystem for a Mexican University. 8th International Conference on Technological Ecosystems for Enhancing Multiculturality, TEEM 2020, October 21, 2020 - October 23, 2020; 2020; Virtual, Online, Spain: Association for Computing Machinery.\n\nGold ER, Ali-Khan SE, Allen L, et al.: An open toolkit for tracking open science partnership implementation and impact [version 2; peer review: 2 approved]. Gates Open Res. 2019; 3: 1442. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHammatt Z: Spotlight on research integrity: international insights on strengthening research culture in the forensic sciences and beyond. Forensic Sci. Res. 2021; 6(4): 281–282. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHatch A, Curry S: Changing how we evaluate research is difficult, but not impossible. elife. 2020; 9(08): 12. Publisher Full Text\n\nKoroshetz WJ, Behrman S, Brame CJ, et al.: Framework for advancing rigorous research. elife. 2020; 9: 9. Publisher Full Text\n\nKoterwas A, Dwojak-Matras A, Kalinowska K: Dialogical teaching of research integrity: an overview of selected methods. Facet. 2021; 6: 2138–2154. Publisher Full Text\n\nMa L: Money, morale, and motivation: A study of the Output-Based Research Support Scheme in University College Dublin. Res. Eval. 2019; 28(4): 304–312. Publisher Full Text\n\nMarques M, Powell JJW, Zapp M, et al.: How does research evaluation impact educational research? Exploring intended and unintended consequences of research assessment in the United Kingdom, 1986–2014. Eur. Educ. Res. J. 2017; 16(6): 820–842. Publisher Full Text\n\nMebane CA, Sumpter JP, Fairbrother A, et al.: Scientific integrity issues in Environmental Toxicology and Chemistry: Improving research reproducibility, credibility, and transparency. Integr. Environ. Assess. Manag. 2019; 15(3): 320–344. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSeverin A, Egger M, Eve MP, et al.: Discipline-specific open access publishing practices and barriers to change: an evidence-based review. F1000Res. 2018; 7: 1925. Publisher Full Text\n\nStracke CM: Open Science and Radical Solutions for Diversity, Equity and Quality in Research: A Literature Review of Different Research Schools, Philosophies and Frameworks and Their Potential Impact on Science and Education. Lecture Notes in Educational Technology: Springer. 2020; pp. 17–37.\n\nTecwyn EC: Doing reliable research in comparative psychology: Challenges and proposals for improvement. J. Comp. Psychol. 2021; 135(3): 291–301. PubMed Abstract \| Publisher Full Text\n\nWilliams M, Mullane K, Curtis MJ: Addressing Reproducibility: Peer Review, Impact Factors, Checklists, Guidelines, and Reproducibility Initiatives. Research in the Biomedical Sciences: Transparent and Reproducible: Elsevier. 2018; 197–306. Publisher Full Text\n\nWoolston C: Australian junior scientists report damaging lack of support at work. Nature. 2020; 579: 457–458. PubMed Abstract \| Publisher Full Text\n\nAbbott LE, Andes A, Pattani AC, et al.: Authorship Not Taught and Not Caught in Undergraduate Research Experiences at a Research University. Sci. Eng. Ethics. 2020; 26(5): 2555–2599. PubMed Abstract \| Publisher Full Text\n\nBaker S: Managers who ‘fetishise’ certain journals warp incentive culture. The Times Higher Education Supplement. 2019 14/11/2019.\n\nBanks GC, Field JG, Oswald FL, et al.: Answers to 18 Questions About Open Science Practices. J. Bus. Psychol. 2019; 34(3): 257–270. Publisher Full Text\n\nBaskin P: Top-tier US universities push for open science. Times. High. Educ. 2022 20/04/2022.\n\nBonn NA, Pinxten W: Rethinking success, integrity, and culture in research (part 2) - a multi-actor qualitative study on problems of science. Research Integrity and Peer Review. 2021; 6(1). Publisher Full Text\n\nBornmann L, Guns R, Thelwall M, et al.: Which aspects of the open science agenda are most relevant to scientometric research and publishing? An opinion paper. Quantitative Sci Stud. 2021; 2(2): 438–453. Publisher Full Text\n\nCenter for Open Science: Effort to repeat key cancer biology experiments reveals challenges and opportunities to improve replicability. The Breeze: James Madison University; 2021 07/12/2021.\n\nGersten P: EPA Transparency Rule Will Bolster Science and Improve Rulemaking. Competitive Enterprise Institute; 2018 16/07/2018.\n\nMiguel E: Evidence on research transparency in economics. J. Econ. Perspect. 2021; 35(3): 193–214. Publisher Full Text\n\nMullard A: Half of top cancer studies fail high-profile reproducibility effort. Nature. 2021; 600: 368–369. PubMed Abstract \| Publisher Full Text\n\nStall S, Yarmey L, Cutcher-Gershenfeld J, et al.: Make scientific data FAIR. Nature. 2019; 570: 27–29. Publisher Full Text\n\nTegbaru D, Braverman L, Zietman AL, et al.: ASTRO Journals’ Data Sharing Policy and Recommended Best Practices. Adv. Radiat. Oncol. 2019; 4(4): 551–558. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZuiderwijk A, Shinde R, Jeng W: What drives and inhibits researchers to share and use open research data? A systematic literature review to analyze factors influencing open research data adoption. PLoS One. 2020; 15(9 September): e0239283. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCumyn A, Ouellet K, Côté AM, et al.: Role of Researchers in the Ethical Conduct of Research: A Discourse Analysis From Different Stakeholder Perspectives. Ethics Behav. 2019; 29(8): 621–636. Publisher Full Text\n\nFeng GC: Research Performance Evaluation in China: A Big Data Analysis. SAGE Open. 2020; 10(1): 215824401990125. Publisher Full Text\n\nLabib K, Roje R, Bouter L, et al.: Important Topics for Fostering Research Integrity by Research Performing and Research Funding Organizations: A Delphi Consensus Study. Sci. Eng. Ethics. 2021; 27(4): 47. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartin-Sardesai A, Guthrie J, Tooley S, et al.: History of research performance measurement systems in the Australian higher education sector. Account. Hist. 2019; 24(1): 40–61. Publisher Full Text\n\nSuls J, Rothman AJ, Davidson KW: Now Is the Time to Assess the Effects of Open Science Practices With Randomized Control Trials. Am. Psychol. 2021; 1–9.\n\nFlake JK: Strengthening the foundation of educational psychology by integrating construct validation into open science reform. Educ. Psychol. 2021; 56(2): 132–141. Publisher Full Text\n\nHolst MR, Faust A, Strech D: Do German university medical centres promote robust and transparent research? A cross-sectional study of institutional policies. Health Res. Policy Syst. 2022; 20(1): 39. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHorn L: Promoting Responsible Research Conduct: A South African Perspective. J. Acad. Ethics. 2017; 15(1): 59–72. Publisher Full Text\n\nMoher D, Naudet F, Cristea IA, et al.: Assessing scientists for hiring, promotion, and tenure. PLoS Biol. 2018; 16(3): e2004089. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaxton A, Tullett A: Open Science in Data-Intensive Psychology and Cognitive Science. Policy Insights Behav. Brain Sci. 2019; 6(1): 47–55. Publisher Full Text\n\nSatalkar P, Perneger T, Shaw D: Accommodating an Uninvited Guest: Perspectives of Researchers in Switzerland on ‘Honorary’ Authorship. Sci. Eng. Ethics. 2020; 26(2): 947–967. PubMed Abstract \| Publisher Full Text\n\nŠčepanović R, Labib K, Buljan I, et al.: Practices for Research Integrity Promotion in Research Performing Organisations and Research Funding Organisations: A Scoping Review. Sci. Eng. Ethics. 2021; 27(1): 4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmidt R, Curry S, Hatch A: Creating SPACE to evolve academic assessment. elife. 2021; 10(09): 23.\n\nSchroter S, Montagni I, Loder E, et al.: Awareness, usage and perceptions of authorship guidelines: An international survey of biomedical authors. BMJ Open. 2020; 10(9): e036899. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStremersch S, Winer RS, Camacho N: Faculty Research Incentives and Business School Health: A New Perspective from and for Marketing. J. Mark. 2021; 85(5): 1–21. Publisher Full Text\n\nLi D, Li Y: Masked Resistance in Neoliberal Academia: Academics’ Responses to the Research Assessment Exercise 2020 in Hong Kong. High Educ. Pol. 2021; 36: 270–288. Publisher Full Text\n\nChubb J, Cowling P, Reed D: Speeding up to keep up: exploring the use of AI in the research process. AI Soc. 2021; 37: 1439–1457. Publisher Full Text\n\nCurtis GJ, Slade C, Bretag T, et al.: Developing and evaluating nationwide expert-delivered academic integrity workshops for the higher education sector in Australia. High. Educ. Res. Dev. 2021; 41: 665–680. Publisher Full Text\n\nFussy DS: The hurdles to fostering research in Tanzanian universities. High. Educ. 2019; 77(2): 283–299. Publisher Full Text\n\nHelgesson G, Bülow W: Research Integrity and Hidden Value Conflicts. J. Acad. Ethics. 2021; 21: 113–123. Publisher Full Text\n\nMunafò MR, Nosek BA, Bishop DVM, et al.: A manifesto for reproducible science. Nat. Hum. Behav. 2017; 1(1). Publisher Full Text\n\nAleman-Juarez A, Becerra-Mariscal AE, Garcia-Higuera MC, editors. Revista de intergridad academica: An effort to foster academic integrity in Universidad Panamericana 10th International Conference on Education and New Learning Technologies (EDULEARN); 2018 2018 Jul 02-04; Palma, SPAIN.2018.\n\nAntes AL, Kuykendall A, DuBois JM: The lab management practices of “Research Exemplars” that foster research rigor and regulatory compliance: A qualitative study of successful principal investigators. PLoS One. 2019; 14(4): e0214595. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrunt MW, Weary DM: Perceptions of laboratory animal facility managers regarding institutional transparency. PLoS One. 2021; 16(7): e0254279. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElliott KC, Resnik DB: Making open science work for science and society. Environ. Health Perspect. 2019; 127(7): 75002. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGallagher RV, Falster DS, Maitner BS, et al.: Open Science principles for accelerating trait-based science across the Tree of Life. Nat. Ecol. Evol. 2020; 4(3): 294–303. PubMed Abstract \| Publisher Full Text\n\nKraft-Todd GT, Rand DG: Practice what you preach: Credibility-enhancing displays and the growth of open science. Organ. Behav. Hum. Decis. Process. 2021; 164: 1–10. Publisher Full Text\n\nMullane K, Curtis MJ, Williams M: Biomedical Research in the 21st Century: Multiple Challenges in Resolving Reproducibility Issues. Research in the Biomedical Sciences: Transparent and Reproducible. Elsevier; 2018; 307–353.\n\nOfori G: Professionalism in built environment research: beyond integrity and good practice. Eng. Constr. Archit. Manag. 2021; 29: 3617–3646. Publisher Full Text\n\nRoche DG, O’Dea RE, Kerr KA, et al.: Closing the knowledge-action gap in conservation with open science. Conserv. Biol. 2021; 36. Publisher Full Text\n\nRoje R, Tomić V, Buljan I, et al.: Development and implementation of research integrity guidance documents: Explorative interviews with research integrity experts. Account. Res. 2021; 30: 293–330. Publisher Full Text\n\nSatalkar P, Shaw D: How do researchers acquire and develop notions of research integrity? A qualitative study among biomedical researchers in Switzerland. BMC Med. Ethics. 2019; 20(1): 72. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTang L, Cao C, Lien D, et al.: The Effects of Anti-corruption Campaign on Research Grant Reimbursement: Regression Discontinuity Evidence from China. Sci. Eng. Ethics. 2020; 26(6): 3415–3436. PubMed Abstract \| Publisher Full Text\n\nTijdink JK, Horbach SPJM, Nuijten MB, et al.: Towards a Research Agenda for Promoting Responsible Research Practices. J. Empir. Res. Hum. Res. Ethics. 2021; 16(4): 450–460. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCervini E: Transparency key to cutting dodgy research: Dutch expert. The Australian. 2018 06/06/2018.\n\nFidler F, Fraser H: Our survey found ‘questionable research practices’ by ecologists and biologists – here’s what that means. The Conversation. 2018. Reference Source\n\nMacleod M: Want research integrity? Stop the blame game. Nature. 2021; 599: 533. PubMed Abstract \| Publisher Full Text\n\nMunafò M: Raising research quality will require collective action. Nature. 2019; 576: 183. PubMed Abstract \| Publisher Full Text\n\nValkenburg G, Dix G, Tijdink J, et al.: Expanding Research Integrity: A Cultural-Practice Perspective. Sci. Eng. Ethics. 2021; 27(1): 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZwart H, Ruud ter M: Addressing research integrity challenges: from penalising individual perpetrators to fostering research ecosystem quality care. Life Sci. Soc. Policy. 2019; 15(1): 1–5. Publisher Full Text\n\nFeinberg M, Sutherland W, Nelson SB, et al.: The New Reality of Reproducibility: The Role of Data Work in Scientific Research. Proc ACM Hum Comput Interact. 2020; 4(CSCW1): 1–22. Publisher Full Text\n\nGilmore RO, Diaz MT, Wyble BA, et al.: Progress toward openness, transparency, and reproducibility in cognitive neuroscience. Annals of the New York Academy of Sciences. Blackwell Publishing Inc.; 2017; pp. 5–18.\n\nGurgu E, Tonis RB-M, Avram LG, et al.: Applicability of the ethics management tools in Romanian academia. Indep. J. Manag. Prod. 2020; 11(7): 2709–2732. Publisher Full Text\n\nLeonelli S: Global data quality assessment and the situated nature of “best” research practices in biology. Data Sci. J. 2017; 16. Publisher Full Text\n\nMische SM, Fisher NC, Meyn SM, et al.: A review of the scientific rigor, reproducibility, and transparency studies conducted by the ABRF research groups. J. Biomol. Tech. 2020; 31(1): 11–26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoher D: COVID-19 and the research scholarship ecosystem: help! J. Clin. Epidemiol. 2021; 137: 133–136. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRastogi S: Making ASU ethics committees more productive: Responsible research needs more than developing the guidelines. J. Ayurveda Integr. Med. 2021; 12(1): 191–194. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRhaiem M, Amara N: Determinants of research efficiency in Canadian business schools: evidence from scholar-level data. Scientometrics. 2020; 125(1): 53–99. Publisher Full Text\n\nSatalkar P, Shaw D: Is failure to raise concerns about misconduct a breach of integrity? Researchers’ reflections on reporting misconduct. Account. Res. 2018; 25(6): 311–339. PubMed Abstract \| Publisher Full Text\n\nSpitschan M, Schmidt MH, Blume C: Transparency And Open Science Principles In Reporting Guidelines In Sleep Research And Chronobiology Journals [Version 1; Peer Review: 3 Approved With Reservations]. Wellcome Open Res. 2020; 5: 1–25. Publisher Full Text\n\nStagge JH, Rosenberg DE, Abdallah AM, et al.: Assessing data availability and research reproducibility in hydrology and water resources. Sci. Data. 2019; 6: 6. Publisher Full Text\n\nChristensen G, Freese J, Miguel E: Transparent and reproducible social science research: How to do open science. University of California Press; 2019; 1–272.\n\nWoutersen-Windhouwer S, Rodríguez EM, Sondervan J, et al.: Consolidating institutional repositories in a digital, free, open access publication platform for all scholarly output. LIBER Q. 2020; 30(1): 1–15. Publisher Full Text\n\nZinchenko V, Ostapenko S, Udovichenko H: Introduction of Academic Honesty as a Necessary Prerequisite and an Important Component of Quality Education for Future Economists. Revista Romaneasca Pentru Educatie Multidimensionala. 2021; 13(1): 81–95. Publisher Full Text\n\nAnsar, editor Implementation of Total Quality Management in Higher Education (A Case of State University of Gorontalo, Indonesia). 9th International Conference for Science Educators and Teachers (ICSET); 2017 2017 Sep 13-15; Indonesia. 2017.\n\nChapman AL, Greenhow C: Citizen-scholars: Social media and the changing nature of scholarship. Publ. 2019; 7(1). Publisher Full Text\n\nDougherty MR, Slevc LR, Grand JA: Making Research Evaluation More Transparent: Aligning Research Philosophy, Institutional Values, and Reporting. Perspect. Psychol. Sci. 2019; 14(3): 361–375. PubMed Abstract \| Publisher Full Text\n\nOlsen J, Mosen J, Voracek M, et al.: Research practices and statistical reporting quality in 250 economic psychology master’s theses: a meta-research investigation. R. Soc. Open Sci. 2019; 6(12): 190738. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeugelsdijk S, van Witteloostuijn A , Meyer KE: A new approach to data access and research transparency (DART). J. Int. Bus. Stud. 2020; 51(6): 887–905. Publisher Full Text\n\nWingen T, Berkessel JB, Englich B: No Replication, No Trust? How Low Replicability Influences Trust in Psychology. Soc. Psychol. Personal. Sci. 2020; 11(4): 454–463. Publisher Full Text\n\nBhattacharya N, Langhout RD, Vaccarino-Ruiz SS, et al.: \"Being a team of five strong women horizontal ellipsis we had to make an impression:\" The College Math Academy as an intervention into mathematics education. Am. J. Community Psychol. 2021; 70: 228–241. Publisher Full Text\n\nBlatch-Jones A, Lakin K, Thomas S: A scoping review on what constitutes a good research culture. (dat aset). OSF. 2024." }	[ { "id": "277506", "date": "23 May 2024", "name": "Steven De Peuter", "expertise": [ "Reviewer Expertise Research integrity", "research culture", "behavior change", "health psychology", "change 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\nI have read this scoping review with interest. The authors have compiled and synthesized an impressive collection of works, both from academic sources and from popular sources. I was pleasantly surprised to see that they even included two podcasts.\nThe authors not only review aspects of the research culture that are problematic. They also search the literature for evidence of what constitutes a good research culture and what can be done to promote it. That they limit their search to recently published material is not problematic: only recently has the shift been made from “codification and compliance” and from preventing the bad from happening towards promoting a healthy climate. It allows researchers and policy makers to get a better view on what is currently known about good research culture. The paper’s recommendations are clear and impressively complete, excellently summarizing the collected evidence, both in the text and in the clearly structured and comprehensive tables. The structure of the themes is also intuitive.\nI applaud the authors for their work and I want to emphasize that I consider this a relevant, solid, and quite exhaustive review. I have, however, a number of (minor) comments that I list below. Their purpose is solely to improve the relevance and reach of the paper, which I believe deserves a wide audience.\n\nBackground, Discussion, Conclusions\nThe Background section is very much to the point. For readers who are familiar with the topic of research culture, it is sufficient to have the high-level overview of the main points that the paper currently provides. For interested readers who are less familiar with the topic the background section may be too high-level. The overview remains abstract and could benefit from more specific information and examples. For example, what is “the potential negative impact of a poor research culture / the consequences and challenges associated to an inadequate research culture”? What are some recommendations from the “international actions to address the underlying drivers of poor research culture”? (Which drivers are there?)\nRelated to this, I think the Dicussion section would benefit from a brief recap of the main findings in the first paragraph(s), instead of just stating “From the evidence, it was clear that there were several initiatives to seek a cultural change across the research institutions/Higher Education Institutions.” The same applies to the conclusions. The authors correctly and rightfully emphasize the fact that “research institutions cannot act in isolation”, but in my opinion some of the findings deserve equal emphasis – and therefore being mentioned in the conclusions. In general, I think one of the conclusions could also be that there is a lot that can be done and that the evidence base for promoting a good research culture is substantial.\nWhen reading the paper, it felt a bit like I was reading a – very well written – internal report for policy makers who are knowledgeable of the potential problems with(in) research culture. I think it can be leveraged to also appeal to a broader audience.\n\nMethods\nThe Types of sources section confused me when I first read it, leading me to think that only empirical papers (“studies”) were included. Further on, it became evident that the authors included a wide variety of contributions. I suggest adding a first sentence to this section describing this, then continue by detailing the various types of studies and data that were included as it is currently documented.\n\nResults\nThe PRIMSA flow diagram (Figure 1) is incorrect. The total of the “Full-text articles excluded, with reasons (n = 513)” differs from the sum of the specific reasons (sum = 670). It appears that the latter is correct, because 924 papers screened – 670 excluded equals 254 included. Please note that there is still one paper that seems to have disappeared: Figure 1 and the main text mention 253 included papers, not 254. Unfortunately, in spite of the impressive amount of information that is confined in the Tables and despite my admiration for the work the authors must have put into presenting the evidence this way, there are inconsistencies between the number of references that are mentioned with the statements and the last column of the tables. You could consider this comment as an obsessive form of nitpicking from my part. I am aware of that. However, I believe that having a complete overview of the evidence associated with each statement will allow future readers to consult the relevant sources.\nTable 2 Theme Promote fair and transparent process for career progression Statement 2: number of references with statement = 39; last column = 35 Statement 3: number of references with statement = 29; last column = 30 Statement 6: number of references with statement = 20; last column = 21 Theme Reduce hyper competition and provide a culture of kindness Statement 2: number of references with statement = 23; last column = 24 Theme Cultivate a culture of support that fosters a diverse set of skills and career pathways Statement 1: number of references with statement = 33; last column = 34 Statement 4: number of references with statement = 26; last column = 27\nTable 3 Theme Embed and support an inclusive culture Statement 1: number of references with statement = 44; last column = 43 Statement 2: number of references with statement = 40; last column = 41 Theme Investing in people to reduce burden and improve wellbeing Statement 1: number of references with statement = 39; last column = 42 Statement 3: number of references with statement = 24; last column = 27\nTable 4 Theme Everyone feeling valued and having equality of opportunities to contribute Statement 2: number of references with statement = 25; last column = 24\nTable 5 Theme Creation and facilitation Statement 1: number of references with statement = 73; last column = 74 Statement 2: number of references with statement = 54 (!!!); last column = 71 Statement 3: number of references with statement = 45; last column = 46 Statement 4: number of references with statement = 43; last column = 44 Theme Fostering transparency and visibility Statement 2: number of references with statement = 49; last column = 51 Statement 3: number of references with statement = 37; last column = 38 Statement 6: number of references with statement = 12; last column = 13\n\nStudy strengths and limitations\nFirst paragraph: I would suggest to also include the percentage of articles from the USA, analogous to Canada and other international countries.\n\nGeneral comments\nSome of the sentences feel odd. For example, in Wellbeing and equality of opportunity, second paragraph, “The evidence suggests that these issues have an impact not only at the institutional level such as having a lack of diversity in organisational leaderships, but also for individuals, leading to a lack of role models and peer mentors skills shortages in particular disciplines, sectors and roles, and drives off talent.” is a run-on and feels like a collation of several sentences. Please check. Some of the Statements in the tables are also long and may better be divided into several shorter sentences. Some examples: Table 2, Statement 3 under theme Reduce hyper competition and provide a culture of kindness “Consider ways to demonstrate support for other researchers to secure funding as part of progression (and review current reward systems), ensuring education, teaching and research are equally prioritised”: who is referred to by “other”? Table 5, under theme Fostering transparency and visibility Statements 2 and 7 feel odd. It seems like parts of the statements are missing. Please reformulate.\n\nTypo’s\nAbbreviations list COPE is the “Committee on Publication Ethics”, not “of” – the same typo is in Table 5 (theme “Fostering transparency and visibility” number 3 “Gain greater understanding…”) ENRI: do the authors mean European Network of Research Integrity Offices (ENRIO - https://www.enrio.eu/), or maybe ENERI, the “European Network for Research Ethics and Integrity” (https://eneri.eu)? If corrected, please also correct the mention of ENRI in Table 5 (same place as COPE) and in the last paragraph before the Discussion section. KPI à capitalize “Performance” Background 3d paragraph: The consequences of poor research culture does (change into “do”) not only impact researchers, it also effects (change into “affects”) research support staff… Results Security and career progression 3d paragraph: “The review suggests that the problem is reinforced by a culture where researchers are incentivized to produce many funding applications and academic publications where high rejection rates” this sentence seems to be missing a verb. Research quality and accountability – open and trustworthy research 4th paragraph: change “algin” into “align” Tables In Table 2, under theme Cultivate a culture of support that fosters a diverse set of skills and career pathway the references of Statement 8 are not included as links (they are also between brackets). This may be a formatting problem beyond the authors’ control, though. In Table 3, under theme Embed and support an inclusive culture Statement 6: …including shift (change into “shifting”) institutional practice… In Table 3, under theme Making use of and learning from existing tools and initiatives to support cultural change there is no space before the opening bracket in Statement 2 In Table 5, under theme Incentives and innovation Statement 1 mentions (at the end) “open assess movement”. Do the authors maybe mean “open access movement”? In Table 5, under theme Fostering transparency and visibility Statement 5 please change “CREDiT” into “CRediT” Other Seeing “life-work balance” mentioned in Table 3 made me smile. However, in the section Wellbeing and equality of opportunity and in the Discussion section the authors shift to work-life balance, also using “work/life balance” in the discussion. Please be consistent.\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": [ { "c_id": "11806", "date": "25 Jun 2024", "name": "Amanda Blatch-Jones", "role": "Author Response", "response": "Background: The overview remains abstract and could benefit from more specific information and examples. For example, what is “the potential negative impact of a poor research culture / the consequences and challenges associated to an inadequate research culture”? What are some recommendations from the “international actions to address the underlying drivers of poor research culture”? (Which drivers are there?) We have amended the first paragraph to provide more content and greater clarity for the reader. Related to this, I think the Discussion section would benefit from a brief recap of the main findings in the first paragraph(s), instead of just stating “From the evidence, it was clear that there were several initiatives to seek a cultural change across the research institutions/Higher Education Institutions.” We have added to the first part of the discussion emphasising some of the key points as suggested. The same applies to the conclusions. The authors correctly and rightfully emphasize the fact that “research institutions cannot act in isolation”, but in my opinion some of the findings deserve equal emphasis – and therefore being mentioned in the conclusions. In general, I think one of the conclusions could also be that there is a lot that can be done and that the evidence base for promoting a good research culture is substantial. Thank you for your comments and we have included your suggested conclusion comment into the manuscript. We have also amended the sentence “research institutions cannot act in isolation.” When reading the paper, it felt a bit like I was reading a – very well written – internal report for policy makers who are knowledgeable of the potential problems with(in) research culture. I think it can be leveraged to also appeal to a broader audience. Thank you for your feedback. We have made notable changes to the manuscript which we hope provides greater coverage for a broader audience. Methods: The Types of sources section confused me when I first read it, leading me to think that only empirical papers (“studies”) were included. Further on, it became evident that the authors included a wide variety of contributions. I suggest adding a first sentence to this section describing this, then continue by detailing the various types of studies and data that were included as it is currently documented. Thank you for your suggestion. We have included an opening sentence for this sub-heading. “Several types of contributions were used for the scoping review, which included articles, reports, blogs and web-based articles from both empirical studies and grey literature.” Results: The PRIMSA flow diagram (Figure 1) is incorrect. The total of the “Full-text articles excluded, with reasons (n = 513)” differs from the sum of the specific reasons (sum = 670). It appears that the latter is correct, because 924 papers screened – 670 excluded equals 254 included. Please note that there is still one paper that seems to have disappeared: Figure 1 and the main text mention 253 included papers, not 254. Unfortunately, in spite of the impressive amount of information that is confined in the Tables and despite my admiration for the work the authors must have put into presenting the evidence this way, there are inconsistencies between the number of references that are mentioned with the statements and the last column of the tables. You could consider this comment as an obsessive form of nitpicking from my part. I am aware of that. However, I believe that having a complete overview of the evidence associated with each statement will allow future readers to consult the relevant sources. Thank you for pointing this out on the PRISMA flow diagram. Having gone back to the reference manager the error has been corrected. The number of exclusions were 671 and the missing article was not recorded. This has now been amended. Thank you for your thoughtful comment and paying particular attention to the mismatch between the number of references cited for each statement and the count of these references in the tables. We really appreciate your attention to detail and have made the relevant changes and have double checked these for consistency. Table 2 Theme Promote fair and transparent process for career progression Statement 2: number of references with statement = 39; last column = 35 Statement 3: number of references with statement = 29; last column = 30 Statement 6: number of references with statement = 20; last column = 21 Theme Reduce hyper competition and provide a culture of kindness Statement 2: number of references with statement = 23; last column = 24 Theme Cultivate a culture of support that fosters a diverse set of skills and career pathways Statement 1: number of references with statement = 33; last column = 34 Statement 4: number of references with statement = 26; last column = 27 Thank you. We have adjusted the frequencies and have doubled checked all the other statements for clarity. Table 3 Theme Embed and support an inclusive culture Statement 1: number of references with statement = 44; last column = 43 Statement 2: number of references with statement = 40; last column = 41 Theme Investing in people to reduce burden and improve wellbeing Statement 1: number of references with statement = 39; last column = 42 Statement 3: number of references with statement = 24; last column = 27 Thank you. We have adjusted the frequencies and have doubled checked all the other statements for clarity. Table 4 Theme Everyone feeling valued and having equality of opportunities to contribute Statement 2: number of references with statement = 25; last column = 24 Thank you. We have adjusted the frequencies and have doubled checked all the other statements for clarity. Table 5 Theme Creation and facilitation Statement 1: number of references with statement = 73; last column = 74 Statement 2: number of references with statement = 54 (!!!); last column = 71 Statement 3: number of references with statement = 45; last column = 46 Statement 4: number of references with statement = 43; last column = 44 Theme Fostering transparency and visibility Statement 2: number of references with statement = 49; last column = 51 Statement 3: number of references with statement = 37; last column = 38 Statement 6: number of references with statement = 12; last column = 13 Thank you. We have adjusted the frequencies and have doubled checked all the other statements for clarity. Study strengths and limitations: First paragraph: I would suggest to also include the percentage of articles from the USA, analogous to Canada and other international countries. These figures and sentence has been adjusted to reflect the accuracy of the percentages in table 1. General comments: Some of the sentences feel odd. For example, in Wellbeing and equality of opportunity, second paragraph, “The evidence suggests that these issues have an impact not only at the institutional level such as having a lack of diversity in organisational leaderships, but also for individuals, leading to a lack of role models and peer mentors skills shortages in particular disciplines, sectors and roles, and drives off talent.” is a run-on and feels like a collation of several sentences. Please check. (1) Some of the Statements in the tables are also long and may better be divided into several shorter sentences. Some examples: Table 2, Statement 3 under theme Reduce hyper competition and provide a culture of kindness “Consider ways to demonstrate support for other researchers to secure funding as part of progression (and review current reward systems), ensuring education, teaching and research are equally prioritised”: who is referred to by “other”? (2) Table 5, under theme Fostering transparency and visibility Statements 2 and 7 feel odd. It seems like parts of the statements are missing. Please reformulate. (3 and 4) Thank you for your general comments on some of the sentences in the manuscript. We have amended these, which hopefully makes more sense for the reader. “The evidence suggests that these wellbeing issues can have an impact at an institutional level, resulting in a lack of diversity across leadership roles, a shortage of role models and peer mentors, and driving off talent due to staff leaving academia.” ‘other’ has been taken out as that was a typo error. Thank you for drawing us to this statement. Due to the structure of the statements and how they emerged as part of the synthesis, it would be challenging to go back and re-evaluate these statements. We understand that some of them are longer than others, as we attempted to capture sufficient information to enable the reader to understand the content and context. Statement 2 has been amended “Actively encouraging researchers to make their research more accessible and open through sharing protocols and data openly and transparently, could foster greater knowledge exchange opportunities.” Statement 7 has also been amended “Become a signatory of initiatives such as DORA and seek to engage with local and international networks such as the Reproducibility Network.” Typo’s: Abbreviations list COPE is the “Committee on Publication Ethics”, not “of” – the same typo is in Table 5 (theme “Fostering transparency and visibility” number 3 “Gain greater understanding…”) ENRI: do the authors mean European Network of Research Integrity Offices (ENRIO - https://www.enrio.eu/), or maybe ENERI, the “European Network for Research Ethics and Integrity” (https://eneri.eu)? If corrected, please also correct the mention of ENRI in Table 5 (same place as COPE) and in the last paragraph before the Discussion section. KPI à capitalize “Performance” Background 3d paragraph: The consequences of poor research culture does (change into “do”) not only impact researchers, it also effects (change into “affects”) research support staff… Results Security and career progression 3d paragraph: “The review suggests that the problem is reinforced by a culture where researchers are incentivized to produce many funding applications and academic publications where high rejection rates” this sentence seems to be missing a verb. Research quality and accountability – open and trustworthy research 4th paragraph: change “algin” into “align” Tables In Table 2, under theme Cultivate a culture of support that fosters a diverse set of skills and career pathway the references of Statement 8 are not included as links (they are also between brackets). This may be a formatting problem beyond the authors’ control, though. In Table 3, under theme Embed and support an inclusive culture Statement 6: …including shift (change into “shifting”) institutional practice… In Table 3, under theme Making use of and learning from existing tools and initiatives to support cultural change there is no space before the opening bracket in Statement 2 In Table 5, under theme Incentives and innovation Statement 1 mentions (at the end) “open assess movement”. Do the authors maybe mean “open access movement”? In Table 5, under theme Fostering transparency and visibility Statement 5 please change “CREDiT” into “CRediT” Other Seeing “life-work balance” mentioned in Table 3 made me smile. However, in the section Wellbeing and equality of opportunity and in the Discussion section the authors shift to work-life balance, also using “work/life balance” in the discussion. Please be consistent. Thank you for your additional suggestions on the typo’s in the manuscript. We have addressed all your comments accordingly. For the references, on statement 8, it is a formatting issue outside of our control (a request to F1000 has been made in the revised manuscript)" } ] }, { "id": "277499", "date": "28 May 2024", "name": "Elisabeth Grey", "expertise": [ "Reviewer Expertise Health behaviour", "health communication", "qualitative methods", "systematic reviews" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for asking me to review this interesting scoping review on research culture in research institutions. The manuscript is well-written and comprehensive, providing clear details on the methods and supplementary materials to enable other researchers to replicate the searches. I only have a few very minor suggestions that I think would help clarify a few things in the text:\nIn the Abstract, there are two stated aims, one under Background and one under Aims – these are not quite the same and I think it would be better to stick with one or the other (the first matches what is in the main text).\nInclusion criteria or Types of sources – I think this needs a statement on the types of initiative that were studied e.g., ‘all initiatives aimed, partly or wholly, at improving research culture were included’. Or this may need to broader if reports were included about initiatives that did not specifically aim to improve research culture, but the impact on this was measured.\nIn the PRISMA flow diagram, the reasons for exclusion are only provided for the academic records – could they be added for the grey records too?\nYou mention that many of the articles were relevant to more than one of the four focus areas – could you add a little to the Methods to explain how you decided which area to categorise a report under in these cases? Or were they included in the synthesis for each category they related to (would be good to state this)?\nThere is a typo in the fourth paragraph under ‘Research quality and accountability’ – ‘algin’?\nTable 4 and Table 5 have the same title – I think Table 5 should be Key concepts and statements associated with research quality and accountability\nIt struck me that none of the concepts under ‘Security and career progression’ seemed to relate to job security, only career progression. This would be worth highlighting – ultimately to improve job security, research institutions and funders need to rethink how research positions are funded. Innovation is needed here but this review suggests that nothing is happening on this front.\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": [ { "c_id": "11807", "date": "09 Jul 2024", "name": "Amanda Blatch-Jones", "role": "Author Response", "response": "Reviewer response: In the Abstract, there are two stated aims, one under Background and one under Aims – these are not quite the same and I think it would be better to stick with one or the other (the first matches what is in the main text). Author response: Thank you. We have replaced the aims with the following: The purpose of the scoping review was to explore ‘What does the evidence say about the ‘problem’ with ‘poor’ research culture, what are the benefits of ‘good’ research culture, and what does ‘good’ look like?’ Reviewer response: Inclusion criteria or Types of sources – I think this needs a statement on the types of initiative that were studied e.g., ‘all initiatives aimed, partly or wholly, at improving research culture were included’. Or this may need to broader if reports were included about initiatives that did not specifically aim to improve research culture, but the impact on this was measured. Author response: Thank you. We have included and revised your suggestion: All initiatives aimed, partly or wholly, at enhancing or assessing research culture were included. Reviewer response: In the PRISMA flow diagram, the reasons for exclusion are only provided for the academic records – could they be added for the grey records too? Author response: The flow diagram has been amended to include the exclusions and reasons. Reviewer response: You mention that many of the articles were relevant to more than one of the four focus areas – could you add a little to the Methods to explain how you decided which area to categorise a report under in these cases? Or were they included in the synthesis for each category they related to (would be good to state this)? Author response: We have added more detail about the four areas and how we allocated each article to an area or areas. “Both reviewers applied the articles under one of the four areas during extraction, based on the content and context of the article. Some articles were relevant to more than one category, which was reflected in the data extraction table. The reviewers independently checked the included articles to ensure that they were included appropriately across the four areas.” Reviewer response: There is a typo in the fourth paragraph under ‘Research quality and accountability’ – ‘algin’? Author response: Thank you. This has now been amended. Reviewer response: Table 4 and Table 5 have the same title – I think Table 5 should be Key concepts and statements associated with research quality and accountability Author response: Thank you for pointing this out. Table 5 title has been changed accordingly. Reviewer response: It struck me that none of the concepts under ‘Security and career progression’ seemed to relate to job security, only career progression. This would be worth highlighting – ultimately to improve job security, research institutions and funders need to rethink how research positions are funded. Innovation is needed here but this review suggests that nothing is happening on this front. Author response: Thank you. We have added the following sentence to the second paragraph under table 2. “To improve job security, research institutions and funding organizations need to readdress how research positions are funded, particularly in the early career stage.” Innovation was discussed in the some of the articles and these are reflected in the appropriate statements. We have tried to be inclusive to the areas that were most discussed, innovation for this area was more limited than the others (possibly due to challenges, barriers and competing interests around job security and progression). It is a valid point and thank you for bringing it up." } ] }, { "id": "277505", "date": "30 May 2024", "name": "Elizabeth Gadd", "expertise": [ "Reviewer Expertise Research assessment", "research culture", "scholarly communication", "open 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\nThank you for the opportunity to review this scoping review on what constitutes a good research culture, and thank you to the authors for taking the time to share their review with a wider audience through this piece.\nI make a number of minor comments against some of the article's headings below, however I think there are some more fundamental issues that it would be helpful to address to secure the scientific soundness of this article and therefore its contribution to the literature.\n\n1) Clarity & consistency around the dimensions of research culture being investigated It's not clear how the particular lenses of open research, career research paths (recognition & awards) & EDI mentioned in the background section were chosen given the research question appears to put no boundaries around the elements of poor research culture & the benefits of a good culture and what it looks like. In the methods section, the dimensions of research culture under investigation appear to have changed to 'four key areas highlighted from existing published work from the Wellcome Trust'. The argument given is that it will ensure consistency and continuity to predefined areas already established by the research environment.' (I'm not sure to what the authors refer when they use the phrase 'the research environment' here.) It's unclear at this point what these four areas are, and why they were selected. Again, why be guided by the WT if the research question is to consider the problems and benefits of poor/good research cultures more broadly? It would be helpful if a stronger case was made for the dimensions of research culture being used to analyse the literature given the specific research questions of the study.\n2) The use of the research questions as a study frame Having stated the research questions, they don't seem to provide a strong framework for the rest of the article. For example, Figure 2 summarises the evidence relating to 'what makes a good research culture' but not relating to the other elements of the research question (what are the problems with research culture and what benefits does it bring). If all three questions were being considered together, the heading of the figure could be changed.\nThe research questions are not referred back to in the findings, discussion or conclusions, which leads to a loss of structure and clarity.\n\n3) Superficial and incomplete analyses of the literature reviewed Some of the evidence summaries feel superficial and possibly incomplete. Take as an example the sentence: \"Evidence suggests that this [evaluating academic performance based on the use of inadequate proxies] can result in a lack of workload oversight, a culture discouraging of appreciation, that in turn makes researchers feel pressured to be successful, often resulting in a significant amount of time in pursuit of success at the cost of their wellbeing.\" I know this literature quite well, and I don't think a lack of workload oversight and a culture of discouraging appreciation are the key issues with the overuse of publication metrics.\n\nAgain, in the Wellbeing & equality of opportunity section the authors write: 'Researchers are incentivized to attain research excellence, which can often result in hyper-competitiveness and unfair working practices.' However, it's generally agreed that the problem lies not so much in the pursuit of excellence so much as how narrowly excellence is defined.\nI provide some other examples below but this is not a complete list.\n\n4) Poor phraseology The findings of the review are often obscured by somewhat tortuous phrasing and unclear writing. For example, in the research quality and accountability statements table, one statement reads: 'Develop a coordinated approach to incentivize open access policies to optimise a positive cultural shift based on Government recognition of UK Research and Innovation’s position on open access research practice, (including European and international position and status of progression/advancement in open research)'. It's not clear to me what this is saying, nor whether reference to one nation's policy position is meaningful.\nAgain, in the Wellbeing & equality of opportunity section, one sentence reads: 'As the evidence has shown, working relationship challenges in research culture require structural changes by transforming people, places, and practices.'\nI provide some other examples below, but this is by no means a complete list.\nI think it would be helpful if the authors scrutinise every sentence to ask, is this strictly accurate? How might this be misinterpreted? Am I representing the authors of the literature carefully? Have we identified the major themes?\n\n5) Stronger discussion & conclusions Finally, I find the discussion section rather unstructured and unclear. New points are introduced in the discussion that are not reported in the findings, e.g., reference to digital tools. The reader is not left with a clear sense as to what the authors proposed answers to the research questions are.\n\nMinor corrections Background Minor Correction: \"Funding organisations such as UK Research and Innovation (UKRI) enhanced its 2021-2022 allocation of research culture funding to Higher Education Providers (HEPs) to further explore research processes and experiences of working in research, through piloting new initiatives or enhancing existing activities.\" - this funding is from Research England to English HEPs:\nMinor: \"The consequences and challenges associated to an inadequate research culture is well evidence\" - should be 'associated with' and 'are well evidenced'\nMethods Minor: The term 'non-academic staff' is largely seen as derogatory - defining a group of people by what they are not. Research-enabling staff is a term in more common parlance now. Or professional services if you are looking more broadly.\nSearch strategy Minor: citations should be references I think?\nData extraction & evidence selection Minor: Citation needed for Rayyan\nMinor: I appreciate the work was carried out prior to the Vitae Research Culture study which identified 4 different core domains, however it would be good to mention this work as there is a lot of overlap with this paper.\nHow research is managed and undertaken How research ensures value How people are supported How individuals engage with others\nMinor: the numbers in the PRISMA flow diagram don't add up. The authors should take another look at this.\nCharacteristics of the included studies Minor: It should read 'conference papers' not 'conference proceedings'.\nMinor: UK is part of Europe. Is the 17 a subset of the 36 or separate to?\nSummarising the evidence Minor: Could be clearer as to what you mean by 'career type'. Career pathway? Job family?\nMinor: I'm not sure what the term 'statements' refers to in Table 2. 'Statement' implies a citation from the literature, but these are very complex so I don't think that's what's being provided.\n\nWellbeing and equality of opportunity Minor: just be careful with phrasing - 'The pandemic also initiated ‘kindness in research’' - I think you mean that the pandemic led to calls for more kindness in research? When writing reviews of this type, it's important to be strictly accurate as to exactly what was being suggested.\nMinor: Para beginning 'These practices' - it's not clear to what practices this refers?\nResearch quality & accountability Minor: This isn't quite accurate. 'the evidence...highlighted several issues inhibiting open research practices, which some have termed as a ‘replication or reproducibility crisis’. I think you mean that a link was made between open research and reproducibiity, but not that open research practices were termed a 'replication or reproducibilty crisis'?\n\nDiscussion Minor: The report mentioned here: 'As noted in the recent Research and Development report on people and culture strategy, high quality research and innovation requires an acknowledgment of the full range of people needed.8' is not a Research & Development report, but the BEIS R&D People & Culture Strategy.\nMinor: To what research group does this refer? 'The health of the research group and those that lead them has been identified as an area that universities need to pay more attention to'.\nMinor: The term 'impact' should be clarified throughout the article. In REF the term is used to describe non-academic impact. However, in the following sentence I think it refers to citation impact? ''The increasing competitiveness within the research environment, with research funding organisations (RFOs) placing greater focus on impact rather than creativity and innovation, is causing a global initiative for cultural change.' Either way, I'm not sure this sentence is strictly accurate.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [ { "c_id": "11808", "date": "09 Jul 2024", "name": "Amanda Blatch-Jones", "role": "Author Response", "response": "Reviewer comment: 1) Clarity & consistency around the dimensions of research culture being investigated It's not clear how the particular lenses of open research, career research paths (recognition & awards) & EDI mentioned in the background section were chosen given the research question appears to put no boundaries around the elements of poor research culture & the benefits of a good culture and what it looks like. Author response: These areas were chosen as a result of the Wellcome Trust survey and the areas reported in their report. The review focused on what the solutions could be rather than focusing on the barriers and challenges to a good research culture (due to the existing coverage in the literature). The aim of the review was to therefore consider the evidence about solutions and what the research community could consider. However, we have amended the last paragraph to add some additional context to address your comment. Reviewer comment: In the methods section, the dimensions of research culture under investigation appear to have changed to 'four key areas highlighted from existing published work from the Wellcome Trust'. The argument given is that it will ensure consistency and continuity to predefined areas already established by the research environment.' (I'm not sure to what the authors refer when they use the phrase 'the research environment' here.) It's unclear at this point what these four areas are, and why they were selected. Again, why be guided by the WT if the research question is to consider the problems and benefits of poor/good research cultures more broadly? It would be helpful if a stronger case was made for the dimensions of research culture being used to analyze the literature given the specific research questions of the study. Author response: We have revised the manuscript to be more descriptive of what the four areas are, along with what we mean by research environment (changed to research community based on the participants and respondents to the Wellcome Trust research cultures work). Reviewer comment: 2) The use of the research questions as a study frame Having stated the research questions, they don't seem to provide a strong framework for the rest of the article. For example, Figure 2 summarises the evidence relating to 'what makes a good research culture' but not relating to the other elements of the research question (what are the problems with research culture and what benefits does it bring). If all three questions were being considered together, the heading of the figure could be changed. Author response: The challenges and problems around research culture are well documented in the literature and we approached the research questions simultaneously, with more focus on solutions and what good research culture could look like. For each of the four areas, we have provided a summary of the challenges to address this part of the research question, with the main emphasis being the second part of the research question. The tables and figure 2 purposively focus on what constitutes a good research culture to address the challenges and barriers, to encourage a cultural shift with actionable actions. The purpose of the review was to focus on solutions rather than what the current challenges are, as these are well documented. Reviewer comment: The research questions are not referred back to in the findings, discussion or conclusions, which leads to a loss of structure and clarity. Author response: We have made this clearer in the revised manuscript and referred back to the research questions. Reviewer comment: 3) Superficial and incomplete analyses of the literature reviewed Some of the evidence summaries feel superficial and possibly incomplete. Take as an example the sentence: \"Evidence suggests that this [evaluating academic performance based on the use of inadequate proxies] can result in a lack of workload oversight, a culture discouraging of appreciation, that in turn makes researchers feel pressured to be successful, often resulting in a significant amount of time in pursuit of success at the cost of their wellbeing.\" I know this literature quite well, and I don't think a lack of workload oversight and a culture of discouraging appreciation are the key issues with the overuse of publication metrics. Again, in the Wellbeing & equality of opportunity section the authors write: 'Researchers are incentivized to attain research excellence, which can often result in hyper-competitiveness and unfair working practices.' However, it's generally agreed that the problem lies not so much in the pursuit of excellence so much as how narrowly excellence is defined. I provide some other examples below but this is not a complete list. Author response: Thank you for your comments and feedback. We have revised the two areas you mentioned and have carefully considered and reviewed the rest of the manuscript. Reviewer comment: 4) Poor phraseology The findings of the review are often obscured by somewhat tortuous phrasing and unclear writing. For example, in the research quality and accountability statements table, one statement reads: 'Develop a coordinated approach to incentivize open access policies to optimise a positive cultural shift based on Government recognition of UK Research and Innovation’s position on open access research practice, (including European and international position and status of progression/advancement in open research)'. It's not clear to me what this is saying, nor whether reference to one nation's policy position is meaningful. Author response: Thank you. We have amended the statement to make it clearer to the reader. Reviewer comment: Again, in the Wellbeing & equality of opportunity section, one sentence reads: 'As the evidence has shown, working relationship challenges in research culture require structural changes by transforming people, places, and practices.' Author response: We have amended the sentence to be more cohesive. Reviewer comment: I provide some other examples below, but this is by no means a complete list. I think it would be helpful if the authors scrutinize every sentence to ask, is this strictly accurate? How might this be misinterpreted? Am I representing the authors of the literature carefully? Have we identified the major themes? Author response: Thank you. We have reviewed the manuscript and made several changes to make it more readable and coherent. Reviewer comment: 5) Stronger discussion & conclusions Finally, I find the discussion section rather unstructured and unclear. New points are introduced in the discussion that are not reported in the findings, e.g., reference to digital tools. The reader is not left with a clear sense as to what the authors proposed answers to the research questions are. Author response: We have revised the discussion and conclusion to make it clearer to the reader and follow a more structured approach. Reviewer comment: Minor corrections Background Minor Correction: \"Funding organizations such as UK Research and Innovation (UKRI) enhanced its 2021-2022 allocation of research culture funding to Higher Education Providers (HEPs) to further explore research processes and experiences of working in research, through piloting new initiatives or enhancing existing activities.\" - this funding is from Research England to English HEPs: Author response: Thank you. We have addressed this correction and amended the sentence accordingly. Reviewer comment: Minor: \"The consequences and challenges associated to an inadequate research culture is well evidence\" - should be 'associated with' and 'are well evidenced' Author response: Thank you, we have amended accordingly. Reviewer comment: Methods Minor: The term 'non-academic staff' is largely seen as derogatory - defining a group of people by what they are not. Research-enabling staff is a term in more common parlance now. Or professional services if you are looking more broadly. Author response: Thank you. We have replaced with research-enabling staff due to the scope of the review. Reviewer comment: Search strategy Minor: citations should be references I think? Author response: We have amended the manuscript to refer to references rather than citations to make it clearer to the reader. Reviewer comment: Data extraction & evidence selection Minor: Citation needed for Rayyan Author response: A link to Rayyan is now included. Reviewer comment: Minor: I appreciate the work was carried out prior to the Vitae Research Culture study which identified 4 different core domains, however it would be good to mention this work as there is a lot of overlap with this paper. How research is managed and undertaken How research ensures value How people are supported How individuals engage with others Author response: This has now been included in the manuscript as part of the overall introduction and discussion. Reviewer comment: Minor: the numbers in the PRISMA flow diagram don't add up. The authors should take another look at this. Author response: Thank you for noticing this. We have rectified the error in the PRISMA flow diagram and have updated accordingly. Reviewer comment: Characteristics of the included studies Minor: It should read 'conference papers' not 'conference proceedings'. Author response: We have amended to reflect your comment. Reviewer comment: Minor: UK is part of Europe. Is the 17 a subset of the 36 or separate to? Author response: We separated UK from Europe so that we could see what initiatives were specifically being conducted in the UK as funding, academic institutions etc work differently across country. As reported the 17 UK are separate to Europe, so the total across Europe was 43). We have adjusted the manuscript to be more concise. Reviewer comment: Summarizing the evidence Minor: Could be clearer as to what you mean by 'career type'. Career pathway? Job family? Author response: We have provided an explanation with examples on the first mention of career type. Reviewer comment: Minor: I'm not sure what the term 'statements' refers to in Table 2. 'Statement' implies a citation from the literature, but these are very complex so I don't think that's what's being provided. Author response: We have changed ‘statements’ for all tables and have amended with key areas and considerations associated to [what the theme was]. Reviewer comment: Wellbeing and equality of opportunity Minor: just be careful with phrasing - 'The pandemic also initiated ‘kindness in research’' - I think you mean that the pandemic led to calls for more kindness in research? When writing reviews of this type, it's important to be strictly accurate as to exactly what was being suggested. Minor: Para beginning 'These practices' - it's not clear to what practices this refers? Author response: Thank you. We have amended the sentences accordingly. Reviewer comment: Research quality & accountability Minor: This isn't quite accurate. 'the evidence...highlighted several issues inhibiting open research practices, which some have termed as a ‘replication or reproducibility crisis’. I think you mean that a link was made between open research and reproducibility, but not that open research practices were termed a 'replication or reproducibility crisis'? Author response: Thank you. We have amended the sentence accordingly. Reviewer comment: Discussion Minor: The report mentioned here: 'As noted in the recent Research and Development report on people and culture strategy, high quality research and innovation requires an acknowledgment of the full range of people needed.8' is not a Research & Development report, but the BEIS R&D People & Culture Strategy. Author response: We have amended the manuscript accordingly. Reviewer comment: Minor: To what research group does this refer? 'The health of the research group and those that lead them has been identified as an area that universities need to pay more attention to'. Author response: We have provided more details to make it clearer to the reader. Reviewer comment: Minor: The term 'impact' should be clarified throughout the article. In REF the term is used to describe non-academic impact. However, in the following sentence I think it refers to citation impact? ''The increasing competitiveness within the research environment, with research funding organizations (RFOs) placing greater focus on impact rather than creativity and innovation, is causing a global initiative for cultural change.' Either way, I'm not sure this sentence is strictly accurate. Author response: We have adjusted and amended the manuscript where necessary." } ] }, { "id": "271033", "date": "04 Jul 2024", "name": "Stephen Curry", "expertise": [ "Reviewer Expertise Research assessment", "EDI", "metascience", "structural biology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a review of the peer-reviewed and grey literature on research culture issues at research institutions that aims to explore the evidence base for (i) claims of poor research culture, (ii) the benefits of a ‘good’ research culture, and (iii) what ‘good’ might might look like.\nThe review is systematic in its consideration of the literature published between 2017 and 2022 and certainly addresses an important and topical area. However, I have a number of concerns about the design and execution of the study.\nFirst, the aims lack focus. As stated, they are to “explore the interplay between research culture, open research, career paths, recognition and rewards and EDI”. This maps out an extremely broad range of issues and doesn’t clearly articulate the desired endpoints.\nA second concern is the fact that the literature surveyed is confined to a 5-year period that ended over two years ago. Given the topicality of the subject, I find this a strange limitation. What reassurance can the authors offer that their review is not already out of date?\nThird, and perhaps most critically, the report is largely descriptive and lacks an analytical edge that I think would add considerably to the value and impact of the piece. I was left wondering who is going to read this and what will they take away? The main conclusion in the abstract is that research institutions and funders need to work together, a finding that seems obvious given the systemic nature of the issues under discussion. What is new here that we didn’t know before the review was conducted?\nI suspect the lack of analysis may reflect the fact that the interactions between open research, EDI etc and research culture are extremely difficult to isolate and distinguish and that there have been relatively few efforts to evaluate whether interventions have had positive or negative effects on research culture. The problem is made more difficult because of the existence of external influences (e.g. funder policies, league tables, international competition) on institutional culture. Nevertheless, even to highlight the absence of such evaluation efforts would be a valuable point to make – and I hope that the authors might address this question in a revised version of the paper.\n\nI have a few additional comments:\nIn the first paragraph of the introduction, I think it would be more appropriate to present the ‘actions’ that have been taken in chronological order.\nLater in the introduction, it is stated that “attempts on reform requires commitment from everyone”. While I agree with this claim, it sits oddly with the study design, which is focused only on research institutions. This is one of several instances where I lost sight of the coherence of the arguments being presented.\nIn the first paragraph of the section on Security and Career Progression, the authors identify “concerns over job security, career progression and sustainability…” but it is not clear to me what is meant by sustainability in this context.\nLater in this section it is stated that “The evidence suggests that offering potential solutions or supportive actions for academic institutions and the research community may enhance and stabilise career paths, particularly those in the early career stage, including those in technical and managerial roles.” This is a rather vague and weak statement. What solutions have been identified? Who is responsible for them and how effective are they? What does it mean to enhance a career path?\nOn page 19 it is stated (with regard to the replication crisis) that “Determining where effort is most needed and what changes are required, not only provides opportunity for the research ecosystem but also how RPOs and RFOs can mandate open research practices, and therefore coordinate change at both research integrity and researcher integrity level…”. This is another rather vague claim where analysis is lacking. What specific changes might be made? Could the authors also address the very live debates around the merits and demerits of using mandates?\nIn the Discussion, the sentence “The increasing competitiveness within the research environment, with research funding organisations (RFOs) placing greater focus on impact rather than creativity and innovation, is causing a global initiative for cultural change” doesn’t make sense to me. Is it not increasing awareness of the harmful impacts of research competition that is leading many stakeholders across the world to focus attention on improving research culture. This is just one example of what I find to be a rather fuzzy style of writing. This sense is compounded by the repetition of the phrase “the evidence suggests”. As noted above, I would like to see the authors doing a better job of sifting and weighing the evidence.\nThe last paragraph of the Conclusions is not really a conclusion. It is to my mind a description of a situation that was evident before reading this review. The first paragraph begins with the statement that “The review has shown that there is a wealth of evidence suggesting how and where changes are needed to establish a global cultural change to the research ecosystem. ” I think it would add a great deal of value to the review if the authors could identify what they think are the most important changes. This would have the potential to focus the attention of the sector on the most urgent actions to be undertaken.\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? 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? 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": "12259", "date": "23 Aug 2024", "name": "Amanda Blatch-Jones", "role": "Author Response", "response": "Unfortunately we did not receive your review until we submitted a revised version. We will of course address your comments in version 3, when we have received all of the reviewers comments. Thank you again for your comments and suggestions for improvements." }, { "c_id": "12404", "date": "14 Oct 2024", "name": "Amanda Blatch-Jones", "role": "Author Response", "response": "In addition to our previous comments we would like to add that we have addressed your comments in line with the other comments and feedback received. Thank you for your comments. First, the aims lack focus. As stated, they are to “explore the interplay between research culture, open research, career paths, recognition and rewards and EDI”. This maps out an extremely broad range of issues and doesn’t clearly articulate the desired endpoints. Thank you for your comment. The scoping review was kept broad for the purposes of the review and the related areas highlighted in the Wellcome report. On this basis, we kept the review broad to capture relevant evidence (and contribute to the wider piece of work the review contributed to). A second concern is the fact that the literature surveyed is confined to a 5-year period that ended over two years ago. Given the topicality of the subject, I find this a strange limitation. What reassurance can the authors offer that their review is not already out of date? We appreciate your concern around the period; however, this was chosen to consider existing literature in the space, the Wellcome report and initiatives in research culture. The period covered relevant references and included reports of changes during COVID-19 pandemic. As this was a scoping review to determine the existing evidence, we were only covering the specified areas within that period. Third, and perhaps most critically, the report is largely descriptive and lacks an analytical edge that I think would add considerably to the value and impact of the piece. I was left wondering who is going to read this and what will they take away? The main conclusion in the abstract is that research institutions and funders need to work together, a finding that seems obvious given the systemic nature of the issues under discussion. What is new here that we didn’t know before the review was conducted? The review provides updated literature from the Wellcome report and supports the existing evidence that although there are further developments in this space, there is still a lack of collaborative working. The statements provided in the tables gives greater clarity around what these developments are and how they could be considered to foster and incentivise what a good research culture looks like. As this was a scoping review, analytical content or assessment was out of scope. I suspect the lack of analysis may reflect the fact that the interactions between open research, EDI etc and research culture are extremely difficult to isolate and distinguish and that there have been relatively few efforts to evaluate whether interventions have had positive or negative effects on research culture. The problem is made more difficult because of the existence of external influences (e.g. funder policies, league tables, international competition) on institutional culture. Nevertheless, even to highlight the absence of such evaluation efforts would be a valuable point to make – and I hope that the authors might address this question in a revised version of the paper. As noted in the review, research culture is in itself complex due to multiple factors at play. The review highlights these complexities and the range of areas required to promote and encourage a good research culture. We agree with your comment and have highlighted these concerns within the revised version, thank you. In the first paragraph of the introduction, I think it would be more appropriate to present the ‘actions’ that have been taken in chronological order. Later in the introduction, it is stated that “attempts on reform requires commitment from everyone”. While I agree with this claim, it sits oddly with the study design, which is focused only on research institutions. This is one of several instances where I lost sight of the coherence of the arguments being presented. Thank you for your comment. Addressing this point in the introduction is a valid point, demonstrating how the Wellcome report highlighted the need for greater commitment from not just research institutions (and demonstrating the complexity). In the first paragraph of the section on Security and Career Progression, the authors identify “concerns over job security, career progression and sustainability…” but it is not clear to me what is meant by sustainability in this context. Thank you. We have added some examples of what we mean by sustainability in this context. Later in this section it is stated that “The evidence suggests that offering potential solutions or supportive actions for academic institutions and the research community may enhance and stabilise career paths, particularly those in the early career stage, including those in technical and managerial roles.” This is a rather vague and weak statement. What solutions have been identified? Who is responsible for them and how effective are they? What does it mean to enhance a career path? We have referred the reader to the table, which provides the evidence for this section. We didn’t elaborate within the text as we would be duplicating what is reported in table 2. Several solutions are reported in the table, and as reported, a range of individuals are responsible for initiating them (individuals themselves, research organisations, departments, HR etc). On page 19 it is stated (with regard to the replication crisis) that “Determining where effort is most needed and what changes are required, not only provides opportunity for the research ecosystem but also how RPOs and RFOs can mandate open research practices, and therefore coordinate change at both research integrity and researcher integrity level…”. This is another rather vague claim where analysis is lacking. What specific changes might be made? Could the authors also address the very live debates around the merits and demerits of using mandates? Thank you for your comment. Like the above statement, the scoping review provided a summary of the evidence found rather than analysing the evidence (another type of review approach would be needed for this). The purpose here was to highlight and assess the scope of the literature and map it to specific areas (the four areas reported in the Wellcome report). In the Discussion, the sentence “The increasing competitiveness within the research environment, with research funding organisations (RFOs) placing greater focus on impact rather than creativity and innovation, is causing a global initiative for cultural change” doesn’t make sense to me. Is it not increasing awareness of the harmful impacts of research competition that is leading many stakeholders across the world to focus attention on improving research culture. This is just one example of what I find to be a rather fuzzy style of writing. This sense is compounded by the repetition of the phrase “the evidence suggests”. As noted above, I would like to see the authors doing a better job of sifting and weighing the evidence. This section has been revised in a previous version. However, weighing or providing an analytical account of the included evidence is out of scope for scoping reviews. Scoping reviews aim to understand ‘What has been done previously?’ and ‘What does the literature say?’ compared to systematic reviews that ask the question ‘Does this intervention work for this group of individuals? The last paragraph of the Conclusions is not really a conclusion. It is to my mind a description of a situation that was evident before reading this review. The first paragraph begins with the statement that “The review has shown that there is a wealth of evidence suggesting how and where changes are needed to establish a global cultural change to the research ecosystem. ” I think it would add a great deal of value to the review if the authors could identify what they think are the most important changes. This would have the potential to focus the attention of the sector on the most urgent actions to be undertaken. Thank you for your comment. We have extended the conclusions and included the Vitae citation. However, we have not directed the reader to specific priorities as we feel this would add bias to the review. As already noted there are several areas in the tables under the four areas that would be considered to some as priority but may not be to someone else. On this basis, it would be the readers decision to understand what is priority to them and their institution based on what is feasible and within their control." } ] } ]	1	https://f1000research.com/articles/13-324
https://f1000research.com/articles/13-1224/v1	14 Oct 24	{ "type": "Case Report", "title": "Case Report: Acute hepatitis A virus infection presenting with direct antiglobulin test-negative autoimmune hemolytic anemia and α-thalassemia trait", "authors": [ "Habiba Debbabi", "Eya Chakroun", "Hajer Hassine", "Hela Kchir", "Dhouha Cherif", "Haythem Yacoub", "Nadia Maamouri", "Habiba Debbabi", "Eya Chakroun", "Hela Kchir", "Dhouha Cherif", "Haythem Yacoub", "Nadia Maamouri" ], "abstract": "Reports from the literature have discussed patients presenting Hepatitis A virus infection with hemolytic anemia, specifically with glucose-6-phosphate dehydrogenase deficiency. However, autoimmune hemolytic anemia (AIHA) has been rarely reported. We present a challenging case of Coombs-negative hemolytic anemia as initial manifestation of hepatitis A virus infection in a silent carrier of α-thalassemia.", "keywords": [ "DAT-negative", "autoimmune hemolytic anemia", "hepatitis A infection" ], "content": "Introduction\n\nThe hepatitis A virus (HAV) is the most common type of acute viral hepatitis. It is usually a self-limiting disease with variable clinical presentation. Symptoms can range from mild to severe, and usually include jaundice and digestive signs. Various extrahepatic manifestations can occur with acute hepatitis A infection, such as neurological complications and acute kidney injuries. However, extrahepatic immune complications remain rare.1 Hemolytic anemia has also been observed as a hematological complication associated with HAV infection in several case studies, especially in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency.2,3 However, autoimmune hemolytic anemia (AIHA) during the course of HAV infection has rarely been described.4–6 As the immune nature of anemia is caused by the positivity of the Direct Antiglobulin test (DAT), DAT-negative AIHA cases could evade diagnosis if not recognized. Herein, we present a challenging case of 39 a year-old man with α-thalassemia trait who presented with acute HAV infection revealed by DAT-negative AIHA.\n\n\nCase report\n\nA 39-year-old man with no significant past medical history presented with jaundice, and fatigue started 5 days prior to presentation. He had no remarkable family history of hematological disorders. He had received no drugs and had no prior hospitalization. At the time of admission, the patient was severely jaundiced and pale. The body temperature was 37.2°C. pulse rate was 88 beats per minute (bpm). blood pressure was 120/70 mmHg. His abdomen was soft. Hepatomegaly (liver span, 17.5 cm) and splenomegaly (3 cm below the left costal margin) were noted. He had no palpable lymphadenopathy, and the remainder of the physical examination was normal.\n\nAdmission laboratory evaluation of the patient was as follows: hemoglobin (Hb): 5.7 g/dL, mean corpuscular volume (MCV): 123 fL, absolute reticulocyte count: 219 400/μL, platelet count: 137 000/μL and white blood cell count: 5820/μL. A peripheral blood smear revealed anisocytosis, polychromatophils, and dacryocytes. The direct antiglobulin test (DAT) using a gel microcolumn (Low Ionic Strength Solution (LISS), Bio-Rad Laboratories) was negative for IgG and C3d. An elevation of serum aspartate aminotransferase (AST) 44.17 IU/L (normal: 5-34); alanine aminotransferase (ALT) 100.23 IU/L (normal: < 55); gammaglutamyltransferase (ɤGT) 276.97 IU/l (normal: 12–64); total bilirubin (TBil) 319 μmol/L (normal: <12) with an indirect fraction of 111 μmol/L and a high LDH level (540 U/L) were noted. Renal function tests, electrolyte levels, prothrombin time, and autoimmune tests were normal.\n\nFurther investigations of cholestatic hepatitis showed that the viral serologic studies were positive for anti-HAV IgM antibody and negative for anti-HAV IgG. Tests for hepatitis B virus surface antigen, hepatitis C virus (HCV) antibody (anti-HCV), and screening for HIV, CMV, and EBV were negative.\n\nAbdominal Ultrasonography showed hepatosplenomegaly but no evidence of biliary obstruction. Bili MRI revealed no abnormalities.\n\nGiven hemolysis, constitutional causes, including inherited spherocytosis and G6PD deficiency, were excluded. However, hemoglobin electrophoresis revealed an α-thalassemia trait (97.5% hemoglobin A1, 0.9% hemoglobin F, and 1.6% hemoglobin A2). Cell flow cytometry was negative for paroxysmal nocturnal hemoglobinuria.\n\nFurthermore, a remarkably high serum ferritin level (512μg/L). folate level was low (2.5 μg/L), but vitamin B12 level was normal. Thyroid function, Anti-intrinsic factor (IF) antibodies, and anti-parietal cell antibodies were also negative. DAT was repeated during hospitalization and performed with monospecific anti-human globulin (AHG) reagents, including anti-IgG, -IgA, -IgM, -C3c, and -C3d antisera, and yielded negative results. The eluate was negative.\n\nBased on clinical and laboratory findings, the patient was diagnosed with acute HAV infection complicated by DAT-negative AIHA. Bone marrow biopsy was normal, with no evidence of lymphoproliferative disorder.\n\nThe patient symptoms improved and remained stable during hospitalization. The patient’s blood cell count showed a slight upward trend. The Hb level reached 6.8 g/dL on the 10th day of hospital stay. TBil levels decreased to 101 μmol/L and liver enzyme levels showed a marked reduction. The patient was discharged in good condition two weeks after admission and was jointly cared for in the Hematological outpatient department.\n\nIt is important to note that 3 months after the acute episode, the patient had recurrence of his symptoms with re-elevation of the serum TBil level (382 μmol/L), and the Hb level began to drop to 6.2 mg/dL. The persistence of hepatitis A IgM antibodies prompted the consideration of relapsing hepatitis A. Only by the 5th month of follow-up, hepatitis A IgM antibodies disappeared, and oral prednisone therapy (70 mg, 1.5 mg/kg/day) was started; Hb Levels rapidly increased to 7.1 g/dL. Corticosteroids were maintained at the same dose for 6 weeks and then tapered gradually over several weeks. The patient’s condition improved within the first month of steroid therapy, and the hemoglobin level reached 10.1 g/dL. During the follow-up, the CBC was completely re-normalized.\n\n\nDiscussion\n\nAutoimmune hemolytic anemia has been reported in association with various hepatotropic viruses, notably Epstein-Barr virus, cytomegalovirus, and hepatitis B. A well-established link exists between chronic active hepatitis and AIHA. We present a rare case of acute hepatitis A, manifesting as a direct antiglobulin test (DAT)-negative AIHA.\n\nIn advanced liver disease, reduced hemoglobin levels are indicative of poor outcomes, such as liver decompensation and the onset of acute-on-chronic liver failure.7,8\n\nAnemia can have several etiologies (acute or chronic blood loss, hemolysis, and malabsorption). A combination of AIHA and viral hepatitis has been reported in the literature, and Hepatitis E virus, hepatitis C virus chronic infection, cytomegalovirus infection, and HAV acute hepatitis are epidemiologically associated with AIHA.6\n\nHowever, the pathogenic mechanisms underlying hemolysis in acute hepatitis remain unknown and have not been completely elucidated.9–11 The presentation of HAV infection varies from complete lack of symptoms to acute/fulminant hepatitis, but gastrointestinal symptoms, fever, and malaise are frequent.1 In this condition, the diagnosis of concomitant AIHA may be challenging, as common signs of AIHA, such as fatigue, jaundice, and pallor, may go undetected in patients with a severe presentation. Indeed, AIHA has been reported during the course of HAV infection.12–14 The hypothesis that hemolysis is induced by circulating antibodies or the effect of the virus on red blood cells has been proposed by several authors.12,15,16 To date, only two studies have detected autoantibodies that were IgM antibodies against triosephosphate isomerase (anti-TPI).12,13\n\nAntibodies against TPI damage enzyme activity and reduce the osmotic resistance of erythrocytes. The presence of these antibodies is hypothesized to be linked to the reactivation of latent persistent Epstein-Barr virus (EBV) infection.13 However, in our patient, EBV serology was negative. No anti-TPI antibody was detected, as reported in other studies.\n\nThe occurrence of contributing factors seems to be necessary, as red cell survival in the absence of an underlying red cell abnormality can be shortened by acute infectious hepatitis, but the rate of destruction of RBCs due to the effect of the virus alone is insufficient to induce hemolytic anemia.2,3,16–18\n\nThe hemolytic anemia can increase up to 70–87% in patients with G6PD deficiency complicated by acute hepatitis,19 which may result in a severe clinical presentation.2,3,15,20,21\n\nThe mechanism of hemolysis in these cases could result from the accumulation of oxidants due to hepatic dysfunction, which leads to reduced glutathione levels and induces hemolysis.3,9 G6PD deficiency was not found in our patient, but he carried the α-thalassemia trait.\n\nIt is worth to note that there is a high incidence of thalassemia (2.5-25%) in the tropical subtropical regions of Africa, the Asian subcontinent, and Southeast Asia, the Middle East, and particularly in the Mediterranean basin where milder forms of the disease are frequently observed.22 Silent carriers of α-thalassemia are typically asymptomatic and may exhibit either a normal blood count or mild microcytic hypochromic anemia; therefore, no specific treatment is recommended for these patients.23 The involvement of this inherited blood disorder in the onset of hemolysis in cases of acute hepatitis A remains unknown as no similar reports have been reported in the literature. However, it seems unlikely that hemolysis is related to the α-thalassemia trait because of the absence of previous hemolytic episodes.\n\nHemolysis may also be an autoimmune process. Positive DAT is a diagnostic hallmark of AIHA. However, negative DAT may be found in some cases, and it is considered a challenging situation because diagnosis and management may be delayed.6\n\nThe incidence of DAT-negative AIHA is approximately 3 to 11% in all cases.24,25 The main causes of negative DAT could be a low level of antibodies on the RBCs, a lower sensitivity of DAT, or an autoantibody type IgA or IgM, which many commercial DAT reagents could miss because they only contain anti-IgG and anti-C3.26,27\n\nSubsequent methods have been developed to achieve greater sensitivity in detecting red cell sensitization by IgG below the threshold of the routine commercial DAT or by IgA alone, or rarely (monomeric) IgM alone (Eluate, test with anti-IgA or anti-IgM antisera antiglobulin test, enzyme-linked anti-IgG assay, and flow cytometry to detect red cell IgG).28 It is important to note that these tests have a low predictive value, and thus, the test results should be interpreted according to clinical and biological data for DAT-negative AIHA.27\n\nIn our patient, both DAT monospecific AHG reagents, including anti-IgG, -IgA, -IgM, -C3c, -C3d anti-sera, and eluate, were performed and yielded negative results. Similarly, the lack of an alternative confirmatory test should not delay treatment. Thus, diagnostic assessment must rule out all hereditary and acquired causes of hemolytic anemia. In fact, the conjunction of hemolysis, denial of other hemolytic diseases, and responsiveness to steroid treatments are key to establishing a diagnosis of DAT-negative AIHA.29 In fact, corticosteroids are the cornerstone of AIHA treatment; splenectomy and rituximab are the second-line treatments. Transfusion is required in cases of severe anemia.30\n\nAs no drugs are targeted for the treatment of acute hepatitis A infection, patients are currently treated symptomatically with intravenous fluids and antipyretics as indicated.30\n\nThe most common hemolytic disorders associated with viral hepatitis are brief. However, in some patients, hemolysis persists for longer intervals even after recovery from viral hepatitis.31 In addition, the length of time that the IgM anti-HAV test remains positive varies widely, from 4 to 32 months in some studies.32,33\n\nIn our patient, the anemia persisted over five months after the onset of jaundice, and we hypothesized that this hemolytic state could not be related to the severity of liver disease, but rather suggests that an immunological disorder linked to HAV could exist and persist even after infectious hepatitis.\n\n\nConclusion\n\nHepatitis A is common worldwide, with a wide range of manifestations that can evade the diagnosis of concomitant hemolytic anemia. This case highlights the importance of recognizing the occurrence of AIHA, even if DAT is negative. Therefore, extensive medical and laboratory workup may be warranted, and responsiveness to steroid treatment is considered a supportive element of DAT-negative AIHA. However, the involvement of the alpha-thalassemia trait in our patient remains unclear.\n\n\nConsent\n\nWritten informed consent for publication of his clinical details was obtained from the patient.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\n\nReferences\n\nJeong SH, Lee HS: Hepatitis A: clinical manifestations and management. Intervirology. 2010; 53(1): 15–19. Publisher Full Text\n\nAbutineh I, Kreitman K, Kothadia JP, et al.: Acute hepatitis A causing severe hemolysis and renal failure in undiagnosed glucose-6-phosphate dehydrogenase deficient patient: A Case Report and Review of the Literature. Case Rep. Hepatol. 2021; 2021: 1–8. Publisher Full Text\n\nSharma D, Singh O, Juneja D, et al.: Hepatitis A virus-induced severe hemolysis complicated by severe glucose-6-phosphate dehydrogenase deficiency. Indian J. Crit. Care Med. 2018; 22(9): 670–673. PubMed Abstract \| Publisher Full Text\n\nChang HJ, Sinn DH, Cho SG, et al.: Pure red-cell aplasia and autoimmune hemolytic anemia in a patient with acute hepatitis A. Clin. Mol. Hepatol. 2014; 20(2): 204–207. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMiri-Aliabad G, Rashidi S: Immune thrombocytopenic purpura and hemolytic anemia secondary to hepatitis A. Int. J. Hematol.-Oncol. Stem Cell Res. 2017; 11(2): 89–91. PubMed Abstract\n\nBianco C, Coluccio E, Prati D, et al.: Diagnosis and management of autoimmune hemolytic anemia in patients with liver and bowel disorders. J. Clin. Med. 2021; 10(3): 423. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nScheiner B, Semmler G, Maurer F, et al.: Prevalence of and risk factors for anaemia in patients with advanced chronic liver disease. Liver Int. 2020; 40(1): 194–204. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPiano S, Tonon M, Vettore E, et al.: Incidence, predictors and outcomes of acute-on-chronic liver failure in outpatients with cirrhosis. J. Hepatol. 2017; 67(6): 1177–1184. PubMed Abstract \| Publisher Full Text\n\nWright CS, Gardner E: A study of the role of acute infections in precipitating crises in chronic hemolytic states. Ann. Intern. Med. 1960; 52: 530–537. PubMed Abstract\n\nGundersen SG, Bjoerneklett A, Bruun JN: Severe erythroblastopenia and hemolytic anemia during a hepatitis A infection. Scand. J. Infect. Dis. 1989; 21(2): 225–228. PubMed Abstract \| Publisher Full Text\n\nHara K, Tagawa K, Unuma T: Acute hemolysis associated with hepatitis A. Gastroenterol. Jpn. 1985; 20(6): 611–615. Publisher Full Text\n\nRitter K, Uy A, Ritter S, et al.: Hemolysis and autoantibodies to triosephosphate isomerase in a patient with acute hepatitis A virus infection. Scand. J. Infect. Dis. 1994; 26(4): 379–382. PubMed Abstract \| Publisher Full Text\n\nRitter S, Schröder S, Uy A, et al.: Haemolysis in hepatitis A virus infections coinciding with the occurrence of autoantibodies against triosephosphate isomerase and the reactivation of latent persistent Epstein-Barr virus infection. J. Med. Virol. 1996; 50(3): 272–275. PubMed Abstract \| Publisher Full Text\n\nUrganci N, Akyildiz B, Yildirmak Y, et al.: A case of autoimmune hepatitis and autoimmune hemolytic anemia following hepatitis A infection. Turk. J. Gastroenterol. Off. J. Turk. Soc. Gastroenterol. 2003; 14(3): 204–207.\n\nTibble JA, Ireland A, Duncan JR: Acute auto immune haemolytic anaemia secondary to hepatitis A infection. Clin. Lab. Haematol. 1997; 19(1): 73–75. PubMed Abstract \| Publisher Full Text\n\nCuthbert JA: Hepatitis A: old and new. Clin. Microbiol. Rev. 2001; 14(1): 38–58. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKatz R, Velasco M, Guzman C, et al.: Red cell survival estimated by radioactive chromium in hepatobiliary disease. Gastroenterology. 1964; 46: 399–404. PubMed Abstract \| Publisher Full Text\n\nSiddiqui T, Khan AH: Hepatitis A and cytomegalovirus infection precipitating acute hemolysis in glucose-6-phosphate dehydrogenase deficiency. Mil. Med. 1998; 163(6): 434–435. PubMed Abstract \| Publisher Full Text\n\nChau TN, Lai ST, Lai JY, et al.: Haemolysis complicating acute viral hepatitis in patients with normal or deficient glucose-6-phosphate dehydrogenase activity. Scand. J. Infect. Dis. 1997; 29(6): 551–553. Publisher Full Text\n\nCharan VD, Desai N, Choudhury VP: Hyperbilirubinemia following hepatitis A in a patient with G6pD deficiency. Indian J. Gastroenterol. Off. J. Indian Soc. Gastroenterol. 1993; 12(3): 99.\n\nLyons DJ, Gilvarry JM, Fielding JF: Severe haemolysis associated with hepatitis A and normal glucose-6-phosphate dehydrogenase status. Gut. 1990; 31(7): 838–839. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWeatherall DJ: The inherited diseases of hemoglobin are an emerging global health burden. Blood. 2010; 115(22): 4331–4336.\n\nRachmilewitz EA, Giardina PJ: How I treat thalassemia. Blood. 2011; 118(13): 3479–3488. PubMed Abstract \| Publisher Full Text\n\nBoccardi V, Girelli G, Perricone R, et al.: Coombs-negative autoimmune hemolytic anemia. Report of 11 cases. Haematologica. 1978; 63(3): 301–310. PubMed Abstract\n\nPetz LD, Garratty G: Autoimmune hemolytic anemia with a negative direct antiglobulin test (DAT). Philadelphia: Immune Hemolytic Anemias Churchill-Livingston; 2004; pp. 319–334.\n\nHill QA, Stamps R, Massey E, et al.: The diagnosis and management of primary autoimmune haemolytic anaemia. Br. J. Haematol. 2017; 176(3): 395–411. Publisher Full Text\n\nTakahashi T: Direct antiglobulin test-negative autoimmune hemolytic anemia. Acta Haematol. 2018; 140(1): 18–19. PubMed Abstract \| Publisher Full Text\n\nSegel GB, Lichtman MA: Direct antiglobulin (“Coombs”) test-negative autoimmune hemolytic anemia: a review. Blood Cells Mol. Dis. 2014; 52(4): 152–160. PubMed Abstract \| Publisher Full Text\n\nLin JS: Clinical applications of direct antiglobulin test. Blood Heart Circ. 2018; 2(3): 2–5. Publisher Full Text\n\nAlmeida PH, Matielo CEL, Curvelo LA, et al.: Update on the management and treatment of viral hepatitis. World J. Gastroenterol. 2021; 27(23): 3249–3261. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConrad ME: Persistent haemolysis after infectious hepatitis. Gut. 1969; 10: 516–521. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKao HW, Ashcavai M, Redeker AG: The persistence of hepatitis A IgM antibody after acute clinical hepatitis A. Hepatol. Baltim. Md. 1984; 4(5): 933–936. PubMed Abstract \| Publisher Full Text\n\nSikuler E, Keynan A, Hanuka N: IgM antibodies to hepatitis A virus in late convalescent sera. Isr. J. Med. Sci. 1987; 23(3): 193–195. PubMed Abstract" }	[ { "id": "332449", "date": "30 Oct 2024", "name": "Rosy Sultana", "expertise": [ "Reviewer Expertise Clinical immunology and virology: Hepatitis E virus in pregnancy", "SARS-CoV-2 antibodies in diabetic people and healthcare professionals", "Association of rheumatoid arthritis with autoimmune thyroid 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 case report detailed here is really interesting and deserve attention. The patient had alfa-thalassemia trait. However, carriers of alfa trait have not been demonstrated to cause anemia. Hepatitis A virus (HAV) induced acute hepatitis has been reported to be epidemiologically associated with AIHA without pathogenic mechanisms of underlying hemolysis. There might be several reasons for DAT-negative results, such as- i) low sensitivity of the reagents which were used for DAT. ii) low affinity of the IgG antibody Chemiluminescence immunoassay (CLIA) based method can be thought to increase the sensitivity of the assays. Diagnostic evaluation performed by the researchers to explore AIHA was elaborate and specific. Since all the test parameters were not in favor of a direct antiglobulin test-positive AIHA, patient's response to steroid treatment was found to be indicative for a diagnosis of DAT-negative AIHA. Further approach can be made considering the following issue: If the causative HAV is an unconventional mutant variant, it might produce epitope(s) which might be different from that of globally circulating conventional variant. The epitope produced by unconventional mutant variant may mimic erythrocyte epitope. That is, the monoclonal antibody produced in response to causative mutant variant may recognize epitope on erythrocytes causing hemolysis through molecular mimicry. Usually the binding through molecular mimicry is weak. However, sequencing of immunodominant region of HAV antigen can be recommended.\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? Yes", "responses": [ { "c_id": "13196", "date": "25 Jan 2025", "name": "Hajer Hassine", "role": "Author Response", "response": "As discussed, we have conducted almost exhaustive investigations to document this hemolysis. However, the use of sequencing of the immunodominant region of the HAV antigen had not been considered. It is accepted in the literature that responsiveness to steroid treatments is considered as a convincing argument in favor of the autoimmune mechanism of hemolysis and a key to establishing a diagnosis of DAT-negative AIHA. Thank you for the review." } ] }, { "id": "336132", "date": "19 Nov 2024", "name": "Shiv Sekhar Chatterjee", "expertise": [ "Reviewer Expertise Microbiology", "Laboratory Hematology only" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 is Bili MRI? Please explain in full form. 2. Please include a figure of the peripheral blood film of this patient. 3. Please state how spherocytosis and G6PD deficiency were excluded. 4. Also, state what finding on flow cytometry helped authors rule out paroxysmal nocturnal hemoglobinuria. Please include the flow cytometry graphical read out as a picture. 5. What was done for the low folate levels of this patient? 6. Why was Serum Haptoglobin not measured in this patient? 7. The Platelet count in this patient was relatively low at 137000/microliter. Was Evan's syndrome a differential diagnosis? 8. Is there any significance of the high serum ferritin levels in this patient? Kindly mention in discussion. 9. Why do you consider this patient to be a case of DAT negative AIHA? Which diagnostic criteria are fulfilled? Please mention in your Discussion. 10. How do authors conclude that the patient was suffering from Alpha Thalassemia Trait? Is it only from hemoglobin electrophoresis? Which electrophoresis was done? HPLC or capillary electrophoresis? Was PCR done for the diagnosis of Alpha Thalassemia trait?\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": [ { "c_id": "13197", "date": "24 Jan 2025", "name": "Hajer Hassine", "role": "Author Response", "response": "1. Biliary Magnetic Resonance Imaging (MRI) 3. For spherocytosis: since peripheral red blood cell morphology examinations, are not sufficiently sensitive or specific. An erythrocyte osmotic fragility test (OFT) was conducted. Unfortunately, Eosin‐5'‐maleimide (EMA) binding test (EMABT) and ektacytometry are not carried out here. Howerver, G6PD deficiency was excluded by G6PD level determination. For both, there was no family history of inherited hemolytic anemia. 4. Flow cytometry is performed in the hematology laboratory of the Pasteur Institute of Tunis. We do not have the acquisitions of the graphs when the search for a deficit in GPI-anchored molecules is negative. 5. During hemolysis, folates decrease. It is true that vitamin B9 therapy was prescribed but the patient was not perfectly compliant. 6. Unfortunately, haptoglobin is a parameter that is not always available in our hospital. 7. Other platelet counts were normal during follow-up and well before the initiation of corticosteroid therapy in this patient. Therefore, Evans syndrome was not considered as a differential diagnosis. 8. Hepatic cytolysis could explain the hyperferritinemia which remains < 1000 μg/L 9. As discussed, we have conducted almost exhaustive investigations to document this hemolysis. It is accepted in the literature that responsiveness to steroid treatments is considered as a convincing argument in favor of the autoimmune mechanism of hemolysis and a key to establishing a diagnosis of DAT-negative AIHA. 10. capillary electrophoresis was performed. PCR is not systematically done for the diagnosis of Alpha Thalassemia trait here. Thank you for the review." } ] } ]	1	https://f1000research.com/articles/13-1224
https://f1000research.com/articles/10-971/v1	27 Sep 21	{ "type": "Study Protocol", "title": "Protocol for a cross-sectional study on factors affecting health-related quality of life among Afghan refugees in Pakistan", "authors": [ "Atta Ur Rehman", "Rubeena Zakar", "Muhammad Zakria Zakar", "Ume Hani", "Florian Fischer", "Atta Ur Rehman", "Rubeena Zakar", "Muhammad Zakria Zakar", "Ume Hani" ], "abstract": "Background: Pakistan served as a host for more than 1.4 million Afghan refugees for more than 40 years. Access to health care is the most important issue faced by refugees, because they might be at a higher risk for certain diseases. This risk can be attributed to a lack of awareness of health care facilities, health beliefs, inadequate hygiene, cultural differences, and malnutrition. Health of individuals is closely associated with their quality of life. Quality of life over the whole lifespan is pivotal to overall life satisfaction. It includes physical wellbeing, mental health, education, occupation, income, personal safety, as well as (religious) freedom. Until now, the health status of Afghan refugees has never been comprehensively investigated in Pakistan. Therefore, an assessment in this regard is needed to explore their health-related quality of life, for securing their human right to health. Methods: A cross-sectional study has been designed to describe and explain the health-related quality of life of Afghan refugees in Pakistan. Multistage cluster sampling was applied for selection of study participants. The number of respondents from two regions in Pakistan was drawn through a proportionate sampling technique. A quantitative research method using pre-validated questionnaires was used for data collection. The questionnaire included items to assess well-being, mental health, health literacy, and factors affecting health and health care. Descriptive analysis was used, whereas inferential statistical tests (binary logistic regression model) was also performed. The study received ethically permission by the Advanced Studies and Research Board of the University of the Punjab, Lahore, Pakistan. Discussion: The assessment of Afghan refugee’s quality of life in Pakistan should lead to recommendations disseminated to public and health care officials. This evidence is needed for policymaking related to adequate measures for improving health conditions of Afghan refugees in Pakistan.", "keywords": [ "Afghanistan", "refugees", "migration", "health", "quality of life" ], "content": "Abbreviations\n\nAAHLS: All Aspects of Health Literacy Scale\n\nQOL: Quality of life\n\nSPSS: Statistical Package for the Social Sciences\n\nUNHCR: United Nations High Commissioner for Refugees\n\nWHO: World Health Organization\n\n\nIntroduction\n\nThe World Health Organization (WHO) advocated health as a fundamental human right in its constitution of 1946. The availability of health care facilities to all individuals – irrespective of gender, religion, race, political, economic and social conditions – are essential to attain this right.1 However, war is considered as a serious threat to this human right.2 War may lead to displacement and refugees are usually most vulnerable in host countries and, therefore, are at high risk of developing certain diseases.3 Refugees might face exploitation, prejudice and violence during travelling and stay in host countries which may negatively impact on their health.4\n\nFor about 40 years, Pakistan served as a host for more than 1.4 million Afghan refugees.5 Health care is one of the most important issues faced by refugees during migration. Health is a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity.6 Health of individuals living in a particular society is dependent on their quality of life. According to the WHO, quality of life is defined as “the individual’s perception of their position in life in the context of the culture and value systems in which they live and in relation to their goals”.7 It describes well-being of individuals and society considering the positive and negative features of life. Quality of life across the whole span is pivotal to satisfaction in life. That includes physical well-being, mental health, academic achievements, job, income, personal safety, and (religious) freedom.8 Health disparities are prevalent in almost all societies across the globe. Health inequalities and financial constrains may result in psychological health problems.9\n\nRefugee’s health is mostly dependent on living conditions and health facilities in host countries. Refugees might be at a higher risk for getting certain diseases because of lack of awareness of health facilities, health beliefs, inadequate hygiene, cultural differences, and malnutrition. Their health problems and needs may vary over time.10 At the time of arrival, refugees might face health problems related to injuries, gastrointestinal disorders, infectious diseases, cardiovascular disorders, hypothermia, skin diseases, mental health disorders, malnutrition and women’s health needs during pregnancy and delivery. After resettlement, refugees are at risk of mental health problems, communicable diseases, and non-communicable diseases. Particularly women and children are vulnerable populations. They may experience exposure to violence during their stay in refugee camps from local population as well as from other refugees.11\n\nThe pattern of migration has changed over time, but the factors affecting the quality of life and psychological well-being remain the same. The large influx of Afghan refugees has affected neighbouring countries such as Pakistan. Afghan's presence in the labour market directly affects their quality of life, because they are often informally employed without access to social protection.12 Although Afghan refugees are present in Pakistan for more than four decades, there is a lack of research to assess their quality of life. The quality of life of refugees affects not only their ability to fully participate in society but also acts as a barrier to learn new skills. Health-related quality of life is influenced by individual factors (age, sex, genes), lifestyle factors (socioeconomic, cultural, linguistic barriers and substance abuse),13 living conditions (access to clean water, sanitation and housing), working conditions (access to work, job), social and community factors (discrimination, social inclusion) and governance (documentation).8 Knowledge about the health care system as well as health literacy are also important factors.14\n\nMental health and psychological well-being are the basis for social functioning of any human being. Health care professionals used the terminology well-being to relate health-related quality of life and mental health.15 Overall, major depression was found in 30.8% of refugees, whereas post-traumatic stress disorder prevalence rate was 30.6%.16 Investigations on war-influenced youths have identified changes in psychological well-being on social encounters. Trauma memories, mental health, and resilience were investigated by Panter-Brick et al.17 in Afghan youths (11–16 years old) with their caregivers in Kabul (Afghanistan) and Peshawar (Pakistan). This study provided evidence on the association between posttraumatic distress and depression in Afghan youth. Furthermore, it showed that posttraumatic distress was less frequently observed in males as compared to females.17\n\nBadshah et al.18 investigated maternal risk factors in Pakistani mothers compared to Afghan-refugees in Peshawar, Khyber Pakhtunkhwa, Pakistan. The study showed a 2.6 times higher likelihood for low birth weight of neonates among the Afghan refugees. The reasons for low birth weight include living in tribal areas, no access to fresh water, low income, abortion/miscarriages, unregistered pregnancies, short inter-pregnancy intervals, and old age. However, there is a need for further research to assess the factors impacting on maternal health in Afghan refugees to overcome their health risks.18 This assessment is needed to explore the determinants of health-related quality of life, health beliefs, and the current health status of refugees in Punjab and Khyber Pakhtunkhwa, Pakistan.\n\n\nMethods\n\nFirstly, we consider that individual and lifestyle factors are associated with health-related quality of life among Afghan refugees in Pakistan. Secondly, we presume that there are differences in health-related quality of life due to living and working conditions among Afghan refugees in Pakistan. Thirdly, we expect that there is an association between social and community factors affecting health-related quality of life among Afghan refugees in Pakistan.\n\nThe main objectives of the study are:\n\n1. to determine the health-related quality of life among Afghan refugees in Punjab and Khyber Pakhtunkhwa, Pakistan,\n\n2. to examine the factors affecting health-associated quality of life and study their association among Afghan refugees in Punjab and Khyber Pakhtunkhwa, Pakistan,\n\nThe results should support to suggest measures to improve the health status of Afghan refugees in Punjab and Khyber Pakhtunkhwa, Pakistan.\n\nThe investigation design was cross-sectional. The sampling frame for the current investigation was refugee’s population in Khyber Pakhtunkhwa and Punjab, Pakistan. based on data from the United Nations High Commissioner for Refugees (UNHCR).19 Khyber Pakhtunkhwa is accommodating more than 58% of the Afghan refugee population. Punjab is the largest local educated population province with maximum human development index in the country. Thus, both provinces qualify as a favorable setting for Afghan refugees’ survey. We used validated instruments to collect information from Afghan refugees.\n\nMultistage sampling was used to collect on-site data. In the first stage, clusters of Afghan refugees (District) were selected from each province by online data available. Clusters were selected on the basis of both sexes’ participation in the pilot survey, because in some districts husbands did not allow their wives to take part in the study due to sociocultural factors. In the second stage, the number of Afghan participants were estimated from each district through proportionate sampling technique based on the population in each district. Finally, in the third stage, the calculated sample size was completed systematically due to non-data (refugee list) sharing policy of organizations working with the refugees. From the first ten refugee household’s, the second was selected through random number generator. The desired sample size was achieved through visiting the households at a regular interval. The Afghan Proof of Registration (PoR) card was observed as a proof of their refugee status in the resident area.\n\nSampling formula for known population was used:\n\nN is total population of refugee families 35,082 and e ± 3% level of precision (sampling error). The chances of rejection were assumed as 10%. Therefore, the sample size was estimated at 1,185.\n\nProportionate random sampling technique was used to calculate actual sample size. The formula used to calculate the number of sample families in each province is:\n\nTable 1 illustrates the selection of Afghan refugees within the provinces.5,20,21\n\nThe refugee families accessible in the study area during the time of data collection willing to participate were included in the study. Refugees with inability to understand consent procedures and to reply a questionnaire were excluded from the investigation. The objectives of the study were clearly explained to the families before the questionnaires were administered and written informed consent was obtained. Sampled families were guaranteed confidentiality and anonymity of the data throughout the study.\n\nData was collected by using pre-validated questionnaires (Table 2). Quality of life was assessed with the World Health Organization Quality-of-Life Scale (WHOQOL-BREF) by applying standardized age and gender sampling quota.22 According to sampling quota, 50% of the participants must be female and age-wise 50% of the participants must be older than 45 years of age. Psychological well-being was assessed by WHO-Wellbeing index23 and mental health by the Refugee Health Screener.24 The All Aspects of Health Literacy Scale (AAHLS) was used to measure health literacy.25 Questionnaires related to factors affecting health and health care were developed from Syrian Refugee Health Access Survey in Jordan and Lebanon according to local needs of the population.26–28 The existing internationally used instruments version with documented validity and reliability of English, Urdu and Afghan national Dari language was used. Permissions to use the tools were given by the stakeholders/authors. Afghan national bilingual research assistants were engaged for the data collection and linguistic interpretations of the Afghan national language according to the guidelines of WHO. Forward and backward translations were conducted under supervision of the principal investigator. The paper-based research questionnaires were administered to male respondents by Afghan national bilingual research assistants under the supervision of the first author and to female respondents by the fourth author with the help of research assistants in the research area. A team of two principal investigators and four trained research assistants supported the participants to fill in the questionnaires where needed. The research assistants were trained for two weeks before the field work.\n\nThe data of the filled-out forms has been entered in SPSS version 24 for data analysis. Descriptive analysis includes calculation of frequencies and percentages, whereas inferential statistical tests were applied to measure the level of association between variables.29 Logistic regression was performed to examine the relationship between variables at a 0.05 level of significance. The power 1-β of the test is 0.80 at 95% confidence level. The relevant differences should be observed by odds ratios.\n\nThe data of the current investigation will be shared with scientific journals and associated data repositories. The data was coded and sub-coded to ensure that participant identification may not be revealed. The analysis was carried out by the principal investigator who is trained. The supervisors and team members also supported and guided during the analysis.\n\nWe tried to remove selection bias from the project by choosing a representative sample by utilizing WHO quality of life standard age and gender sampling quota. According to this, 50% of the participants must be female and age-wise 50% of the participants must be older than 45 years. As the final sample was collected by applying systematic random sampling, we make sure that the randomization of the participants in terms of age and gender must be followed to complete the sample size from the selected cluster. Although the refusal rate was quite high in the refugee population, we tried to include at least 50% of the respondents that responded to any survey for the first time. Appropriate probability sampling techniques and internationally accepted questionnaires are used to avoid recall bias. Interviewees were given sufficient time for recall of memory. The sample size calculated was 1,185 so that maximum responses should be available to conclude the results. Specific inclusion and exclusion criteria were established at the design stage so that our outcomes are correctly identified.\n\nThe study is ethically permitted by the Advanced Studies and Research Board of the University of the Punjab, Lahore. Written informed consent for voluntary participation was obtained from respondents. The objectives of the study had been clearly explained to the participating families before the questionnaires were administered and written informed consent was obtained. Sampled families were guaranteed voluntary participation, confidentiality, and anonymity of the data throughout the study.\n\n\nPlans for dissemination of the study outcome\n\nThe results are going to be disseminated to the public by open defence and health care officials via outcome sharing, as this evidence is needed for policymaking related to adequate measures for improving health conditions of Afghan refugees in Pakistan. This investigation results will be submitted in the form of draft to the University of the Punjab, Lahore, Pakistan and Higher Education commission library, Islamabad for the record and guidance for the future investigations. The research will be submitted in the form of research papers to international journals.\n\n\nStudy status\n\nData collection was initiated in March 2020 and completed in May 2021. Currently, the data is analyzed. A first manuscript draft will be finished by October 2021.\n\n\nDiscussion\n\nThe Pakistani health care system met a number of public health challenges over the past decades. Afghan refugees are a significant population group which has to be served by provincial health facilities. In the 1980s and 1990s, the government of Pakistan focused mainly on addressing basic health care needs of refugees related to epidemics like malaria. More recently, the attention shifted to providing antenatal care and child health immunization coverage among refugees in Pakistan.30 The strong focus on infectious diseases relates to a study by UNHCR in 2012, which emphasizes that the main health problems faced by refugees were skin diseases, typhoid, malaria, diarrhoea, measles, dysentery, hepatitis C, thalassemia, cholera and tuberculosis.31 Afghan refugees experience several health risks which may increase the risk of infectious diseases. For that reason, Afghan refugees contributed to the spread of polio in Pakistan.32 However, their health status has never been comprehensively evaluated.\n\nThis study will provide an overview of the health-related quality of life of Afghan refugees in Punjab and Khyber Pakhtunkhwa. A comprehensive approach using pre-validated questionnaires was used for assessment. The outcomes of families in different provinces and clusters will be compared for living conditions and social inclusion in their host areas.\n\n\nLimitations\n\nStudy limitations are that participants with inability to response to consent procedures and questionnaires were not included in the investigation. As for all epidemiological surveys, the inclusion of marginalised groups, such as refugees, is a major challenge for all kinds of surveys, particularly for health surveys. Although a random sampling technique was applied, various sampling procedures have shown limited success in migrant health research. Despite these limitations, the findings of the study will provide information on the current health status of Afghan refugees. There is a need for research in this regard to provide better health care facilities to refugees.\n\n\nData availability\n\nNo data are associated with this article.", "appendix": "Acknowledgments\n\nWe acknowledge support from the German Research Foundation (DFG) and the Open Access Publication Fund of Charite – Universitatsmedizin Berlin.\n\n\nReferences\n\nLougarre C: Using the Right to Health to Promote Universal Health Coverage: A Better Tool for Protecting Non-Nationals' Access to Affordable Health Care? Health Hum Rights. 2016; 18: 35–48. PubMed Abstract \| Free Full Text\n\nYusuf S, Anand S, MacQueen G: Can medicine prevent war? Imaginative thinking shows that it might. BMJ. 1998; 317: 1669–1670. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLanglois EV, Haines A, Tomson G, et al.: Refugees: towards better access to health-care services. Lancet. 2016; 387: 319–321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbbas M, Aloudat T, Bartolomei J, et al.: Migrant and refugee populations: a public health and policy perspective on a continuing global crisis. Antimicrob Resist Infect Control. 2018; 7: 113. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUNHCR: Operational Portal Refugee Situations. Brussels: United Nations High Commissioner for Refugees; 2020.\n\nKuhn S, Rieger UM: Health is a state of complete physical, mental and social well-being and not merely absence of disease or infirmity. Surg Obes Relat Dis. 2017; 13: 887. PubMed Abstract \| Publisher Full Text\n\nGholami A, Jahromi LM, Zarei E, et al.: Application of WHOQOL-BREF in Measuring Quality of Life in Health-Care Staff. Int J Prev Med. 2013; 4: 809–817. PubMed Abstract \| Free Full Text\n\nMartinez-Martin P, Prieto-Flores ME, Forjaz MJ, et al.: Components and determinants of quality of life in community-dwelling older adults. Eur J Ageing. 2012; 9: 255–263. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMagklara K, Skapinakis P, Niakas D, et al.: Socioeconomic inequalities in general and psychological health among adolescents: a cross-sectional study in senior high schools in Greece. Int J Equity Health. 2010; 9: 3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPavli A, Maltezou H: Health problems of newly arrived migrants and refugees in Europe. J Travel Med. 2017; 24. PubMed Abstract \| Publisher Full Text\n\nDaynes L: The health impacts of the refugee crisis: a medical charity perspective. Clin Med. 2016; 16: 437–440. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorgan WA: Experience of a clinic for Afghan refugees in Pakistan. West J Med. 1988; 149: 234–238. PubMed Abstract \| Free Full Text\n\nBraveman P, Gottlieb L: The social determinants of health: it's time to consider the causes of the causes. Public Health Rep. 2014; 129(Suppl. 2): 19–31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWangdahl J, Lytsy P, Martensson L, et al.: Health literacy and refugees' experiences of the health examination for asylum seekers - a Swedish cross-sectional study. BMC Public Health. 2015; 15: 1162. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoutter AK, O'Steen B, Gilmore A: The student well-being model: a conceptual framework for the development of student well-being indicators. Int J Adolesc Youth. 2014; 19: 496–520. Publisher Full Text\n\nSteel Z, Chey T, Silove D, et al.: Association of torture and other potentially traumatic events with mental health outcomes among populations exposed to mass conflict and displacement: a systematic review and meta-analysis. JAMA. 2009; 302: 537–549. PubMed Abstract \| Publisher Full Text\n\nPanter-Brick C, Grimon MP, Kalin M, et al.: Trauma memories, mental health, and resilience: a prospective study of Afghan youth. J Child Psychol Psychiatry. 2015; 56: 814–825. PubMed Abstract \| Publisher Full Text\n\nBadshah S, Mason L, McKelvie K, et al.: Maternal risk factors in Afghan-refugees compared to Pakistani mothers in Peshawar, NWFP Pakistan. J Pak Med Assoc. 2011; 61: 161–164. PubMed Abstract\n\nUNHCR: UNHCR in Pakistan: An enduring partnership.2020. Accessed April 2020. Reference Source\n\nUNHCR: Afghan Refugees Camp Population in KP March, 2018. Brussels: United Nations High Commissioner for Refugees; 2018.\n\nCommissionerate for Afghan Refugees. Punjab Figures at a Glance. Accessed April 2020. Reference Source\n\nVahedi S: World Health Organization Quality-of-Life Scale (WHOQOL-BREF): Analyses of Their Item Response Theory Properties Based on the Graded Responses Model. Iran J Psychiatry. 2010; 5: 140–153. PubMed Abstract \| Free Full Text\n\nTopp CW, Ostergaard SD, Sondergaard S, et al.: The WHO-5 Well-Being Index: a systematic review of the literature. Psychother Psychosom. 2015; 84: 167–176. PubMed Abstract \| Publisher Full Text\n\nHollifield M, Verbillis-Kolp S, Farmer B, et al.: The Refugee Health Screener-15 (RHS-15): development and validation of an instrument for anxiety, depression, and PTSD in refugees. Gen Hosp Psychiatry. 2013; 35: 202–209. PubMed Abstract \| Publisher Full Text\n\nChinn D, McCarthy C: All Aspects of Health Literacy Scale (AAHLS): developing a tool to measure functional, communicative and critical health literacy in primary healthcare settings. Patient Educ Couns. 2013; 90: 247–253. PubMed Abstract \| Publisher Full Text\n\nDoocy S, Lyles E, Akhu-Zaheya L, et al.: Health service access and utilization among Syrian refugees in Jordan. Int J Equity Health. 2016; 15: 108. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDoocy S, Lyles E, Akhu-Zaheya L, et al.: Health Service Utilization among Syrian Refugees with Chronic Health Conditions in Jordan. PLoS One. 2016; 11: e0150088. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDoocy S, Lyles E, Roberton T, et al.: Prevalence and care-seeking for chronic diseases among Syrian refugees in Jordan. BMC Public Health. 2015; 15: 1097. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDembe AE, Partridge JS, Geist LC: Statistical software applications used in health services research: analysis of published studies in the U.S. BMC Health Serv Res. 2011; 11: 252. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMalik MS, Afzal M, Farid A, et al.: Disease Status of Afghan Refugees and Migrants in Pakistan. Front Public Health. 2019; 7: 185. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUNHCR: Report on Issues faced by Afghan Refugees during Repatriation. Brussels: United Nations High Commissioner for Refugees; 2012.\n\nTribune TE: Fighting Disease: Gilani blames refugees for polio spread. Bilal Ali Lashri. 2011." }	[ { "id": "130109", "date": "27 Apr 2022", "name": "Alejandro Gil-Salmerón", "expertise": [ "Reviewer Expertise integrated care", "health services research", "social and preventive medicine", "social determinants of 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\nI would like to congratulate all of the authors on this nicely presented protocol.\nMy only concern is that the begining of the abstract starts addressing \"accessibility to health care\", and there are studies focused on this aspect of refugees' health and social determinants of health, whereas the protocol addresses \"health-related quality of life\" as the main varaible, and access to healthcare services is the \"dependent variable\", so the authors should explain how health-related quality of life could be affected by accessibility.\n\nThis might create some discordance with the rest of the text.\nI would suggest the authors include some of the results of a large-scale project in Europe. The first one is a scoping literature review, the second one an analysis of the health status and needs, and the third one is an analyis of the accessibility by percieived discrimination in healthcare settings and avaiability of transaltion services:\nLebano et al. (20201). Riza et al. (20202). Gil-Salmerón et al. (20213).\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": "12572", "date": "14 Oct 2024", "name": "Florian Fischer", "role": "Author Response", "response": "The fact that a certain number of the predictor variables in surveys weren't always independent or dependent must be kept in mind. A predictor variable that was independent for one survey could become a dependent variable in another depending on the research survey (Flannelly et al., 2014). This assumption should be kept in mind while analyzing the survey's results because predictors were utilized in previous surveys as both independent and dependent variables, such as self-rated health (Vogel et al., 2021; Williams et al., 2017), substance abuse(smoking, naswar) (Abernathy et al., 1966), cultural compatibility (Iivari & Iivari, 2011), linguistic barriers, face discrimination (Salleh et al., 2021), social inclusion (Nihinlola, 2020), access to clean water, access to sanitation (Purba & Budiono, 2019), access to education, access to healthcare information via social, print or electronic media, access to healthcare, chronic health illness (Grønning et al., 2018), last time visited health facility, socioeconomic support from government or donor agencies (Nihinlola, 2020), health care cost affordability. Confounders were adjusted at the design stage with demographic randomization of the sample in all the selected regions. Age group, gender, and health illness quota matching of all the selected strata was done to minimize the confounder effect. Multivariate statistical models were applied to control the confounders at the analysis stage. Health-related quality of life (HRQoL) encompasses various aspects of an individual's overall well-being, including physical, mental, and social health. Accessibility plays a crucial role in determining HRQoL, as it directly influences how individuals can interact with their environment and access necessary resources and services. Accessibility impacts health-related quality of life (HRQoL) by affecting physical, economic, social, and psychological aspects. Limited physical access to environments and services can hinder mobility and independence, while economic barriers can restrict access to healthcare and employment. Social accessibility affects inclusion and participation, while inadequate communication access can lead to isolation. Improving accessibility helps enhance HRQoL by ensuring individuals can fully engage in daily activities and maintain overall well-being. All the domains are discussed in detail in final result as mentioned in link below: https://www.researchsquare.com/article/rs-3925465/v1 As per suggestion relevant literature was added as mentioned in table 1. The literature from developed countries, including the European nations, United States, and Australia focuses on various aspects of refugee health assessment, such as health-related quality of life, mental health screening, and access to healthcare, food insecurity, and language proficiency in the host country. However, the specific type of health assessment conducted may vary depending on the country's policies and the author's research focus." } ] }, { "id": "148759", "date": "25 May 2024", "name": "Shraddha Kashyap", "expertise": [ "Reviewer Expertise Mental health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this protocol, which describes the methodology of a study aiming to assess the health status (including wellbeing, mental health, health literacy, and factors affecting health and health care) among Afghan people with refugee backgrounds, living in Pakistan. This paper describes rigorous sampling techniques in a complex environment, and it is clear and well written. It is an important area of work.\nI note that the study (for which this is a protocol) has already been conducted. Could authors provide a justification for publishing the methodology as a separate protocol rather than publishing the methods together with results, and a discussion of the implications of the findings? The cross-sectional nature of the design is limiting in that causal associations between environmental factors and wellbeing cannot be made, however, the results will provide helpful information as a snapshot of the health status of Afghan refugees living in Pakistan.\n\nGiven the time frame in which data was collected (March 2020-May 2021), can authors clarify whether there were any measures directly related to the impacts of COVID on participants’ wellbeing?\nThe following queries for authors are more conceptual and are suggestions to consider for this and/or future studies.\nAuthors have acknowledged that factors such as literacy levels have led to certain groups of people being excluded from the study, and this is understandable given that the study requires participants to complete written surveys. At the same time, is it possible that the people excluded from the study are the most vulnerable, and find themselves frequently excluded from such efforts to provide appropriate support? As a quantitatively trained researcher myself who has worked on similar projects using similar methodologies, my question is as follows; is our understanding of factors such as wellbeing, mental health, and health among refugee populations limited by how we have chosen to measure them? That is, by only using quantitative methodologies, which requires participants to complete written surveys as the only option. Could authors discuss whether or not they considered collecting qualitative data, to complement the quantitative findings (e.g., by collecting data relating to narratives about wellbeing, told by people who may not be able to complete surveys)? This would account for all literacy levels, potentially enhance the cultural sensitivity of the project, and improve the validity of findings.\nIf this was considered, could authors describe any barriers faced in doing this?\nFurther, despite rigorous forward and back translation of surveys, can factors as culturally and contextually bound such as concepts of mental health, distress, quality of life, and wellbeing, be accurately and fully captured for diverse Afghan communities, from adaptations of measures designed from a Western paradigm of mental health and wellbeing? The following are examples of papers which discuss this issue: 1) Culture and reform of mental health care in central and eastern Europe. WHO, (2017 1) 2) Carpenter-Song et al. (2010 2) 3) Parker H. et al. (2003 3)\nCould authors provide some reflections on this?\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "12573", "date": "14 Oct 2024", "name": "Florian Fischer", "role": "Author Response", "response": "Registering the research protocol at the national level helps establish project novelty and priority. This is crucial as similar studies might be initiated simultaneously at different institutions. If another study on the same topic and population is published before ours, protocol registration can demonstrate our research's originality and timeline. This process ensures that our project's unique contributions are recognized despite overlapping research. Research article on Health related quality of life of Afghan Refugees was published before our detailed article from Pakistan. The survey adopted a quantitative research method because it provides the advantages of large sample size, more accurate, rapid numerical data collection, presentation of collected data in the form of graphical display, and results interpretation to generate useful information for decision-making (Conroy et al., 2008). The cross-sectional survey design was selected because it allowed researchers to instantly gather information from a large number of respondents at one point in time and compare group variations in a time-efficient and economical way (Kesmodel, 2018). This cross-sectional investigation only gives a snapshot of limited factors affecting the health-associated quality of life among Afghan refugees in a precise time and environment and the number and nature of determinants may vary over the period. A standard causal relationship between sociodemographics characteristics, predictors, and the outcome variable could not be established due to the cross-sectional design of the current investigation. The longitudinal investigation was not planned due to the time and financial limits. The fact that this research relies on refugee interviewed /self-documented data during the COVID-19 pandemic, which might not fully reflect real behavior, was also one of the survey's main limitations. The survey was executed by a team of two principal researchers and four bilingual Afghan refugee research associates who assisted the sampled Afghan refugees in filling out the questionnaires on paper and performed in-person interviews with respondents who were illiterate or requested interviews. Only refugees who were unable to understand consent procedures or respond to a survey questionnaire due to cultural hesitancy were not included in the investigation. A survey on Afghan refugees' health care in Pakistan was challenging to conduct due to a diverse range of issues. The individuals contacted by organizations working with refugees declined to share refugee lists with contact numbers because of the non-data sharing policy about refugees due to security and confidentiality concerns. Instead, we used online statistics about refugees in Pakistan to approximate about population in each area and contacted the locals in charge of refugee regions to assist in surveys. Afghan refugee research associates were reluctant to reveal their identity at any stage of the project due to unknown security concerns. Hiring bilingual Afghan refugees and traveling to these areas to meet locals in charge of survey permission and fieldwork were big challenges. It took almost 18 months to complete the desired sample size with high nonresponsive rates in these areas. The response rate for the current investigation was 55.45 %. The 2137 respondents were approached to complete the sample size of 1185 participants. The population was quite sensitive and emotional if they did not like any question, facial expression, and clothing of the investigator, conversation with the female investigator, or use of mobile they abruptly abandoned the questionnaire or interview before it was even halfway completed. Our team members adhere to the local dress code and ethical guidelines and stay away from everything that would interfere with the research study. In the majority of the districts, only one female was permitted to approach a female at home for the research, and men were more likely to give interviews outside of their homes, in camps, or tea shops. Qualitative data complement quantitative results by providing deeper insights into the subject matter. This combination enhances the validity of findings and offers a more comprehensive understanding of the research topic. Qualitative data collection was initially planned but University DPCC based on the conceptual framework only permitted the Quantitative Survey." } ] }, { "id": "275681", "date": "30 May 2024", "name": "Izaddin Ahmad Aziz", "expertise": [ "Reviewer Expertise Psychology", "imigration issues" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn general, provides a clear and comprehensive overview of the study's objectives and methodology. The introduction effectively highlights the importance of addressing the factors that impact the health-related quality of life of Afghan refugees in Pakistan, setting a strong foundation for the research. The logical flow of information and the detailed explanation of the study design and methods demonstrate thorough planning and preparation for the study. Overall, the introduction is well-written and engaging, effectively capturing the reader's interest and setting the stage for the rest of the research. The good approach to data collection and analysis, including the use of standardized instruments and statistical software, is commendable and will likely yield reliable and valid results. The inclusion of key variables such as socio-demographic characteristics, health status, and socio-economic factors will provide a holistic understanding of the factors influencing health-related quality of life among Afghan refugees in Pakistan.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "12574", "date": "08 Oct 2024", "name": "Florian Fischer", "role": "Author Response", "response": "Thank you very much for this positive feedback." } ] } ]	1	https://f1000research.com/articles/10-971
https://f1000research.com/articles/13-1223/v1	14 Oct 24	{ "type": "Research Article", "title": "Physical activity level among pregnant women attending maternal healthcare services in rural Karnataka; findings of a cross-sectional study", "authors": [ "Balamurugan Janakiraman", "Arunachalam Ramachandran", "Hariharasudhan Ravichandran", "Kshama Susheel Shetty", "Mohammad Sidiq", "Aksh Chahal", "T.S. Veeragoudhaman", "Sathvik B Sridhar", "Ramya Ramasamy Sanjeevi", "Richa Hirendra Rai", "Sonia Pawaria", "Karthick Balasubramanian", "Neha Kashyap", "Krishna Reddy Vajrala", "Mshari Alghadier", "Balamurugan Janakiraman", "Arunachalam Ramachandran", "Hariharasudhan Ravichandran", "Kshama Susheel Shetty", "Mohammad Sidiq", "Aksh Chahal", "T.S. Veeragoudhaman", "Sathvik B Sridhar", "Ramya Ramasamy Sanjeevi", "Richa Hirendra Rai", "Sonia Pawaria", "Karthick Balasubramanian", "Neha Kashyap", "Krishna Reddy Vajrala" ], "abstract": "Background Regular exercise during pregnancy improves fetal and mother outcomes unless contraindicated. Despite being generally safe and beneficial, non-participation in prenatal activity is relatively common among most of the Asian countries due to multiple reasons. In India, findings related to maternal physical activity and its determinant are scant.\n\nObjective The objective of this study is to assess the physical activity level and associated factors among pregnant women attending maternal healthcare services in Dakshina Kannada District in India.\n\nMethod A multi-center community-based cross-sectional study was conducted recruiting 424 pregnant women attending the maternal healthcare facilities at four taluks of Dakshina Kannada district in Karnataka state, India. A structured questionnaire that collected information on socio-demographic, and maternal characteristics was used and the Pregnancy Physical Activity Questionnaire tool was used to determine the physical activity during pregnancy. Logistic regression model was used to determine the predictor variables.\n\nResults The prevalence of physical inactivity was 40.33%. Physical activity is favorable among pregnant women aged between 25 to 29 years, residing in an urban locality, diploma or graduation and being housewife. Determinants of physical inactivity during pregnancy were sedentary occupation (AOR 7.22, 95% CI 2.2, 23.4), low family income (AOR 3.16, 95% CI 1.414, 7.054), having one child (AOR 5.4, 95% CI 1.3, 22.2), during 2nd trimester (AOR 2.513, 95% CI 1.5, 4.23) and self-reported lack of time (AOR 2.884, 95% CI 1.410, 5.901).\n\nConclusion and recommendation A moderate proportion of pregnant women reported physical inactivity during pregnancy in the Dakshina Kannada district, Karnataka. Physical inactivity was associated with sedentary employment, low income, number of children, trimester, and time constraints. Measures should be undertaken to promote the importance of recommended levels of physical activity, enhance access, and support system targeting pregnant women.", "keywords": [ "Pregnancy", "Physical activity", "Physical exercise", "Physical activity pattern", "Physical activity level" ], "content": "Background\n\nPhysical activity is any bodily movement produced by skeletal muscles that requires energy expenditure, it includes domestic, work-related, transportation and recreational activities.1 It plays a significant role in improving maternal and child health and prevention of chronic non-communicable diseases.2 Physical activity during pregnancy has a significant role in preparation for labor effort and reduction of the duration of the labor.3 It is also important to prevent pregnancy-related complications such as gestational diabetes mellitus, preeclampsia, gestational weight gain and improved maternal fitness and well-being, mood stability, decreased musculoskeletal discomfort and lower limb edema.4–11 Not only for mothers it also benefits the fetus including decreased resting fetal heart rate, increased amniotic fluid level, improvement to the viability of the placenta, early neurobehavioral maturation and stress tolerance.4,11,12 Additionally, it lowers the incidence of operative delivery and prematurity.4\n\nPregnancy is a time of biological, social, psychological and behavioral changes associated with the decline of physical activity and exercise habits in pregnant women because of this most pregnant women especially in low and middle-income countries perceive rest and relaxation as being significantly more important than having regular exercise or being active during pregnancy.13 The World Health Organization’s guideline on physical activity recommends that pregnant women engage in at least 150 minutes of moderate-intensity physical activity on most days/weeks in the absence of medical/obstetrical complications. But, high-risk activities like vigorous exercise and contact sports should be avoided.1 Several developed countries like the United States, the United Kingdom, Canada, Australia, Denmark, and Japan have their physical activity guidelines for pregnant women.14–18 In contrast, in developing countries like India the evidence base on implementing national physical activity guidelines is sparse.\n\nSustainable Development Goals for global development by 2030 have listed 17 goals with more than 100 indicators. Ensuring healthy lives and promoting well-being for all at all ages is the third goal listed under Sustainable Development Goals. In this goal, strategies to reduce global maternal mortality ratio < 70/100,000 live births, and to increase access to reproductive healthcare services by 2030 were recommended to national policymakers worldwide by the World Health Organization. Despite the standardized healthcare facilities and substantial progress made in contributing to Sustainable Development Goal 3 (SDG target 3.1) through a record decline in mortality rate from 26/1000 live births in 2019 to 21/1000 live births in 2020, the state of Karnataka is still facing challenges as least performer among the five southern states of India towards maternal mortality rate. According to a report by the president of the Karnataka State Obstetrics and Gynecological Association in 2022, the main reasons considered for the high maternal mortality rate are irregular medical checkups and non-adherence to medical advice.19–21\n\nThough the American College of Obstetricians and Gynecologists committee opinion number 804 recommends continuing physical activity during pregnancy and the postpartum period, globally, about 60% of women become inactive during pregnancy.14 In India, the prevalence of physically active women during pregnancy ranges from 2.8% to 10.2% respectively.22,23 Evidence in the literature insists on the necessity of physical activity for normal anatomic and physiologic changes in the growing fetus, the physical activity practice is commonly lacking in the general population. The physical activity dosages recommended based on obstetric evaluation have many positive effects on maternal and fetal health. However evidence reports that the majority of pregnant women tend to decrease their physical activity during pregnancy due to different factors.13,19,20,24,25 Also sedentary lifestyle is reported as a major risk factor for 50% of Caesarean deliveries in Mangalore town, Karnataka. Therefore, the aim of this study is to assess the prevalence and associated factors of self-reported physical activity during pregnancy among pregnant women in Dakshina Kannada District of Karnataka.\n\n\nMethods\n\nThis was a multi-center community-based cross-sectional descriptive study conducted among pregnant women in 8 maternal healthcare facilities in 4 taluks (administrative zones) of Dakshina Kannada district, situated in Karnataka state, India. This study was carried out from August 2023 to January 2024. The study protocol was approved by the institutional ethical review committee of the Alvas College of Physiotherapy and Research Centre (ref no; ACP/OP/CL/20230323/03, dated 23/03/2023). All the participants provided informed consent, and they adhered to the principles outlined in the Declaration of Helsinki. STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) for cross-sectional reporting guidelines was used to assess the paper components of the manuscript.\n\nAccording to the 2011 census, Dakshina Kannada district has a population of 2.89 million of which 52.33% are rural habitants and 1.54 million are females. The district is divided into 9 taluks (administrative zones) and the gender-wise literacy was 93.13 and 84.13 for males and females respectively. The female literacy rate of the district was 79.8% in rural and 88.8% in urban zones. However, the female literacy rate of the study area (Dakshina Kannada) was higher than that of the Karnataka state which is 68.08.26 The state is an achiever (100) for one of the 16 SDGs: affordable and clean energy; a performer (50–64) for six goals: zero hunger, quality education, gender equality, industry, innovation and infrastructure, climate action, life below water; and an aspirant (0–49) for none of the goals. Of the 16 SDGs, the state is an achiever (65–99) for nine of them: no poverty, good health and well-being, clean water and sanitation, decent work and economic growth, reduced inequality, sustainable cities and communities, sustainable consumption and production, life on land, peace, justice, and strong institutions.25 According to the 2023 Niti Aayog report, the Dakshina Kannada district with 39 deaths per 1000 live births is far ahead of other districts. The NHFS-5 for the years 2019-2020 reported that the mother who had an antenatal check-up in their 1st trimester and those who had at least 4 antenatal care visits were 86.1% and 82% respectively in the Dakshina Kannada district. As per the reports of the special bulletin by the Vital Statistics Division India for 2018-2020, the maternal mortality ratio (MMR) of Karnataka was 69 (95% CI 35, 103) compared to the MMR of 97 (95% CI 88, 106) of India.\n\nAll pregnant women aged 18 and above, Kannada speaking, native of the study area for the past 1 year, and those who attended the antenatal care clinic in those settings were included in this study. Pregnant women who presented with impaired verbal comprehension, visual impairment, or physical or psychological conditions that could interfere with comprehension and/or autonomy in consent to participate, mothers who were categorized as risk pregnancy and medically advised to avoid physical activity were excluded. All the participants signed the written informed consent and an impartial witness was present for mothers with no formal schooling (unable to read).\n\nThe study sample size was determined by using the single population proportion formula; by assuming a 5% level of significance, confidence interval of 95%, and 50% prevalence of physical inactivity less than the recommended guidelines by the pregnant women in the study area (non-availability of regional data). The derived power calculated sample was 384, the final sample size was n = 424 after accommodating for 15 % contingency plan. On average 30 to 35 pregnant women visit these maternal healthcare facilities (MHF) on average. To improve sample and time representativeness the data collection was limited to a maximum of ‘5’ in a single day for a single MHF. A multistage sampling technique was designed to attain the required power-calculated sample for this study.\n\nThe Dakshina Kannada district has 2 revenue sub-divisions and nine taluks; Mangalore, Moodbidri, Mulki, Ullala, Bantawal, Puttur Belthangadi, Sullia, and Kadaba. We conveniently selected 4 taluks from where the Antenatal care clinics of outpatient Obstetrics and gynecology department of Alvas Health Center (Moodbidri), and the out-patient women’s health care department of Alvas Physiotherapy Clinic (Moodbidri) receive the majority of the clients. The MHF stationed at PHCs and Anganwadi centres were visited and that serves the majority of the women of that taluks were selected. Based on the previous year’s registry data, the required sample for each selected centre was proportionally allocated. So, during every data collection day, the Kath number was calculated by dividing the number of mothers who visited the center the previous working day by ‘5’ (maximum slab allowed). Data was collected until the proportional sample for the center was achieved Figure 1.\n\nData were collected using a structured questionnaire through face-to-face interviews. Four Physiotherapy interns trained in data collection procedures were involved as the data collectors under the supervision of one Female Clinical Physiotherapist. The questionnaire was adapted from previous relevant literature. The structured questionnaire consisted of items related to socio-demographics, maternal characteristics, and pregnancy physical activity questionnaire tool. The pregnancy physical activity questionnaire was first developed in English24 and then translated to the local language (Kannada) and then back to English to facilitate the understanding of the respondents. A one-day training was provided for the data collectors and a supervisor regarding the objectives of the study, way of approach to the participant, sampling techniques and procedures, client privacy issue, client confidentiality issue, client informed and voluntary participation, data collection method, and significance of the study. Then after, a pretest was conducted on 5% of the sample size before commencing the actual data collection. The pretest was performed at a private antenatal health care clinic, which is similar in culture and lifestyle to the main data collection setting. The purpose and objectives of the study were clearly stated on the first page of the questionnaire which the interviewers explained to participants. During data collection, there was close communication among the data collectors, a supervisor and a principal investigator. The collected questionnaires were checked for completeness and on spot corrective measures were taken both by data collectors and supervisors. Daily meetings have been conducted among the data collectors, a supervisor and a principal investigator for discussion regarding presenting difficulties and to assess the progress of data collection.\n\nData were checked, coded and entered into Epi-info7 then exported to the SPSS version 23 software package for further analysis. Frequencies and cross-tabulations were used to summarize descriptive statistics. The data were presented by texts, tables and graphs. The overall proportion with 95% CI was calculated to determine the prevalence of moderate-intensity physical activity. Furthermore, bivariate logistic regression analysis was used to identify factors associated with moderate-intensity physical activity. Multivariate logistic regression was used to statistically adjust for covariates found to be statistically significantly associated with moderate physical activity at p < 0.05.\n\n\nResults\n\nA total of 424 questionnaires were distributed to pregnant women, all filled with a 96.9% response rate. The mean age of the participants was 26.89 ± 4.704 years. More than one-third of the participants, 37.5% (159) were between the age of 25-29 and most of them, 80.7% (342) were from urban areas. About 91.7% of the participants were married and nearly half of the participants were housewives. The other socio-demographic characteristics of the subjects are presented in Table 1.\n\nMore than one-third the participants were nulliparous 37.7% (160) and had no children and almost two-thirds of the participants were in the third trimester of their pregnancy (Table 2).\n\nAbout 80.7% (342) participants had no regular physical activity before pregnancy and 79.7 % (338) pregnant women agreed that being active during pregnancy is important and only one-third of the participants had husbands who exercised regularly. Health institutions and families were the most commonly reported sources of information regarding the benefits of exercise during pregnancy and fear of miscarriage and too tired were the most reported reasons for not exercising during pregnancy (Table 3).\n\nThe median physical activity was marginally raised in third trimester [3.38 (1.29)] compared to 1st [2.63 (0.989)] and 2nd trimester [2.39 (2.84)], respectively (Table 4). The median frequency obtained for light intensity activity across all the trimesters were similar (3.3 vs 3.5 vs 3.5), respectively. The amount of energy spent on occupational activities diminished as the trimester progressed (2.45 vs 1.75 vs 0.88) and the energy spent by women in household activities did not differ across the trimesters (2.45 vs 2.52 vs 2.52).\n\nAll the independent variables were included in the bivariate analysis with a cut-off significance of P < 0.25 for further final model multivariate analysis. The bivariate analysis results (Table 5) demonstrated the following independent variables as age, residence, educational status, work status, family monthly income, parity, number of children, trimesters, regular exercise before pregnancy, lack of exercise knowledge and having no time had P value < 0.25 and were included for multivariate analysis. The multivariable regression analysis results identified several independent variables that are associated with the physical activity of pregnant women.\n\nWomen merchants (selling goods, online retailers, business) are 7.2 times more likely to be sedentary (95% CI: 2.2 to 23.4) than those employed in civil services and housewives. Pregnant women with lower family income per month demonstrated 3.16 times more sedentary lifestyles (95% CI 1.414 to 7.054) compared to the higher income groups. Pregnant women who had 1 child were 5.4 times more sedentary (95% CI: 1.3 to 22.2) than those who had 2 children. It is also revealed that pregnant women in the first trimester were least sedentary compared to those in the second and third trimesters. Pregnant women with no participation in regular physical activity before pregnancy were 2.39 times protected from being sedentary during pregnancy. Pregnant women lacking time to be active were 2.884 times sedentary compared with those who had time (Table 6).\n\n\nDiscussion\n\nThe purpose of this cross-sectional study is to determine the level of physical activity and determinants of the sedentary lifestyle during pregnancy among women attending antenatal health care centers in Dakshina Kannada district of Karnataka, India. The study findings revealed that 40.33% of women were physically inactive and 59.7% self-reported to practice the recommended level of physical activity. Overall, a moderate proportion of pregnant mothers reported below-par physical levels in the study area.\n\nThe prevalence of physical inactivity found in this study is higher than the prevalence reported in the Bangalore (India) study 7.2% in 2021,27 Zonal hospitals of Tigray (Ethiopia) 21.9% in 2019,28 Serbia 27.2% in 2020,29 Northern Sweden 27.3% in 2021,30 and Riyadh (Saudi Arabia) 41.62% in 2020.31 At the same time, the prevalence is lesser than the reported prevalence among the Western pregnant women population (75%) in 2016,32 pregnant women attending the Institutional antenatal care facility of Tigray (Ethiopia) (79.3%) in 2020,28 Middle eastern pregnant women (84%) in 2016,30 and pregnant women in South Asia (86%) in 2016.32 The differences in the level of literacy, economic background, awareness and accessibility towards antenatal health education and care, socio-cultural practices and beliefs, lifestyle practices and development in advanced technologies could be contributing factors for the varying range of prevalence worldwide. The second objective of this study is to identify the factors associated with a sedentary lifestyle during pregnancy. Type of employment, family income, number of children, stage of trimester, regular exercise before pregnancy and lack of time were the factors identified as significantly associated with physical inactivity among pregnant women attending antenatal care in Dakshina Kannada, Karnataka. Pregnant women involved in occupations such as merchants or businesses lack physical activity seven times compared to women involved in civil services and household activities. Women occupied as merchants or owned self-business were involved in prolonged sitting. They were lacking both occupational and leisure time physical activity. Involvement in sedentary occupation could also predispose pregnant women to adverse effects such as gestational diabetes, gestational hypertension, gestational weight gain and so on.33 At the same time excessive physical exertion at any occupation such as trunk forward bending, rotation, reaching and lifting could increase intra-abdominal pressure and can result in miscarriage or spontaneous abortion.34 This insists on the need for educating pregnant women about the safer level of physical exertion that could be accomplished in the workplace. In the present study, the pregnant women with low family income were three times physically inactive compared to average and high family income categories. Previous studies35–37 in the literature have reported that pregnant women with low family income were physically active compared to average and high income. The population included in those studies differs from the present study by socio-cultural aspects, financial background and lifestyle practices. Both state and central governments of India have implemented antenatal care and nutritional schemes such as Mathrushree, Mathrupoorna, Accredited Social Health Activist - ASHA package, Samagra Mathru Arogya Palana and so on for pregnant women below the poverty line. Though these schemes provide nutritional and financial assistance for antenatal care, there is no clear data to identify the reach of the American College of Obstetricians and Gynecologists’ recommended guidelines for physical activity in pregnant women from low family income. Lack of awareness on physical activity guidelines could be a contributing factor for physical inactivity among pregnant women with low family income. This necessitates the need for the promotion and implementation of physical activity in pregnant women with low family income living in south India.\n\nThe study findings identified that pregnant women with one child were five times physically active compared to 2 children and no children. The study finding is inconsistent with the previous reports from Ethiopia28,38 and Nigeria.39 In those studies,28,38,39 moderate physical activity is reported in pregnant women parenting two or more children. The higher rate of fertility and high magnitude of multiparity exists among the Ethiopian and Nigerian populations and which is average or low among the population included in this study. This could be a contributing reason for differences in physical activity patterns of parenting pregnant women. The parenting responsibilities differ in pregnant women with younger and elder children; and in primiparous and multiparous situations. Pregnant women with one young child are in need to deliver more parental responsibilities compared to pregnant women with two or three elder children and hence lack time for participating in physical activities. Probably the nulliparous pregnant women could able to find time to perform physical activity and hence they are not sedentary compared to pregnant women with one child. In this study, it is observed that physical activity declines in each trimester. Pregnant women in the second trimester were two times physically inactive compared to the first trimester. Lack of adequate knowledge and practice towards programming physical activity in each trimester is prevailing commonly in pregnant women. Additionally, fear of falling, miscarriage/spontaneous abortion, and anxiety refrains them from participating in physical activity programs during pregnancy. This is attributed to the trend of declining physical activity in advanced trimesters among pregnant women in Dakshina Kannada district. This study also revealed that pregnant women lacking schedules were two times physically inactive compared to those who were able to manage their time. More time spent in household or family activities and occupation could have compromised the time spent involvement in physical activity programs.\n\nThere were a few limitations in this present cross-sectional study. Firstly the collected data were self-reported and hence might have been affected by potential reporting bias. Secondly, there could be varied perceptions towards physical activity programming guidelines among the participants and lastly, the collected data lacking objective measurements. Nevertheless, these power-calculated sampled study reports valuable insights into the variables that are determinants of the physical activity levels among pregnant mothers in the study area. Further, the sampling procedure used and data collection strategy to limit the recording to five respondents per day per center would have enhanced the time and sample representation in this study.\n\n\nConclusion\n\nThis study found that a moderate proportion of pregnant mothers were not engaged in physical activity to the levels recommended by the ACOG guidelines. The determinants that negatively influenced physical activity were low family income, sedentary occupation, being primiparous, mothers in their second trimester, and reporting of lack of time as the reason.\n\nThough the national policies and schemes are favorably implemented towards the promotion of safer antenatal care, there still exists a deficiency in knowledge and practice towards the recommended level of physical activity guidelines in pregnancy. Strategies towards the target population are warranted to improve the physical activity status and to sensitize the benefits of being active during pregnancy.\n\n\nEthics and consent\n\nThe study protocol was approved by the institutional ethical review committee of the Alvas College of Physiotherapy and Research Centre (ref no; ACP/OP/CL/20230323/03) dated 22-03-2023. All the participants provided written informed consent, and they adhered to the principles outlined in the Declaration of Helsinki.", "appendix": "Data availability statement\n\nThe dataset contains comprehensive data collected from a study that examines physical activity levels among pregnant women across different trimesters and varying education levels. The dataset is structured to facilitate analysis of the relationship between pregnancy stages (trimesters), physical activity patterns, and educational backgrounds. 40\n\nRepository: Figshare\n\nTitle of Project: Physical activity level among pregnant women attending maternal healthcare services in rural Karnataka; findings of a cross-sectional study\n\nDOI: https://doi.org/10.6084/m9.figshare.25488730.v1\n\nThis project contains the following underlying data:\n\n1. File Name: Physical Activity Dataset\n\n2. Code Book of Physical Activity Dataset\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nCilar Budler L, Budler M: Physical activity during pregnancy: a systematic review for the assessment of current evidence with future recommendations. BMC Sports Sci. Med. Rehabil. 2022; 14(1): 133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSiyad S, Mustafa N, Banu SS, et al.: Pregnant Women’s Perceptions of Physical Activity: Adaptation of the Pregnancy Physical Activity Questionnaire in Dubai, a Multicultural Society. J. Public Health Res. 2022; 11(1): jphr.2021.2261. Publisher Full Text\n\nRibeiro MM, Andrade A, Nunes I: Physical exercise in pregnancy: Benefits, risks and prescription. J. Perinat. Med. 2022; 50(1): 4–17. PubMed Abstract \| Publisher Full Text\n\nMazur K, Machaj D, Mazur D: Physical activity during pregnancy-literature review. J. Edu. Health Sport. 2020; 10(1): 11–15. Publisher Full Text\n\nKominiarek MA, Peaceman AM: Gestational weight gain. Am. J. Obstet. Gynecol. 2017; 217(6): 642–651. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGascoigne EL, Webster CM, Honart AW, et al.: Physical activity and pregnancy outcomes: an expert review. Am. J. Obstet. Gynecol. MFM. 2023; 5(1): 100758. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAsante DO, Osei F, Abdul-Samed F, et al.: Knowledge and participation in exercise and physical activity among pregnant women in Ho, Ghana. Front. Public Health. 2022; 10: 927191. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrather H, Spitznagle T, Hunt D: Benefits of exercise during pregnancy. Pm&r. 2012; 4(11): 845–850. Publisher Full Text\n\nAna Y, Lewis MG, van Schayck OC , et al.: Is physical activity in pregnancy associated with prenatal and postnatal depressive symptoms?: Results from MAASTHI cohort study in South India. J. Psychosom. Res. 2021; 144: 110390. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee R, Thain S, Tan LK, et al.: Asia-Pacific consensus on physical activity and exercise in pregnancy and the postpartum period. BMJ Open Sport Exerc. Med. 2021; 7(2): e000967. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYu Y, Xie R, Shen C, et al.: Effect of exercise during pregnancy to prevent gestational diabetes mellitus: a systematic review and meta-analysis. J. Matern. Fetal Neonatal Med. 2018; 31(12): 1632–1637. Publisher Full Text\n\nBrown WJ, Hayman M, Haakstad LA, et al.: Australian guidelines for physical activity in pregnancy and postpartum. J. Sci. Med. Sport. 2022; 25(6): 511–519. PubMed Abstract \| Publisher Full Text\n\nMottola MF, Davenport MH, Ruchat SM, et al.: No. 367-2019 Canadian guideline for physical activity throughout pregnancy. J. Obstet. Gynaecol. Can. 2018; 40(11): 1528–1537. PubMed Abstract \| Publisher Full Text\n\nMohanty S, Sahoo J, Epari V, et al.: Prevalence, patterns, and predictors of physical inactivity in an Urban population of India. Cureus. 2022; 14(6). Publisher Full Text\n\nMagro-Malosso ER, Saccone G, Di Tommaso M, et al.: Exercise during pregnancy and risk of gestational hypertensive disorders: a systematic review and meta-analysis. Acta Obstet. Gynecol. Scand. 2017; 96(8): 921–931. Publisher Full Text\n\nDi Mascio D, Magro-Malosso ER, Saccone G, et al.: Exercise during pregnancy in normal-weight women and risk of preterm birth: a systematic review and meta-analysis of randomized controlled trials. Am. J. Obstet. Gynecol. 2016; 215(5): 561–571. PubMed Abstract \| Publisher Full Text\n\nArizabaleta AVM, Buitrago LO, de Plata ACA , et al.: Aerobic exercise during pregnancy improves health-related quality of life: a randomised trial. J. Physiother. 2010; 56(4): 253–258. Publisher Full Text\n\nBarakat R, Pelaez M, Montejo R, et al.: Exercise during pregnancy improves maternal health perception: a randomized controlled trial. Am. J. Obstet. Gynecol. 2011; 204(5): 402.e1–402.e7. Publisher Full Text\n\nMorton S, Pencheon D, Squires N: Sustainable Development Goals (SDGs), and their implementation: A national global framework for health, development and equity needs a systems approach at every level. Br. Med. Bull. 2017; 124(1): 81–90. PubMed Abstract \| Publisher Full Text\n\nLópez JL, Espinilla M, Verdejo Á: Evaluation of the impact of the sustainable development goals on an activity recognition platform for healthcare systems. Sensors. 2023; 23(7): 3563. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBiswas S, Dandapat B, Alam A, et al.: India’s achievement towards sustainable Development Goal 6 (Ensure availability and sustainable management of water and sanitation for all) in the 2030 Agenda. BMC Public Health. 2022; 22(1): 2142. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang C, Wei Y, Zhang X, et al.: A randomized clinical trial of exercise during pregnancy to prevent gestational diabetes mellitus and improve pregnancy outcome in overweight and obese pregnant women. Am. J. Obstet. Gynecol. 2017; 216(4): 340–351. PubMed Abstract \| Publisher Full Text\n\nNascimento SL, Surita FG, Cecatti JG: Physical exercise during pregnancy: a systematic review. Curr. Opin. Obstet. Gynecol. 2012; 24(6): 387–394. Publisher Full Text\n\nChasan-Taber L, Schmidt MD, Roberts DE, et al.: Development and validation of a pregnancy physical activity questionnaire. Med. Sci. Sports Exerc. 2004; 36(10): 1750–1760. Publisher Full Text\n\nAnjana RM, Sudha V, Lakshmipriya N, et al.: Physical activity patterns and gestational diabetes outcomes–the wings project. Diabetes Res. Clin. Pract. 2016; 116: 253–262. PubMed Abstract \| Publisher Full Text\n\nHailemariam TT, Gebregiorgis YS, Gebremeskel BF, et al.: Physical activity and associated factors among pregnant women in Ethiopia: facility-based cross-sectional study. BMC Pregnancy Childbirth. 2020; 20: 1–11. Publisher Full Text\n\nTodorovic J, Terzic-Supic Z, Bjegovic-Mikanovic V, et al.: Factors associated with the leisure-time physical activity (LTPA) during the first trimester of the pregnancy: the cross-sectional study among pregnant women in Serbia. Int. J. Environ. Res. Public Health. 2020; 17(4): 1366. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeander L, Lindqvist M, Mogren I, et al.: Physical activity and sedentary time during pregnancy and associations with maternal and fetal health outcomes: an epidemiological study. BMC Pregnancy Childbirth. 2021; 21: 1–11. Publisher Full Text\n\nAl-Youbi GM, Elsaid T: Knowledge, attitude, and practices on exercise among pregnant females attending Al-Wazarat Health Center, Riyadh, Saudi Arabia. J. Family Med. Prim. Care. 2020; 9(8): 3905–3915. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSilva-Jose C, Sánchez-Polán M, Barakat R, et al.: Level of physical activity in pregnant populations from different geographic regions: a systematic review. J. Clin. Med. 2022; 11(15): 4638. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThrower A, Quinn T, Jones M, et al.: Occupational physical activity as a determinant of daytime activity patterns and pregnancy and infant health. PLoS One. 2023; 18(12): e0296285. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCai C, Vandermeer B, Khurana R, et al.: The impact of occupational activities during pregnancy on pregnancy outcomes: a systematic review and metaanalysis. Am. J. Obstet. Gynecol. 2020; 222(3): 224–238. PubMed Abstract \| Publisher Full Text\n\nMuzigaba M, Kolbe-Alexander TL, Wong F: The perceived role and influencers of physical activity among pregnant women from low socioeconomic status communities in South Africa. J. Phys. Act. Health. 2014; 11(7): 1276–1283. PubMed Abstract \| Publisher Full Text\n\nBrunette E, Kotze J, Wood PS, et al.: An epidemiological study of physical activity patterns and weight gain in physically active and sedentary pregnant women in Tshwane, South Africa. Afr. J. Phys. Health Edu. Recreat. Dance. 2012; 18(sup-1): 132–143.\n\nHegaard HK, Damm P, Hedegaard M, et al.: Sports and leisure time physical activity during pregnancy in nulliparous women. Matern. Child Health J. 2011; 15: 806–813. Publisher Full Text\n\nGebregziabher D, Berhe H, Kassa M, et al.: Level of physical activity and associated factors during pregnancy among women who gave birth in Public Zonal Hospitals of Tigray. BMC. Res. Notes. 2019; 12: 1–6.\n\nAdeniyi AF, Ogwumike OO, Osinike CI: Physical activity and energy expenditure: findings from the Ibadan Pregnant Women’s Survey. Afr. J. Reprod. Health. 2014; 18(2): 117–126. PubMed Abstract\n\nSridhara S, Gopakkali P, Manoj KN, et al.: Identification of sustainable development priorities for agriculture through sustainable livelihood security indicators for Karnataka, India. Sustainability. 2022; 14(3): 1831. Publisher Full Text\n\nCensus of India: Office of the Registrar General and Census Commissioner, India. India: 2009. Web Archive. Reference Source\n\nSidiq M, Chahal A, Janakiraman B, et al.: Physical activity dataset. Figshare. 2024. Publisher Full Text" }	[ { "id": "332084", "date": "31 Oct 2024", "name": "Prof. Dr. Waribam Ranjeeta", "expertise": [ "Reviewer Expertise Physical Therapy", "rehabilitation", "Musculoskeletal and Sports Therapy", "cardiothoracic rehabilitation", "Neurological Rehabilitation" ], "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\nReport: The study is well drafted with complete chapters in detail and the statistical analysis is upto the mark with well labelled figures into it. Only thing which needs to be documented is the future scope and recommendations needs to be included for future researchers. It meets the requirements to be indexed.\nThank You\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "12755", "date": "08 Nov 2024", "name": "Dr Mohammad Sidiq", "role": "Author Response", "response": "Thank you so much learner reviewers for your expert comment. We will surely instill your recommendations in our updated manuscript. Best regards" } ] } ]	1	https://f1000research.com/articles/13-1223
https://f1000research.com/articles/11-203/v1	17 Feb 22	{ "type": "Study Protocol", "title": "Effect of a collaborative multidimensional approach versus usual care on the resolution of adult depression in primary care in Chile: study protocol for a single blinded cluster randomized controlled trial", "authors": [ "VERONICA VITRIOL", "ALFREDO CANCINO", "ANDRES SCIOLLA", "SERGIO GUIÑEZ", "JORGE CALVO", "MARCELA ORMAZABAL", "JOHANNA KREITHER", "SOLEDAD BALLESTEROS", "MARIA DE LA LUZ AYLWIN", "ALFREDO CANCINO", "ANDRES SCIOLLA", "SERGIO GUIÑEZ", "JORGE CALVO", "MARCELA ORMAZABAL", "JOHANNA KREITHER", "SOLEDAD BALLESTEROS", "MARIA DE LA LUZ AYLWIN" ], "abstract": "Background: Major depression (MD) is a prevalent and disabling condition in Chile. Most MD cases are treated at the primary care level. In Chilean primary care, the authors have gathered evidence of a prevalent complex depression subtype associated with a worse prognosis and characterized by interpersonal difficulties, suicidality and trauma history. This MD presentation suggests the need for a multidimensional, trauma-informed and interprofessional approach. The present study protocol describes the context, hypotheses and methods for a cluster randomized control trial (RCT) comparing a collaborative multidimensional approach and usual care in treatment outcomes of MD in primary care in Chile. Methods: This is a two-arm, single-blinded, cluster RCT to compare the efficacy of a collaborative multidimensional approach for depression (CMAD) versus usual care to treat MD in primary care clinics in Chile. In total, 394 depressed adults from 18 to 65 years of age in twelve clinics located in Chile’s Maule Region will be consented to participate in the study. Patients and care teams from each clinic will be randomized to the intervention or to the control arm. Interprofessional teams in the intervention arm will attend 27 hours of didactic and active learning sessions focused on clinical competences to effectively engage, treat and follow up patients with complex presentation of MD. Team in the control arm will receive 27 didactic sessions on current clinical guidelines for MD, professionals in both arms will receive 27 hours of continued education. Discussion: To improve treatment outcomes of MD in Chile, primary care teams should develop clinical competencies relevant to complex, difficult-to-treat types of MD within collaborative and trauma-informed approaches.", "keywords": [ "Depression treatment", "primary care", "collaborative care", "trauma-informed care", "randomized controlled trial" ], "content": "Abbreviations\n\nCMAD: Collaborative multidimensional approach for depression\n\nGAD-7: General Anxiety Disorder Scale-7\n\nGSES: General self-efficacy scale\n\nERS: Emotion regulation scale\n\nMD: Major depression\n\nMINI: Mini-International Neuro-psychiatric Interview\n\nPHQ9: Patient Health Questionnaire\n\nOQ-45: Outcome Questionnaire 45\n\nRCT: Randomized controlled trial\n\n\nBackground\n\nDepression is the leading cause of disability worldwide, contributing significantly to the overall global burden of morbidity and mortality.1 It is estimated that it affects almost 280 million people worldwide.1 In Chile, depression constitutes a significant public health problem.2 Findings before the SARS-CoV-2 pandemic showed that 18.2% of the adult Chilean population reported depressive symptoms, and 6.2% met the criteria for major depression (MD).3,4 This prevalence is expected to increase with the pandemic.5 Furthermore, it affects twice as many women as men, is the second leading cause of disability-adjusted life years and the first among women between 20 and 44 years.2\n\nSince 2001 there has been a Chilean national mental health program to treat MD. From 2006, this program has been known as Explicit Health Guarantees (Garantías Explícitas en Salud, GES, in Spanish), and is regulated by ministerial clinical guideline (Guía Clínica, 2013).6 According to existing data, primary care treat 90% of MD cases.7 Only those with current suicide attempts, suspected bipolarity or psychosis are referred to the specialty level.2,7\n\nDespite the implementation of the governmental guidelines, evidence shows limited competence in primary care teams to address MD,7 with remission rates close to 50% at one year of follow-up.8,9 There is also evidence of a high prevalence of comorbid anxiety disorders and reports of adverse life experiences in over 80% of patients with MD.10,11 Using latent class analysis, our group found evidence of a complex depressive subtype.12 This subtype, whose frequency is about half of the sample studied, is characterized by a history of suicide attempts, history of adverse life experiences, interpersonal difficulties, impairment in social functioning, and poor treatment response.12 These characteristics, which have been reported in refractory depression,13 can be understood in light of the neurobiological sequelae of exposure to psychological trauma.14 Currently, there are a lack of recommendations in depression treatment guidelines regarding the needs of patients with this complex clinical picture.\n\nAccording to a consensus of international experts, the clinical characteristics of patients with refractory depression are better conceptualized as difficult-to-treat depression.13 This conceptualization implies an understanding of depression as a chronic disease, which requires a collaborative, multidimensional, biopsychosocial clinical approach and an orientation to the management of symptoms and functional recovery.13 Working with similar populations, others have proposed the adoption of trauma-informed care principles and approaches, considering the cumulative interactions between trauma exposure, socioeconomic disadvantage, depression and suicidality14–16\n\nBoth difficult-to-treat depression and trauma-informed care imply a collaborative organization health model similar to that proposed by Wagner et al in the management of chronic diseases,17 including anxiety and depressive disorders as proposed by Archer et al.18 It involves the presence of a case manager, a structured patient-centered approach, scheduled follow-up visits, the use of validated measures to monitor treatment response, and interprofessional communication between the different levels of care.18 Considering all of the above, we hypothesize that a continuing education program for primary care teams that focuses on a biopsychosocial, trauma-informed care approach implemented in a collaborative model, will improve the outcomes of depression in comparison to usual care.\n\nSpecifically, we hypothesize that the collaborative multidimensional approach for depression (CMAD) in primary care will demonstrate greater efficacy relative to the standard treatment based on the clinical guidelines, considering:\n\n1. Adult depressed patients in the CMAD arm will significantly improve depressive symptoms compared to the control group at 3 and 6 months after admission.\n\n2. Adult depressed patients in the CMAD arm will significantly improve anxiety symptoms compared to the control group at 3 and 6 months after admission.\n\n3. Adult depressed patients in the CMAD arm will significantly improve interpersonal dysfunction, social impairment, and emotional dysregulation compared to the control group at 3 and 6 months after admission\n\n4. Adult depressed patients in the CMAD arm will achieve a significantly greater adherence than the control group at 3 and 6 months after admission.\n\nWe designed a cluster RCT protocol with two arms, single-blind to the outcome evaluator to compare the efficacy of a CMAD to improve the treatment outcomes of adult depression in primary care in Maule Region in Chile.\n\nThe general aim of this study is to compare the efficacy of a CMAD approach for MD with usual care according the standard treatment on the outcomes in primary care clinics in the Maule Region through a cluster RCT. The specific aims of this study are:\n\n1. To design a CMAD treatment approach that imparts primary care teams with the competencies to recognize the clinical, functional and psychosocial dimensions associated with difficult-to-treat depression. This design includes trauma-informed principles and patient-centered care communication skills.\n\n2. To implement the CMAD approach in primary care clinics in the Maule region, including a case manager, a structured patient-centered inter-professional management, a scheduled follow-up using validated instruments and continuous consultation with the specialty level.\n\n3. To compare the depressive symptoms in adults treated for MD in primary care Maule clinics using the CMAD approach versus the standard treatment at baseline, three and six months.\n\n4. To compare the anxiety symptoms in adult depressed patients treated for MD in primary care Maule clinics using the CMAD approach versus the standard treatment at baseline, three and six months.\n\n5. To compare the symptoms of functional variables of emotional regulation, interpersonal and social functions in adult depressive patients treated for MD in primary care Maule clinics, using the CMAD approach versus the standard treatment at baseline, three and six months.\n\n6. To compare the therapeutic adherence in adult depressive patients treated for MD in primary care Maule clinics using the CMAD approach and the standard treatment.\n\nThis study protocol is a cluster RCT, two parallel arms, single-blind to the outcome evaluator, which will compare the efficacy of a CMAD to improve the treatment outcomes of adult depression in primary care in the Maule Region in Chile.\n\n\nMethods\n\nTo meet the objectives of this protocol, primary care clinics belonging to the Maule Region in the municipalities of Talca, Curicó, Constitución, Sagrada Familia, Romeral and Pelarco will be invited to participate. These are centers that represent urban and rural areas of a disadvantaged region, including several rural areas where the socioeconomic and educational level is very low.19 To obtain the sample, 12 centers were identified, which were matched according to similar average socioeconomic and educational characteristics. Moreover, selection considered that there will be no cross contamination between the patients in the control clinics and the intervention clinics.34\n\nAdults between 18 and 65 years who enter treatment for depression in primary care clinics of the Maule Region will be invited for an evaluation after they sign a written informed consent statement.34 Those with a confirmed diagnosis of MD, according to the Mini-international Neuro-psychiatric interview, will be included in the study.20 On the other hand, those unable or unwilling to sign the informed consent, those with sensory disabilities, no access to a telephone, or who have been referred to a specialist level will be excluded from the study.\n\nEligible primary care clinics will be randomly assigned to the intervention and control arms of the study using a computer algorithm. Primary care teams of the intervention arm will receive training and implementation of the CMAD approach. Primary care teams of the control group will receive training in-line with the current clinical guideline for depression according.\n\nThe intervention arm will include 27 hours of training in the CMAD approach for primary care teams of at least one physician, a psychologist and a social worker. This approach integrates knowledge, attitudes, and skills to manage clinical manifestations associated with adversity or trauma throughout the lifespan, which are common in patients with complex difficult-to-treat depression. These competencies will be integrated with, not substituted for, the diagnostic and treatment recommendations included in the current clinical guidelines for depression. The training will be conducted by a team of two professors from the Universidad de Talca and one professor from the University of California, Davis in a total of eight sessions, four recorded lectures and four online workshops using a video conference platform. After training, primary care teams will implement a collaborative treatment model with a case manager, an individual treatment plan, a follow-up using a combination of validated self-report and clinician-administered instruments, with continuous monthly group supervision by a psychiatrist. All patients enrolled in the clinics assigned to the intervention arm will be treated by the same intervention type according to the CMAD model of treatment. In this arm, patients will receive the usual pharmacological and behavioral treatment, but the health care team will impart the treatment according to the CMAD management model.\n\nThe control arm will include 27 hours of training for primary care teams consisting of at least one physician, a psychologist and a social worker on the current clinical guidelines for MD. This guideline outlines a staging algorithm according to severity for the treatment of MD. The training will be conducted by two professors from Universidad de Talca and take place in 5-recorded lectures and three online workshops. After the training, the primary care teams will treat the patients according to the usual treatment. Teams are expected to be familiar with the guidelines and apply them. However, as is the usual treatment, no formal implementation will be offered. All patients enrolled in the clinics assigned to the control arm will be treated according to the usual care. In this arm, patients will receive the usual pharmacological and behavioral treatment, and the health care team will impart the treatment according to the usual clinic management.\n\nFor a given trial participant, the assigned study intervention may need to be modified or discontinued by treatment teams for various reasons, including change in diagnosis, risk of suicidality, or withdrawal of participant consent. There will be no strategies to modify the patient’s adherence to treatment as part of this protocol.\n\nPrimary care teams will provide patients with the pharmacological and behavioral care that are mandatory in the primary health system for patients with MD.\n\nPrimary outcome\n\nChange in depressive symptoms\n\nDifference in depressive symptoms between the two arms of the study will be assessed at baseline and three and six months, as shown in the participants timeline (Table 1), using the Patient Health Questionnaire validated in Chile.21 This questionnaire is a 9-item self-report survey that uses a 4-point Likert scale to screen for the presence of MD and monitor treatment effects. The total score ranges from 0 to 27, and a greater score means a greater severity of depression. The presence of five or more symptoms in at more than half the days in the last two weeks suggests MD.\n\nSecondary outcomes\n\nChange in anxiety symptoms\n\nDifference in anxiety symptoms between the two arms of the study will be evaluated at baseline and three and six months (Table 1) by the Spanish validated version of the generalized anxiety disorder scale-7 (GAD-7).22 The GAD-7 is a 7-item self-report survey that uses a 3-point Likert scale to screen for generalized anxiety disorder quantify symptom severity. The total score ranges from 0 to 21 points, and greater scores mean greater severity of anxiety.\n\nChange in interpersonal dysfunction and social role difficulties\n\nDifference in functional impairment in interpersonal and social areas between the two arms of the study will be evaluated at baseline, at three and at six months (Table 1) by the subscales of the interpersonal functioning, and social role included in the Outcome Questionnaire 45 (OQ-45).23 The OQ-45 has a 45-item self-report survey that uses a 4-point Likert scale originally developed to monitor patient progress during therapy and after termination. The OQ-45 comprises the subscales of symptom distress, interpersonal relations, and social role. The interpersonal relations subscale includes 12 items addressing loneliness, conflict with others, and marriage and family difficulties, with scores that range from 0 to 48. The social scale consists of nine items tapping into difficulties in the workplace, school or home duties, with scores that range from 0 to 36 points. Greater scores mean worse interpersonal and social functioning.\n\nChange in emotion regulation\n\nDifference in the difficulties in emotion regulation between the two arms of the study will be evaluated at baseline, three and six months (Table 1) by the emotion regulation scale (ERS) validated in Spanish with cutoff scores for the Chilean population.24 ERS contains five subscales addressing emotional rejection, dysregulation, interference, inattention, and confusion. This scale is a 28-item self-report survey that uses a 5-point Likert scale. The scores range from 0 to 140 points, and greater scores indicate increased difficulties with emotional regulation.\n\nTherapeutic adherence\n\nDifference in the adherence to treatment between the two arms of the study will be evaluated at three and six months (Table 1) by the therapeutic adherence scale,25 a 21-item self-reported survey to measure the percentage that patients assign the effectiveness of each behavior. A score of 100 represents the highest adherence possible.\n\nOther outcomes\n\nSelf-efficacy of the primary care teams\n\nThe self-efficacy of the primary care team, in implementing the study model, will be evaluated at baseline and after training (Table 1) by the general self-efficacy scale (GSES) validated in Chile.26 The GSES is a 10-item self-report survey that uses a 7-point Likert scale to measure self-efficacy. Thus, greater scores mean greater self-efficacy.\n\nThe estimation of the sample size considered a difference of 20% according to previous studies carried out in Chile,27–29 based in a unilateral model, with an alpha of 5%, a power of 80%, a confidence level of 95% and a maximum variance of 50% resulted in 341 patients. Based on a previous study that determined the clinical and psychosocial variables associated with different evolutions in eight primary care clinics in the Maule region,11 which showed retention of 85%, we adjusted the sample size to 394 patients. Based on a previous study we defined a group of at least 12 primary care clinics in the Maule Region, to be able to access the flow of adult patients with MD required for the feasibility of the study.11\n\nFirst, we will enroll the health care clinics through invitation to participate will be made to the health administration of the Maule region. Subsequently, those primary care clinics (Centro de Salud Familiar, in Spanish) authorized by their director will be invited to participate. A minimum of 12 primary care clinics will be enrolled, each with one team composed of a physician, a psychologist and a social worker.\n\nThe average socioeconomic level, adult population and patient’s income from 2019 will be used to match pairs of clinics. Later, the clinics will be assigned to the intervention or control groups using a pseudo-random algorithm (randi(2, [1 12], generates a 12-by-1 matrix of random integers between 1 and 2) in Matlab (MathWorks, Natick, MA, USA, RRID:SCR_001622).\n\nA different researcher, not part of the training team, will make the list of pairs of clinics with similar characteristics in excel and assign each clinic to a number 1 or 2. Then, another researcher will assign the clinics corresponding to the randomization list (sequence of 1 and 2 numbers) to the intervention group and the remaining clinics of each pair to the control group. Finally, this last researcher will define a number code to the intervention and control groups, and a different group of researchers which, blinded to the arm assignments, will perform the data collection and analysis using the number code.\n\nAfter the training phase, there will be a four month implementation of the CMAD approach in the clinic teams. After the implementation, patients who enter treatment for depression in their respective primary care clinic will be informed of the study and invited to participate by one person of each primary care team. Those who agree to participate, will be asked for their telephone number and researchers blind to the study arms will contact them, providing the informed consent form and then the questionnaires. An alphanumeric code will be assigned for each intervention arm, clinic and patient. Therefore, participants, outcome assessors, and data analysts will be blinded to the intervention allocation.\n\nPatient recruitment is expected to begin on March 1, 2022. To achieve an adequate participant enrolment, each clinic will have a person in charge of inviting all the patients that meet the criteria for enrollment.\n\nThe study will comply with all local research governance requirements for human data collection. A researcher team of psychiatry residents, blind to the intervention arms, will evaluate the participants at the beginning, at three and at six months using a set of instruments. The evaluation team will receive training for data gathering and standardization. The data from different instruments will be entered into a virtual worksheet located on SurveyMonkey by means of a tablet. Each evaluator will enter the data using a password, leaving no information on the devices. The data will be checked for correct entry every day and will be downloaded to the PI personal computer with a password located in an office with key. All data will be entered with the alphanumeric code, which prevents participant de-identification. The data from the participants that are referred to the specialist level will be eliminated from the study.\n\nThe data monitoring will be performed by the research team in charge of data collection and will meet every two weeks to evaluate the trial progression and data collection. A different research team in charge of data analysis will perform a checking of the data collected and perform preliminary data analysis to evaluate the progression of the data collection.\n\nPatients will first be monitored by their respective primary care teams as part of their treatment monthly. In high risk situations such as serious risk of suicide, psychosis and adverse effects of the medications are detected during the evaluations by the researchers (residents), the residents will inform to the researchers in charge of data collection, who in turn will inform the primary care teams. These patients will be excluded from the study as well as patients who do not want to continue with the evaluations.\n\nWe have not included plans for collecting, assessing, reporting, and managing solicited and spontaneously reported adverse events and other unintended effects of trial interventions as the medical treatment will not be modified from the national guidelines for MD. The interventions only modify the administration of the clinics’ treatment teams.\n\nAn initial analysis of the sociodemographic and clinical characteristics of the sample will be carried out and the scores of the scales will be calculated. The results will be presented according to the Consolidated Standards of Reporting Trials guide for RCT, with its extensions to cluster interventions. Intention-to-treat analysis of the primary outcome will be performed. In the initial descriptive analysis, the differences in the characteristics of the clinics between the intervention groups will be estimated.\n\nFor the analysis of the primary outcome, linear multivariable regression will be used to establish differences at 3 and 6 months, adjusting the results according to the initial data in case of imbalance. In addition, a sensitivity analysis based on different assumptions will also be carried out to evaluate the possible effects of the lack of data. This analysis will also be done for secondary outcomes. Data analysis will be performed with SPSS software (IBM, Armonk, NY, United States, RRID:SCR_002865).\n\nEthical approval for this study was obtained from the institutional Ethics Committee (Comité Ético Científico, Universidad de Talca, protocol # 26-2020). The informed consent document will be available in a Mendeley Data repository.34 Furthermore, informed written consent will be obtained from the participants (mental health team and patients). In case of protocol modifications (for example in the analyses or outcomes) the principal investigator should ask for an amendment to the original ethics informed consent to the Ethics Committee, and the changes should be communicated to all the study team.\n\nThe informed consent process will be performed by the research team in charge of the data collection. This team, made up of seven psychiatry residents, will obtained the informed consent in the health care clinic were the participant is admitted in a paper copy that will not have any information about the intervention assignment. During the informed consent procedure, an alphanumeric code will be assigned to the patient, and all the study information will be available under this code but it will not include any personal information that could help to obtain the identity of the participant. One researcher will have the list with the patient’s name and the assigned code in its personal computer secured with a password.\n\nThe final data set will be in the computer of the PI, and the researchers in charge of the analyses will have access to the data in the coded form. In case that the results of the study show significantly better outcomes in the intervention arm compared to the control arm, the primary care teams of the control arm will be trained in the CMAD approach.\n\nThe principal investigator will communicate trial results to participants and healthcare professionals through workshops in the different clinics. The communication of the results to the general public, and other relevant groups will be performed trough seminars in the University of Talca. Finally, the communication of the results to the medical and scientific community will be done through the publication in specialized journals and the data sharing of the results in databases (eg, Mendeley). Moreover, the protocol will be available after the study has ended. Regarding the authorship legibility for the protocol, we will include all researchers that contributed significantly to the design, implementation the clinics training, data collection and analysis.\n\nThis study has concluded the health clinics’ recruitment as well as the health care team’s informed consent and training in both study arms. Patient recruitment is expected to begin on March 1, 2022.\n\n\nDiscussion\n\nCollaborative models have proven to be the most effective to improve the outcomes for the treatment of MD in primary care.18 However, in Chile, a single study that applied this model on the current government clinical guideline's recommendations showed no significant efficacy in the resolution of depressive symptoms.28 As far as we know, there is no evidence on the efficacy of a collaborative model on the complex, difficult-to-treat depression subtype, which includes the recognition by primary care teams of clinical and functional variables associated with exposure to adversity and trauma.13,29,30\n\nThis project seeks to test a clinical approach that includes a comprehensive, multidisciplinary clinical evaluation, and promotes the synergy of the entire health team, so that patients with difficult-to-treat depression, with neurobiological and psychological vulnerabilities associated with a history of biographical adversity, receive consistent treatment over time. It also entails close collaboration between the primary and secondary health system levels, which may reduce emotional distress in the treating professionals themselves.\n\nAmong the limitations, it should be noted that the continued education intervention will recruit team members who wish to participate. The sample of health care professionals may not be representative of health care professionals working in primary care in Chile. Professionals who are especially motivated in their continued education may be overrepresented among those who consent to participate. In addition, it is possible that this group of providers may have a higher-than-average competency level in some of the skills and attitudes fostered by the proposed approach.\n\nAs an additional limitation, results from this randomized trial involving many low income, rural and semi-rural patients in central Chile may not be extended to other more socioeconomically advantaged populations or patients living elsewhere in the country. Surveys using nationally representative samples have found up to 15-fold differences in prevalence between richer and poorer regions even if at the country level prevalence of MD has not changed significantly in the period of observation.31 Furthermore, Chile’s income inequality gap is also more than 65% wider than the average in a group of mostly rich countries,32 and meta-analysis data demonstrate greater risk of MD in populations with higher income inequality relative to populations with lower inequality.33 Overall, the focus on primary care in the Maule Region of Chile seems justified on population health and social justice considerations. We hope that results from this trial will help address the existing low remission rates of MD in primary care, especially in patients presenting with difficult-to-treat, complex clinical presentations.\n\n\nConsent for publication\n\nNot applicable.\n\n\nData availability\n\nNo underlying data are associated with this article.\n\nMendeley Data: Collaborative multidimensional approach to improve the resolution of depression in primary care in Chile https://doi.org/10.17632/jdftfbpvkn.134\n\nThis project contains the following extended data:\n\n- InformedConsent\n\no Acta de aprobación V. Vitriol.pdf (Minutes of the Institutional Ethic Committee reporting the approval of the Informed Consent documents)\n\no Consentimiento informado aprobado CEC.pdf (Informed consent document for participants)\n\no Consentimiento informado profesional aprobado CEC.pdf (Informed consent document for primary care teams)\n\n- Primary Care Clinic Lists\n\no Primary Care clinics.pdf (Clinics selected for trial).\n\n- Project Acceptance Letter\n\no Carta N°988 Adj. XVII Fonis U. de Talca.pdf (Allocation of Funds for the study)\n\nMendeley Data: Collaborative multidimensional approach to improve the resolution of depression in primary care in Chile https://doi.org/10.17632/jdftfbpvkn.134\n\nThis project contains the following reporting guidelines:\n\n- SPIRIT-Checklist-31 Dec 2021.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nRoles and responsibilities\n\nThe research team responsible for this study belong to the School of Medicine of the University of Talca and the University of Davis, in collaboration with the Maule Health Service.\n\nPrincipal Investigator: Verónica Vitriol\n\nStudy design: Verónica Vitriol, Alfredo Cancino, Andrés Sciolla and Maria de la Luz Aylwin\n\nClinic recruitment: Marcela Ormazábal, Sergio Guiñez\n\nClinic Team Data collection: Sergio Guiñez, Johanna Kreither\n\nPairing and assignment: Marcela Ormazábal, Maria de La Luz Aylwin\n\nTraining Primary Care Teams CMAD: Veronica Vitriol, Alfredo Cancino, Andres Sciolla\n\nTraining Primary Care Teams Depression Clinical Guideline: Jorge Calvo\n\nPatient recruitment: Marcela Ormazábal, Soledad Ballesteros\n\nPatient data collection and monitoring: Marcela Ormazábal, Soledad Ballesteros\n\nData analysis and interpretation: Veronica Vitriol, Alfredo Cancino, Andres Sciolla and Johanna Kreither\n\nResearch report writing: Veronica Vitriol, Alfredo Cancino, Andres Sciolla, Maria de la Luz Aylwin, Sergio Guiñez, Johanna Kreither, Jorge Calvo\n\n\nAuthors' information\n\n\n\n• Verónica G. Vitriol MD, Escuela de Medicina, Universidad de Talca, Talca, Chile\n\n• Alfredo Cancino MD, Escuela de Medicina, Universidad de Talca, Talca, Chile\n\n• Andrés Sciolla MD, Department of Psychiatry, Medical School, UC Davis, USA\n\n• Sergio Guiñez PhD, Escuela de Medicina, Universidad de Talca, Talca, Chile\n\n• Jorge Calvo MD, Escuela de Medicina, Universidad de Talca, Talca, Chile\n\n• Marcela Ormazábal Ms, Departamento APS, Programas y Ciclo Vital, Subdirección de Gestión Asistencial, Dirección Servicio de Salud del Maule, Talca, Chile\n\n• Johanna Kreither PhD, Centro de Investigación en Ciencias Cognitivas, Centro de Psicología Aplicada Facultad de Psicología, Universidad Talca, Talca Chile\n\n• Soledad Ballesteros MD, Escuela de Medicina, Universidad de Talca, Talca, Chile\n\n• María de la Luz Aylwin PhD, Centro de Investigaciones Médicas, Escuela de Medicina, PIA Ciencias Cognitivas, Centro de Investigación en Ciencias Cognitivas, Universidad de Talca, Talca, Chile", "appendix": "Acknowledgements\n\nWe thank the Regional Health Secretary and the Health Departments of the Municipality of Curicó, Constitución, Linares, Pelarco, Romeral, Sagrada Familia, and Talca and all the mental health teams and directors of the primary care clinics who contributed to this project. We also thank Ms. Carmen Gloria Blanco for her assistance with project management.\n\n\nReferences\n\nWorld Health Organization, Newsroom, Fact Sheets, Depression. http\n\nSalvo GL: Magnitude, impact and recommended management strategies for depression, with reference to Chile. Rev. Med. Chil. 2014; 142: 1157–1164. Publisher Full Text\n\nCOES (Center for Conflict and Social Cohesion Studies)First wave results.2019. Reference Source\n\nde Salud M : Encuesta Nacional de Salud [ENS] 2009-2010.Reference Source\n\nWang C, Pan R, Wan X, et al.: A longitudinal study on the mental health of general population during the COVID-19 epidemic in China. Brain Behav. Immun. 2020; 87: 40–48. PubMed Abstract \| Publisher Full Text\n\nde Salud M : Depresión en personas de 15 años y más. Serie Guias Clinicas, Minsal. 2013. Reference Source\n\nAraya R, Alvarado R, Sepúlveda R, et al.: Lessons from scaling up a depression treatment program in primary care in Chile. Rev. Panam. Salud Publica. 2012; 32: 234–240. PubMed Abstract \| Publisher Full Text\n\nVitriol V, Cancino A, Serrano C, et al.: Remission in Depression and Associated Factors at Different Assessment Times in Primary Care in Chile. Clin. Pract. Epidemiol. Ment. Health. 2018; 14: 78–88. PubMed Abstract \| Publisher Full Text\n\nNavarrete RG, Saldivia BS, Vicente PB, et al.: Evaluación del resultado de las acciones de detección, diagnóstico y tratamiento del Episodio Depresivo realizada en pacientes consultantes en el primer nivel de atención de la Provincia de Concepción, Chile.2017; 55: 160–169.\n\nVitriol V, Cancino A, Leiva-Bianchi M, et al.: Association between adverse childhood experiences with depression in adults consulting in primary care. Rev. Med. Chil. 2017; 145: 1145–1153. PubMed Abstract \| Publisher Full Text\n\nCancino A, Leiva-Bianchi M, Serrano C, et al.: Factors Associated with Psychiatric Comorbidity in Depression Patients in Primary Health Care in Chile. Depress. Res. Treat. 2018; 2018: 1–9. Publisher Full Text\n\nVitriol V, Cancino A, Serrano C, et al.: Latent Class Analysis in Depression, Including Clinical and Functional Variables: Evidence of a Complex Depressive Subtype in Primary Care in Chile. Depress. Res. Treat. 2021; 2021: 1–9. Publisher Full Text\n\nMcAllister-Williams RH, Arango C, Blier P, et al.: The identification, assessment and management of difficult-to-treat depression: An international consensus statement. J. Affect. Disord. 2020; 267: 264–282. PubMed Abstract \| Publisher Full Text\n\nLippard ETC, Nemeroff CB: The Devastating Clinical Consequences of Child Abuse and Neglect: Increased Disease Vulnerability and Poor Treatment Response in Mood Disorders. Am. J. Psychiatry. 2020; 177: 20–36. PubMed Abstract \| Publisher Full Text\n\nMladen SN, Williams AB, Griffin SC, et al.: Models of Trauma Exposure, Depression, and Suicidality in Safety-Net Primary Care. J. Trauma. Stress. 2021 Feb 9; 34: 1139–1148. PubMed Abstract \| Publisher Full Text\n\nLathan EC, Selwyn CN, Langhinrichsen-Rohling J: The \"3 Es\" of trauma-informed care in a federally qualified health center: Traumatic Event- and Experience-related predictors of physical and mental health Effects among female patients. J. Community Psychol. 2021 Mar;49(2): 703–724. PubMed Abstract \| Publisher Full Text\n\nWagner EH, Austin BT, Korff MV: Organizing Care for Patients with Chronic Illness. Milbank Q. 1996; 74(4): 511. Publisher Full Text\n\nArcher J, Bower P, Gilbody S, et al.: Collaborative care for depression and anxiety problems. Cochrane Database Syst. Rev. 2012; 10: Cd006525. Publisher Full Text\n\nDescripción sociodemográfica de la región del Maule: Reference Source\n\nLecrubier Y, Sheehan DV, Weiller E, et al.: The Mini International Neuropsychiatric Interview (MINI). A short diagnostic structured interview: Reliability and validity according to the CIDI. Eur. Psychiatry. 1997; 12(5): 224–231. Publisher Full Text\n\nBaader MT, Molina FJL, Venezian BS, et al.: Validación y utilidad de la encuesta PHQ-9 (Patient Health Questionnaire) en el diagnóstico de depresión en pacientes usuarios de atención primaria en Chile.2012; 50: 10–22.\n\nGarcía-Campayo J, Zamorano E, Ruiz MA, et al.: Cultural adaptation into Spanish of the generalized anxiety disorder-7 (GAD-7) scale as a screening tool. Health Qual. Life Outcomes. 2010; 8: 8. PubMed Abstract \| Publisher Full Text\n\nvon Bergen A , de la Parra G : OQ-45.2, Cuestionario para evaluación de resultados y evolución en psicoterapia: Adaptación, validación e indicaciones para su aplicación e interpretación. [OQ-45.2, An Outcome Questionnaire for Monitoring Change In Psychotherapy: Adaptation, Validation and Indications for its Application and Interpretation.]. Terapia Psicológica. 2002; 20: 161–176.\n\nGuzmán-González M, Mendoza-Llanos R, Garrido-Rojas L, et al.: Cut-off points of the difficulties in Emotion Regulation Scale for the Chilean population. Rev. Med. Chil. 2020; 148: 644–652. PubMed Abstract \| Publisher Full Text\n\nSoria Trujano R, Vega Valero CZ, Nava Quiroz C: Escala de adherencia terapéutica para pacientes con enfermedades crónicas, basada en comportamientos explícitos.2009; 14: 89–103.\n\nClavijo M, Yévenes F, Gallardo I, et al.: The general self-efficacy scale (GSES): Reevaluation of its reliability and validity evidence in Chile. Rev. Med. Chil. 2020; 148: 1452–1460. PubMed Abstract \| Publisher Full Text\n\nRojas G, Martínez P, Vöhringer PA, et al.: Comprehensive technology-assisted training and supervision program to enhance depression management in primary care in Santiago, Chile: study protocol for a cluster randomized controlled trial. Trials. 2015; 16: 311. PubMed Abstract \| Publisher Full Text\n\nRojas G, Guajardo V, Martínez P, et al.: A Remote Collaborative Care Program for Patients with Depression Living in Rural Areas: Open-Label Trial. J. Med. Internet Res. 2018; 20: e158. PubMed Abstract \| Publisher Full Text\n\nVitriol V, Sciolla A, Cancino A, et al.: Cuidado Informado En Trauma: Un Modelo Emergente Para El Abordaje Del Subtipo Depresivo Con Historia De Adversdad Infantil.2020; 58: 348–362.\n\nSciolla AF: An Overview of Trauma-Informed Care. Cham: Springer International Publishing; 2017; 165–181.\n\nMarkkula N, Zitko P, Peña S, et al.: Prevalence, trends, correlates and treatment of depression in Chile in 2003 to 2010. Soc. Psychiatry Psychiatr. Epidemiol. 2017 Apr; 52(4): 399–409. PubMed Abstract \| Publisher Full Text\n\nChile economic snaphot: Upcoming Economic Forescat update.1 December 2021. Reference Source\n\nPatel V, Burns JK, Dhingra M, et al.: Income inequality and depression: a systematic review and meta-analysis of the association and a scoping review of mechanisms. World Psychiatry. 2018; 17(1): 76–89. [published correction appears in World Psychiatry. 2018 Jun;17(2):235]. PubMed Abstract \| Publisher Full Text\n\nVitriol V, Aylwin M: 2022. Collaborative multidimensional approach to improve the resolution of depression in primary care in Chile. Mendeley Data. V1. Publisher Full Text" }	[ { "id": "188474", "date": "31 Jul 2023", "name": "Paula Dagnino", "expertise": [ "Reviewer Expertise Research in clinical psychology. Research in Depression and Personality. Research in patients treatment" ], "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 emphasize the importance of this study. It considers a central pathology, such as depression, specifically patients who are difficult to treat. The fact that the study will include complementary variables to the symptomatology, such as emotional regulation, comorbidity, interpersonal relationships, etc., is in the most updated line of research in this field, in personalized or patient-centered treatment. The training of health professionals in Chile needs to be improved in this type of complexity and also in interdisciplinary, community, and network treatment. Knowing that this is \"the\" way of treating patients, the CMAD protocol will significantly contribute to primary care.\nThe document is well-written and clear in each of the sections. I will be looking forward to the results.\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": "281255", "date": "12 Sep 2024", "name": "Lene F. Eplov", "expertise": [ "Reviewer Expertise psychiatry", "mental health", "recovery", "interventions", "implementation", "collaborative 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\nThe paper is a study protocol for a cluster randomized controlled trial evaluating the effect of a collaborative multidimensional approach for major depression (MD). This is an important study, as MD constitutes are large burden in Chile and because the research group has previously observed a complex depressive subtype with poor response to standard treatment.\nThe rationale for the study is clearly described. The choice of a multidimensional, collaborative, and trauma-informed approach is well-justified and seems an appropriate choice, based on the literature and the groups previous studies. Overall, the study protocol is clearly structured and conforms with the CONSORT guidelines. However, there are some major issues as well as minor issues that needs to be addressed.\nMajor issues Abstract:\nThe primary outcome is not described in the section “Methods” in the abstract. This is essential information and should be provided here.\nBackground:\nThe section clearly describes the scientific background and rationale. However, the authors use a lot of space to describe a subgroup among people with MD and although this is interesting, the RCT is investigation the effect of the intervention on the whole population with MD in primary care. Furthermore, it doesn’t look like they are going to do a subgroup analysis on the mentioned subgroup and the power calculation is based on wanting an analysis of the effect on the whole group, leading to the fact that there is not enough power to examine the effect of the intervention on the mentioned subgroup. Therefore, the introduction needs to have the main focus on describing the need of the intervention for the whole group of people with MD in primary care.\nMethods:\nThe section “Modifications” is hard to understand. Is the modification made in the treatment, then move the section up to the description of the “intervention arm”, if it is part of the must conduct the analyses then move the section to “Data analysis”. Be aware then that you can’t write that you will perform intention-to-treat analysis, as described under the section “Data analysis”. Sample size: It is unclear if the sample size calculation takes the cluster design of the RCT into account. There is no mentioning of assumptions, such as approximate equal-sized clusters, or intra-class correlation (ICC). Data analysis: As for the sample size calculation, it is unclear if and how the analyses take the clustering of individuals in clinics into account.\nMinor issues\nAbstract:\nThe section “Discussion” is more of a conclusion, as if the trial has already been completed and analyzed. Instead, rephrase to e.g., “This trial will provide information on whether…”. If the trial has been registered, e.g., at ClinicalTrials.gov, please provide registration number and date at the end of the Abstract.\nHypotheses and aims:\nInstead of listing five aims and four hypotheses, only list those related to the primary outcome, i.e. aim 3. The protocol only describes the RCT and therefore it is not an aim to, for example, design the intervention (aim 1), unless this process is also described in details. Hypotheses 1 and 2: Change the wording “improve depressive symptoms” to “a reduction in depressive symptoms”, as this is more specific. Aim 3: To make the aim and outcome clearer, emphasize that it is the change in depressive symptoms between baseline and follow-up, which is compared between the two groups, e.g., “To compare the changes in depressive symptoms…”. The two sentences before the aims (“We designed a cluster RCT…”) and the two below the aims (“This study protocol is a cluster RCT…”) are both related to the methods and should be moved (and merged, as they repeat the same information) from the section “Background” to the section “Methods”, for example as a sub-heading “Design” at the beginning of the section.\nMethods:\nStudy setting: The last two sentences (“To obtain the sample…”) should be moved to the section “Recruitment”, as it is confusing here how centers were identified and matched. Study setting: For international readers, it would be informative with a short description of the healthcare system in Chile, i.e. are the primary care clinics public or private and free of charge or with user payment. Eligibility criteria: Are there any exclusion criteria related to e.g., comorbidity, alcohol or substance misuse, somatic illness? Interventions: The first sentence (“Eligible primary care clinics will…”) should be moved to the section “Recruitment”. It would also make more sense when reading, if the section “Recruitment” came before this section on “Interventions”, and if the heading was changed to “Recruitment and randomization”. Intervention arm: The intervention could be described in more details, as each element is not clearly described, but merely listed. For example, what is the role of the case manager (scheduled meetings with the patient and/or the primary care team? Inter-professional communication? Monitoring of follow-up assessments?), and how are the individual treatment plans developed (based on which instructions/guidelines or principles of care? Stepped care algorithm? Treatment modalities?). Outcome measures: Emphasize that the change in symptoms between baseline and follow-up is the measure: “Difference in depressive symptoms change”. Same for the secondary outcomes. All about blinding and randomization must be move to a separate section called “Blinding and randomization”. Together with the already given information, the authors need to address the fact that all the outcomes are self-report, which can lead expectation bias.\n\nRecruitment: When is the recruitment expected to end (length of inclusion period)? Monitoring: Here the authors write “ These patients will be excluded from the study as well as patients who do not want to continue with the evaluation. Are the patients excluded from the treatment or the study as a whole. If the first change the wording, if he last, remove the phases about using intention-to treat under “data analysis”, as this is not the case.\n\nReferences: Please check the reference list carefully, as:\nSeveral of the references link to URLs that does not exist. Some institution names are incorrect. Links to web pages should list access date or publication date. Reports and documents should list name of institution/publisher and location.\nFormatting: There are several phrasing and grammatical errors, which confuse the reading, such as:\nPhrasing: In the title, the term “on the resolution of adult depression” is unspecific. Replace with “on the treatment of”. Proofreading: Please carefully proofread the entire paper again, as there are several errors, such as a word missing in a sentence or an extra word at the end of a sentence, which should be deleted. Grammatical errors: Please carefully go through the text and check for grammatical errors, as there are quite a few of these, such as the word “The” missing, or plural “s” missing, or confusion between are/is. Efficacy versus effect are used interchangeably, please use the correct wording in all places.\n\nConclusion The manuscript needs major revision before it can be indexed.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "12529", "date": "11 Oct 2024", "name": "VERONICA VITRIOL", "role": "Author Response", "response": "Dear Reviewers, Lene F Eplov and Marte Ustrup We would like to extend our sincere gratitude for your thoughtful and detailed feedback on our manuscript. Your comments and suggestions have been instrumental in improving both the structure and content of the paper. We have carefully considered each of your points and made the necessary revisions to enhance the clarity and overall quality of the manuscript. Please note that this manuscript was originally submitted in 2021, prior to the commencement of the project. Since then, the study has been completed, and we are now in the process of publishing the results in the Annals of Family Medicine. Below, we have provided specific responses to your comments: Primary Outcome in the Abstract Comment: The primary outcome is not described in the “Methods” section of the abstract. Response: We have added a description of the primary outcome in the \"Methods\" section of the abstract. Both the primary and secondary outcomes are now clearly outlined in the Methods section of the main text for better clarity. Background Comment: The focus in the Background section on a specific subgroup of people with Major Depression (MD) is unnecessary, as the study focuses on the entire population with MD in primary care. Response: Thank you for this suggestion. We have revised the introduction to focus on the general population with MD, aligning with the study's objective of evaluating the intervention for all individuals with MD in primary care, rather than emphasizing a specific subgroup. Methods Comment: The “Modifications” section is unclear and misplaced. Response: We have removed the “Modifications” section and incorporated relevant details into other sections for improved clarity and coherence. Comment: It is unclear if the sample size calculation takes the cluster design into account. Response: In this version, we have elaborated on the sample size calculation, including assumptions such as equal-sized clusters and intra-class correlation (ICC). Comment: It is unclear how data analysis accounts for clustering of individuals within clinics. Response: The data analysis section now clearly explains how clustering is handled, including conducting an intra-cluster correlation prior to the regression analyses. Minor Issues Comment: The \"Discussion\" section reads more like a conclusion. Response: We have rephrased the \"Discussion\" section to reflect that the trial is ongoing, using language such as \"This trial will provide information on whether...\". Comment: Please include the registration number for the trial. Response: The trial registration number and date have been added at the end of the abstract. Hypotheses and Aims Comment: Only list aims and hypotheses related to the primary outcome. Response: The aims and hypotheses have been revised to focus on those related to the primary and secondary outcomes. Aims such as designing the intervention (aim 1) have been removed unless explicitly described. Comment: Change \"improve depressive symptoms\" to \"a reduction in depressive symptoms.\" Response: This wording change has been implemented for greater specificity. Comment: Clarify that the aim is to compare changes in depressive symptoms between baseline and follow-up. Response: The aim now explicitly states that we compared changes in depressive symptoms between baseline and follow-up in the two groups. Comment: Sentences regarding the study design should be moved from “Background” to “Methods.” Response: We have moved and merged the relevant sentences under a new sub-heading titled \"Design\" in the Methods section for clarity and to avoid repetition. Study Setting Comment: Move the last two sentences regarding recruitment to the “Recruitment” section. Response: These sentences have been moved to the \"Recruitment\" section for better organization. Comment: Provide a brief description of the healthcare system in Chile. Response: A brief description of Chile’s healthcare system, including the public/private structure and costs to users, has been added. Comment: Are there any exclusion criteria related to comorbidity, substance misuse, or somatic illness? Response: Exclusion criteria for this protocol were bipolar disorder, suicide attempt, or severe drug dependence and consequently, they have been included in the updated version. Interventions Comment: The intervention could be described in more detail. Response: The intervention arm has been elaborated, with a clearer description of the role of the case manager and the development of individual treatment plans. Outcome Measures Comment: Emphasize that the measure is the change in symptoms between baseline and follow-up. Response: We have clarified that the measure is the change in depressive symptoms between baseline and follow-up, and similar wording has been applied to secondary outcomes. Comment: All details regarding blinding and randomization should be in a separate section. Response: A separate section titled \"Blinding and Randomization\" has been added, addressing the use of self-reported outcomes and the potential for expectation bias. Additionally, patients will be followed in a blinded manner by residents administering the follow-up surveys, which will be independent of self-reported information provided to the treatment team. Recruitment Comment: When is recruitment expected to end? Response: The recruitment timeline, including the expected end date and the length of the inclusion period, has been specified. Monitoring Comment: Clarify whether patients are excluded from treatment or the study as a whole. Response: Patients may discontinue treatment or evaluations but will still be included in the analysis based on the intention-to-treat principle. The wording has been updated to reflect this distinction. References Comment: There are several issues with the reference list. Response: The reference list has been reviewed and updated. All URLs have been checked for accuracy, institutional names have been corrected, and links to web pages now include access or publication dates. Reports and documents list the appropriate institution or publisher and location. Formatting Comment: There are phrasing and grammatical errors, and the terms \"efficacy\" and \"effect\" are used interchangeably. Response: The manuscript has been thoroughly proofread to correct phrasing, grammatical errors, and consistency issues. The terms “efficacy” and “effect” have been replaced with “effectiveness,” where appropriate, to ensure proper usage. Once again, we are grateful for your time and valuable input, which have greatly improved the manuscript. We hope the revised version meets your expectations. Sincerely, Dr. Veronica Vitriol Profesor of Psychiatry 27/Sept/2024 Universidad de Talca" } ] } ]	1	https://f1000research.com/articles/11-203
https://f1000research.com/articles/13-1217/v1	11 Oct 24	{ "type": "Research Article", "title": "The usefulness of a rehabilitation programme for people with stress-related disorders - A case from a rehabilitation center in Estonia.", "authors": [ "Mohammad Delwar Hossain" ], "abstract": "Background Rehabilitation programs help to improve people’s lives and reduce turnover rates in organisations. The current analysis revealed that dissatisfaction occurred among practitioners, doctors’ overlapping services, and fragmented plans. No comprehensive assessment and rehabilitation program currently exists for stress-related disorders in Estonia indicating an urgent need to conduct research and development programs for clients to reduce stress (Bugarski, Z, et al., 2016). This study research aimed to determine the usefulness of rehabilitation programs for individuals people with stress-related disorders.\n\nMethod A qualitative approach was used.\n\nMethodology The sample included 10 individuals recruited from various rehabilitation centers in Estonia. Convenience sampling was used to select participants for this research. Open- and closed-ended questions were formulated using the 12 questions enclosed in this research. All transcribed interviews were formatted using the code. Extract codes within participant interviews were compared to identify similarities, differences, and closeness, and therefore formulated categories.\n\nResults The findings revealed that rehabilitation programs contribute to quality services, self-motivation, daily activities plan, self-control, recovery, attention and concentration, and coping skills, whereas traditional treatment can reduce symptoms but not change people’s lives.\n\nConclusion This study suggests that rehabilitation programs are useful for individuals with stress disorders in the context of the Estonian healthcare system. The rehabilitation program is a useful intervention method revealed in the context of Estonia’s healthcare system, as it improves quality services, increases coping skills, self-control, and cognitive skills, and enhances recovery.", "keywords": [ "Usefulness", "psychotherapy", "cognitive-based therapy", "physiotherapy", "occupational therapy", "rehabilitation center", "Stress related disorder", "Estonia" ], "content": "Introduction\n\nAccording to Vos et al. (2012) and Salomon et al. (2012), the global scale of mental health problems is measured as ill health and work disabilities. This means that mental health occurs through two mechanisms - ill health and the working environment according to the global healthcare scale. According to Wittchen HU et al. (2010) In the European Union, more than one-third of the population experiences mental health disease each year and less than one-third of the population receives rehabilitation programs that are considered a level of unmet needs. This statement reflects that, according to European data sources, less than one-third of the population receives rehabilitation programs compared to one-third of the population who have mental health problems; therefore, this does not fulfil their health issues. Currently, stress is a common cause of sick leave and, therefore, a great source of economic burden (Arends et al., 2012, 1-15 & Van der Klink et al., 2001).The statement highlighted that it is a long way process to get the recovery and the question about cost, hence, it is a burden for the whole economy when people are unwell due to mental health problems and then seek admission to hospital, intermediate care, or home care.\n\nDue to stress disorders, many individuals have increased absenteeism, decreased productivity in organizations, and escalated disability pensions (Borg et al., 2010). Approximately 30% of the population is estimated to experience stress disorders in their psychosocial environment in all European countries (Henderson et al., 2005, 802-803). In Estonia, the task of management has changed to centralized procedures in patient care policies (World Health Organization, 2000). The Government of Estonia established infrastructure around the special-care service sector to allow people with psychiatric and intellectual disabilities to become more independent, but the program was not growing fast enough in line with patient demand (Bugarski, Z, et al., 2016; Kuuse & Toros, 2017). Rehabilitation programs have value; however, clinicians prescribe rehabilitation partially or at the end of their interventions when they ascertain that medications are not as effective as they would (Health and Safety Executive, 2008). Therefore, it is necessary to identify specific rehabilitation treatment methods for the welfare of clients and to reduce individual costs. The estimated cost of all neuropsychiatric disorders in Europe was €789 billion in 2010 (Gustavsson et al., 2011, 718-779). Despite this obvious need, very few efficient and specialized rehabilitation programs have been introduced for relieving stress (Koerner, 2011, 45-67). Therefore, it is vital to discover the usefulness of rehabilitation programs that can improve the quality of life, allow a person to maintain daily activities, and manage emotions. Estonia has many patients with stress disorders, mainly receiving antidepressant medications to reduce stress. However, few patients are referred for rehabilitation services (Bugarski, Z, et al., 2016). According to Salomonsson et al. (2018), a more recent study 2018 investigated the effects of psychological interventions on stress disorders and found it to be more effective than Treatment as Usual (TAU); however, the selection of treatment modalities used for a patient as medicine. This statement reflects that organisations are practicing what always they have (i.e., medication), rather than exploring new concepts such as psychological interventions, therefore, it is an indispensable factor in researching how psychological interventions reduce people’s stress and recover early (Bugarski, Z, et al., 2016). This study aimed to examine the usefulness of rehabilitation programs for individuals with stress-related disorders. Cochrane-review from 2015 stated, that if current research proves that rehabilitation programs prevent stress, then it must go higher up as their evidence was about psychotherapy, cognitive behavioral therapy (CBT), and physical or mental therapy programs had a low effect on stress due to low methodological research where literature was not found anything that opposes coherence statements (Ruotsalainen et al., 2015). The research question of this study was devised considering this research problem. Therefore, the research question is how useful the rehabilitation program is for people with stress-related disorders.\n\n\nLiterature review\n\nThis section discusses the role of the four major types of rehabilitation programs: psychology, cognitive-based therapy, physiotherapy, and occupational therapy. According to Kreitner and Robert dan Kinicki Angelo (2014), stress is defined as an adaptive response, influenced by individual characteristics and psychological processes, which are the result of external actions, situations, or events that impose a person’s physical and psychological demands. A stress-related disorder is a mental disorder that is common in the condition of depression and anxiety (Brouwers et al., 2009, 223-229). Stress-related mental disorders are most common in women, 3.2% more than in men, and 1.5% in both Western and Eastern cultures (Lejtzen et al., 2013; Bener et al., 2012). However, the limited number of rehabilitation centers exist, despite the high prevalence of stress and mental disorders in society. The rehabilitation process aims to help people acquire psychological, emotional, spiritual, social, and fundamental skills. Accordingly, people with stress disorders can evaluate their everyday lives and learn various stress management skills from various rehabilitation programs to prevent relapse (European Rehabilitation Medicine Bodies, 2018, 156-165). Traditional care treatment or treatment as usual, which is offered by a practitioner, consists of combined medicine with psychotherapy prescribed for clients with stress-related disorders. Treatment as Usual (TAU) can manage symptoms, but does not support individuals in making life changes. However, the following rehabilitation programs are evidence-based programs that can conveniently change people’s lives.\n\n\nUsefulness of rehabilitation programs\n\nPsychotherapy interventions are applied to people with stress to have positive qualities, strength, empowerment, energy, self-control, and self-motivation to function adequately and gain energy to overcome problems of people with stress (Schrank et al., 2014, 95-103). There is strong evidence that psychotherapy is effective for self-motivation; therefore, motivation constructs people’s strength and encouragement, improving their courage to accomplish tasks (Widodo, 2015). According to Mangkunegara (2013), motivation influences arousing, directing, and balancing behavior in any environment. A previous study has revealed that when individuals have not completed a psychotherapy well-being program (Hüning et al., 2020), it results in more deterioration of stress disorder (Lamers et al., 2015, 553–560). Therefore, to prevent relapse and improve the full recovery from stress, it is necessary to increase psychotherapy well-being interventions (Fava et al., 2017, 801–808). Muzio, (2004), mentioned that well-being therapy is essential to creating a situation in which mastering life acts in connection to a worthwhile working life. Another term for the psychotherapy well-being program is self-mastery or self-control, which is useful for relieving stress that has been confirmed in various qualitative studies about the usefulness of this program (Åhrberg et al., 2010, 167-77). According to Karlson et al. (2010), a psychotherapy rehabilitation program is a useful method for self-control. However, no one has scrutinized how it affects self-mastery or self-control in individual life. Fava et al. 2017, stated that a more recent study showed that on behalf of common mental disorders, psychotherapy well-being is more effective in improving well-being and reducing stress symptoms than Treatment as Usual (TAU). However, many health practitioners and psychiatric doctors prescribe only anti-depressive medication to relieve stress rather than referring to the psychotherapy rehabilitation program because ignoring or thinking about psychological rehabilitation programs is not a useful method of intervention for relieving people with stress (Salomonsson et al., 2018, 1954-1965). However, psychotherapy rehabilitation is paramount and acts from assessment to patient recovery and further follow-up to home rehabilitation, whereas other interventions provide symptomatic management of patient care. According to Stevens-Watkins et al. (2014), psychological resilience is another intervention in a psychotherapy program that describes the ability to cope mentally or emotionally with a crisis or to return to pre-status instantly. A resilience psychotherapy program is defined as the ability to adapt and apply to obtain better outcomes for employees, people, and family stressors for people with stress (Muzzio, 2004). Rehabilitation counselors act as role models by providing an assessment of resilience and, therefore, establishing a resilience training plan for employees for home-living people and other cases that have stress symptoms with respect to providing robust support (Kosciulek, 2011, 8-12). Another important point of resilience training is allowing people to share their feelings and exchange their ideas, concepts, and skills with others in a positive way, where they can enjoy their lives purposefully (Leahy, Chan & Saunders, 2002, 68-81). The author noted that the previous coherence study, 2015, applied psychotherapy, cognitive-behavioral therapy, and other programs resulted in low effects on people with stress, because of the low methodological quality of research where treatment criteria were based on medications and a small number of participants who took part in this research as a selection method (Ruotsalainen et al., 2015). However, according to Yunus (2014), psychotherapy, and cognitive-based therapy were most frequently used in many rehabilitation programs, and people with stress have obtained significant results from this program in addition to other programs that showed the most promising results on reducing stress. However, given the lack of previous literature, it is urgent to investigate from the primary data how psychotherapy therapeutic programs contribute to relieving stress in people’s lives.\n\nCognitive-based programs are utilized to improve individual thoughts and behaviors and make positive changes to individual lives. Cognitive-based programs are most frequently used in the rehabilitation of patients with stress. Generally, cognitive impairments occur in the areas of attention, concentration, working memory, and episodic memory. Therefore, cognitive-based rehabilitation programs play a major role in reducing stress impairments, although the program has not been empirically investigated before (Glise et al., 2012, 18). Cognitive rehabilitation programs are the most frequently used rehabilitation programs for stressed patients because they reduce stress by improving patient attention, concentration, and cognitive function. Cognitive rehabilitation programs focus on stress prevention when applying cognitive behavioral therapy (CBT), various types of behavioral training, and convulsion therapy. Deligkaris argues that during the past decade, cognitive rehabilitation programs applied in patients with stress-related impairment have shown that the condition is associated with de facto cognitive impairment that improves concentration, attention, and memory impairment (Deligkaris et al., 2014, 107-123). This statement indicates that cognitive rehabilitation programs applied in patients with stress are associated with de facto cognitive impairment that improves concentration, attention, and memory impairment in patients. Cognitive rehabilitation impairment programs have been utilized in practice for invigorating concentration, attention, and stress-related conditions that have been associated with de facto behavior for the past decade. De facto means, which exists in reality, regardless of whether they are officially recognized by laws or other formal norms. It is commonly used to refer to what occurs in practice. Cognitive rehabilitation training programs are used for cognitively challenging tasks, especially in neuroplasticity, which means the ability to adapt to any situation through structural organization and simultaneous change behavior (Lindenberger, Wenger, & Lövden, 2017, 261-262). Therefore, it is approached in two ways: strategic and process-based training. Strategic training focuses on teaching strategies, for example, computer-based training that performs specific tasks, whereas process-based training mainly concentrates on executive function and working memory (Ball et al., 2002, 2271-2281).\n\nOccupational therapy is a therapeutic program that focuses on refining a patient’s ability to perform activities of daily living. It facilitates the learning of skills and functions essential for adaptation to the environment and for promoting and maintaining health. The Occupational Therapy Journal defines it as a scientifically based program that provides interventions for mental disabilities and impairments that help a person lifelong through the therapeutic use of various activities, social activities, and cognitive changes (Occupational Therapy Journal, 2017, 24). This statement indicates that occupational therapy provides interventions for various disabilities and impairments in people with mental health problems by preparing various therapeutic activities. Occupational therapy is a rehabilitation-based program that enhances a patient’s recovery and creates a balance in daily working: for example, occupational therapy assists in accomplishing daily tasks routinely and meeting deadlines. Occupational therapy aims to promote individual self-esteem, encourage functional activities, and promote independence. Despite the usefulness of occupational therapy in a mental health care setting, there has not been enough systematic review in various research or journals about the program’s influence to gain energy and motivation to get involved with surroundings (Lopez, 2011).\n\nPhysiotherapy is a scientific-based program that provides assessments and interventions to restore maximum function and improve mobility and well-being. It also prevents risk, injury, and illness through various rehabilitation programs. According to Klaperski. S. et al. (2013), Physiotherapy provides well-documented health benefits and is the remedy for many stress-related illnesses. Physical activity contributes to decreased physiological reactions to psychosocial stress. These statements indicate that performing physiotherapy aerobic exercise reduces cortisol levels and increases the activity of the hypothalamus-pituitary-adrenal gland, which reduces blood pressure and stress. Accordingly, group-based training programs are useful for obtaining more motivational support for teamwork in each workforce to improve cognitive function, including attention and concentration, and increase adaptability and self-esteem (Hötting et al., 2012, 332-346). Physiotherapy has also been shown to improve coping ability in various adverse environments and to enhance self-control, which can alleviate stress from challenging situations (Kirschbaum, C.& Hellhammer, D. H. 2000).\n\n\nMethods\n\nThe qualitative study design is being conducted in this research because people with stress require evidence-based recommendations to fulfil their future needs, which is only possible in the qualitative study design (Hoefsmit et al., 2012, 462-477). Reviews many inconsistent results revealed between quantitative on behalf of usefulness on stress, therefore, quantitative research design is not likely to discover an in-depth understanding of people’s knowledge and skills regarding stress which may affect the success of interventions (Briand et al., 2008, 207-217 & Pearson et al., 2005, 207-215). Given that, the author selected a qualitative study design that discovers the historical background related to people’s problems and supports them through various rehabilitation programs (Corbière et al., 2016, 511-519). This study aimed to determine the usefulness of rehabilitation programs for individuals with stress-related disorders. The research question is how useful is the rehabilitation program for people with stress-related disorders? A convenient sampling method was selected in this research, which is an easily accessible and convenient way to collect samples with allocated time and resources. Semi-structured interview questions were formulated in which participants expressed their feelings and conversed their histories in their own words. Open-ended and closed-ended questions were devised for this study. The questionnaire included 12 questions, and 10 participants were selected throughout the interview process. The researcher formulated an interpretive research design to obtain in-depth information and explore insights into the data, whereas positivism mainly focuses on quantitative research design (Thanh & Thanh, 2015). According to Willis (2007), the interpretive approach is more subjective, therefore, the goal of interpretivism is to create value subjectively. Thomas (2003), stated that qualitative approaches are always supported by interpretivists because the interpretive paradigm portrays a world in which reality is socially constructed, complex, and ever-changing. Based on the above characteristics, a qualitative study with an interpretivism design was conducted in this study, which investigated the usefulness of rehabilitation programs for people with stress. Therefore, it is useful to know how rehabilitation programs act on people’s stress to improve their daily activity plans, self-motivation, attention, coping ability, self-control, etc. (Koerner, 2011, 45-67).\n\nThe author selected convenience sampling was used to gather data that were easily accessible and available within the allocated time and resources. These samples are intended to be generalized to the population and the future. According to Leiner (2014), the main objective of this sampling is to obtain information from participants who are accessible and homogeneous. In another way, this sampling method was affordable, the subjects were ready and available, and the criteria were suitable for conducting this research. The sample was collected from the healthcare industry to provide significant outcomes and results to complete this study efficiently. To avoid biases, the author did not take any representative, therefore, the author met the participant in person for the entire interview process. As a qualitative study method, only 10 participants were selected after obtaining their consent and approval to participate in this study. The participants aged between 25 and 55 years old. This age range was chosen because of a better understanding of the services of the rehabilitation program. Before conducting the interviews, the author arranged meetings with the management in each organization to obtain consent before meeting clients. After obtaining consent from every participant, the author started conducting interviews in person according to the questionnaire. The author provided the participants with an idea of the research topic, the aim of the study, and the inclusion and exclusion criteria.\n\n\n\n1) Age between 25-55 years\n\n2) Stress-related disorder both female and male\n\n3) With the diagnosis of mental stress\n\n\n\n1) Alcoholism, Suicidal risk\n\n2) Fibromyalgia\n\n3) Post-traumatic surgical patient\n\n4) Disease-related stress\n\n5) Physical stress\n\nThe recruitment period was from January to March 2020. The author chose various rehabilitation centers, however, the interviewees were from the Marienthali Clinic, Aarika, and Elil Rehabilitation Centre, depending on the participant’s availability and selection criteria. I selected samples from these organizations to generalize the usefulness of the rehabilitation program. The author justified the reason for choosing this rehabilitation center in light of getting participants easily and conveniently within a short period rather than selecting any other healthcare organization. Moreover, these organizations were invited to execute therapeutic centers, where all multidisciplinary teams, including doctors, nurses, psychologists, and social workers, carried out various rehabilitation programs on a day-to-day basis. In addition, the services were conducted from the patient assessment to discharge to further follow-up where the author had an opportunity to obtain in-depth knowledge of participants’ history and their experience in this field. On the other hand, the author excluded other rehabilitation centers because they were not well-structured and documented in the individual participants’ records. Furthermore, the selected participants met the inclusion and exclusion criteria of this study.\n\nThe organization was inaugurated in 2008 to provide psychiatric services, especially for stressed clients. The Aarika board of the directorate has introduced various rehabilitation services, such as psychotherapy, psychiatric clinical, special education, occupational rehabilitation, physiotherapy, and specialist care education, since 2008. Most clients were referred by the government’s unemployed health services and social welfare department, therefore, very few patients were referred by general practitioners or psychiatric doctors for rehabilitation programs in this organization. However, this organization has a reputation and maintains a protocol in which patients’ records are well-documented, updated, and available from the first admission until their discharge, along with rich confidential systems. Furthermore, the participants’ data were captured easily and conveniently from the systems and paper files for further analysis.\n\nThe organization has been serving various treatment programs for patients since 2017. The clinic consisted of a psychiatric doctor’s department, psychology adults and children, nurses, physiotherapy, occupational therapy, and social rehabilitation. The organization provides services on an outdoor basis, which means that patients receive their care plans and then go home. The clinic’s doctors did not refer clients to any of the rehabilitation services, although the patients benefited from the rehabilitation programs. According to the participants’ viewpoint, most of the patients did not refer to rehabilitation services. The author selected this organization owing to the confronted loads of patients receiving services who have a variety of conditions and have very intriguing histories about their past service. The environment of this clinic was calm and quiet, and the clients could express their emotions and feelings in their own words safely and effectively.\n\nThe Estonian Association of People with Mobility Disabilities introduced ELIL in 1989. In the past, they had various awareness programs based on education and teaching facilities to ensure accessibility for all sectors of people who have mental health issues and are physically disabled. However, many services had already been shut down because of the change in Estonian administrative policy and procedures. Primarily, the servicing systems of the organization were based on occupational rehabilitation, which includes physiotherapy, psychology, occupational therapy, special education, etc. The author selected this organization because, to begin with, it is a rehabilitation center. Moreover, clients would not have been referred to receive rehabilitation programs in the first instance unless they had taken medication from psychiatric doctors. even though it was recommended earlier by the Social Welfare Department. Furthermore, participants were very enthusiastic about conducting face-to-face interviews to share their experiences in this research.\n\nData collection methods were devised in this study while selecting the qualitative form of the research approach. Data collection methods were segregated into two types of sources, secondary and primary. Primary data were collected from the participants’ comments. Secondary data were from reliable sources, such as existing literature, including journal articles, books, academic papers, and scholarships. The secondary sources were recaptured from the EBSCO discovery service and EBSCO academic database, Google Scholar, Taylor and Francis, Emerald Insight, and the Journal of Rehabilitation Medicine. The questionnaire also highlighted the usefulness of primary and secondary data. The authors reviewed more than 80 journal articles to identify the most relevant data for this research. Academic papers that had been published in recent years were also reviewed for the analysis of these research findings. At the same time, the author enclosed some journal articles that were not so recent but gave some significant, concrete ideas and relevant to compare that were being kept in this prospective research. Many articles and sources were rejected due to poor methodology, very old-fashioned publications, etc. Convenience sampling methods were used in this study. Semi-structured interviews were selected because they proved to be versatile and allowed both individual and group interviews (DiCicco-Bloom & Crabtree, 2006, 314-321). According to Gill et al. (2008), the semi-structured format is the most frequently used interview technique in qualitative research studies and a healthcare context, given that the author decided, a semi-structured format to obtain in-depth data. Semi-structured interviews are convenient for collecting rich descriptions of this topic. With semi-structured questions, participants had the freedom to explain their feelings in their own words. All data were collected by the researcher using a physical method to avoid bias. As mentioned earlier, 10 participants were selected from the rehabilitation center. Some of them were allocated to ongoing rehabilitation programs, and a few were waiting to finish their rehabilitation program. The interview was conducted in English and hired interpreters to translate difficult English words to make a simple form in the Estonian language. Face-to-face interviews were conducted because this may provide a higher response rate than any other data-collection method. During the interviews, key points were noted without interrupting the flow of interviews. A voice memo was used to record the conversations and discussions with the participants. Simultaneously, a pen and paper were used to write the notes. The questionnaire was designed to conduct interviews with selected participants. The interviews were recorded after permission was obtained from the participants. The interviews continued until the saturation point was reached. The data collection was carried out over time, therefore, semi-structured, convenient sampling, and questionnaires including open and close-ended questions were used in this research.\n\nThe sample questions were formatted as open and closed-ended in English and Estonian to gain more confidence about the facts, situations, and circumstances of their problems. The author formulated some generalized questions to get inside the participants’ views to discover any specific ideas or concepts from the participants’ statements to justify this research aim. In the case of difficult Estonian languages, translators were hired to harness simple languages. According to Estonia Language Facts and Stats (2019), only 50% of the population in Estonia can read and make a sentence in English, whereas a high percentage of the population has a good command of the Estonian language. The same questions were asked to all participants with an equal timeframe to collect the primary data. It was observed that most participants could speak and understand the English language but sometimes needed to explain difficult English words. The interview duration was 40-50 minutes. The questionnaire included 12 questions covering the most important points that the researcher wanted to carry out in this research. Open-ended questions were formulated, whereas by providing open-ended questions, participants had an opportunity to talk and tell stories about real facts or incidents; therefore, those stories or facts create a good context that makes qualitative research more reliable and valuable. The author encompassed close-ended questions, such as the LIKERT Scale, multiple choice questions, and yes/no questions to participants understand and provide the right answer within a short time. For Instance, physiotherapy/occupational therapy/psychotherapy/cognitive therapy, and good/very good questions. The questionnaire was described as follows.\n\n\n\n1. What type of Therapy Rehabilitation program you have Attended? Do you think it is useful?\n\n2. Do you think the services of the Rehabilitation program might best suit your condition? If so, please tell me in brief.\n\n3. Express your feelings about the role of rehabilitation programs in various hospitals or clinics.\n\n4. How do you feel about receiving a rehabilitation program compared to other interventions?\n\n5. What has been useful from the things you have learned in the rehabilitation program?\n\n6. Are there any things you have not used that you have learned? Why?\n\n7. Please tell me about the situation at home, at work, or in other parts of life after having the rehabilitation program.\n\n8. Please mark your consent! Which therapeutic procedure is more effective in recovering your condition? and how?\n\nA. Physiotherapy. B. Occupational Therapy. C. Psychotherapy D. Cognitive Therapy E. Forest life G. All of the above.\n\n9. Do you want to put your recommendations below? How is your condition now after achieving this Rehabilitation plan?\n\nA. Very good. B. Good. C. Satisfactory. D. No comments. E. Worse.\n\n10. The rehabilitation program provided me with good tools to live a good life after having stress condition. Show your opinion on the LIKERT scale.\n\n1. Strongly agree, 2. Satisfactory, 3. Neutral, 4. All of them, 5. strongly disagree.\n\n11. Do you think the activities at the rehabilitation center are useful for recovery? Please provide your opinion.\n\nAgree – 1. Satisfactory – 2. Extremely Satisfied – 3. Disagree – 4. Extremely Agree – 5.\n\n12. Do you have any suggestions about rehabilitation programs or services that require modification in the future? Please make your comments.\n\nAfter taking the entire interview, the voice memos and notes were transcribed fully to make a final note. The data then progressed to the data analysis phase for examination, interpretation, and management. In the initial phase of the analysis, data were collected from the participants and organized according to the questions for analysis, consolidated, and further analysed. The transcript was read several times to get inside the data and determine the participants’ comments for discovering recurring codes that stand out. Primarily, all transcribed interviews were formatted into a code. All codes were verified thoroughly to ensure that they were different from one another. The Author used a code to provide a clear description. The purpose of coding is also to safeguard the confidentiality of the participants’ personal information, except for their willingness to disclose. Therefore, whatever the participants stated was reflected in the codes. All interviews were coded and levelled line by line to ensure that they were close to the participants’ words. Extract codes within the participants’ interviews were compared to each other to determine similarities, differences, closeness, and completeness from every individual opinion, therefore, they were formulated. After categorization, all categories were combined for further exploration. Once the code was transformed into a category, the findings were formulated, based on the category. To enhance credibility, the author devised a comparison of the study findings with the primary and secondary data to verify consistency with previous research and journals or articles to ensure the authenticity and generalizability of the research findings. Three essential aspects occurred in the data analysis process: data organization. summarization and categorization together contribute to the second known method used for data reduction. It helped to find patterns and themes in the data for easy identification and linking. The third and last parts of the data analysis were both top-down and bottom-up. Data analysis is as important as data collection methods because poor data analysis does not carry out good research findings and reduces the image of overall research.\n\n\nResults\n\nThe results of this study were coded according to participants’ statements or comments. To formulate the code, similar words or sentences were discovered from each of them that were closely related to each participant’s comments. The 10 participants in the study were one client, another client, a few clients, and many clients. When one participant’s comments were discovered identical to those of the other participants, they were kept under the same code. Empirically, all participants responded to each question with the best knowledge and understanding. The interview questions were devised based on the research aims and questions. Owing to a lack of understanding, some participants were unable to address the research questions accurately. Therefore, only relevant data were retained from a large amount of information. The codes were presented in italics. After comparing participants’ comments and based on the words that came up repeatedly from the codes, the author formulated a category. Thus, the following categories are formulated when similarities and differences are generated for each code: quality services, self-motivation, daily activities plan, self-control, recovery, attention and concentration, coping skills, and medication-based treatment, as discussed in the findings and discussion section. These formulated categories were identical to the literature review parts, although some category meanings emerged in different words but still conveyed the same meaning and are useful in the rehabilitation program precisely. The author also coined the last category as additional data to gather knowledge concerning the impact of using medication as a method of Treatment as Usual (TAU) contributes to devising further recommendations for this study. The purpose of collecting additional data in a qualitative study was to maintain the standards of the research findings.\n\n\nDiscussion\n\nThe findings and discussion sections analyze the results of the study by comparing the primary and secondary data, addressing the research aim of this study. Although inconsistent results were discovered from some of the secondary data, positive opinions were gathered from primary data, thereafter, comparing the findings along with primary and secondary data are vital to make the research more rational and scientific. Therefore, the findings and comparison of the primary and secondary data are as follows:\n\nThe author formulated this category in the first place to understand if a rehabilitation program does not provide quality service, then how it generates a useful factor for people with stress. The rehabilitation program offered quality services with effective interventions for patients. The majority of participants had a positive opinion about the treatment procedure of the rehabilitation program, which means that it is an intensive care plan and provides good quality services. In other words, when a rehabilitation program provides quality services, there is no doubt that the rehabilitation program itself is a good treatment procedure as well. Participants specifically mentioned psychotherapy and physiotherapy programs, which have influenced the care of relieving stress and have many useful roles in providing good quality services. However, cognitive-based therapy (CBT) and occupational therapy have many other useful roles in relieving stress. The findings of this study revealed that the rehabilitation program is a good treatment procedure that provides quality services in the context of Estonia. The author brought a segment from the literature review for comparison that the rehabilitation programs do care for individuals to get back their previous life, and enhance physical, mental, cognitive, functional, and well-being. This particular context highlights the need for a rehabilitation program for all purposes and offers quality services for individual daily life. However, one participant gave one negative response. The rehabilitation program is useful and conveys a good treatment procedure, but people are not completely satisfied with the rehabilitation program because they do not get around a skilled service provider, albeit meeting their demands. Eventually, it is explored that the findings of this research study have positively reflected in terms of the usefulness of rehabilitation programs for people with stress disorder.\n\nSelf-motivation is a psychotherapeutic intervention procedure for rehabilitation programs. After gathering participants’ statements, it was revealed that the client is optimistic about the future when the rehabilitation program heals their stress and encourages them to learn new objects because they do not want to adapt to any transformation in their lives. People are satisfied with the rehabilitation program because they enjoy it every day and feel that they are in their comfort zone. In addition, they found that rehabilitation was a useful treatment method in light of utilizing a client-centered approach, which is rare in any other interventions. On the other hand, another participant commented that people’s motivation for rehabilitation services was positive and enquired about receiving more rehabilitation sessions. This statement reflects that motivation is a characteristic of positivism but still does not live up to their satisfaction level because they want more rehabilitation programs.\n\nThe daily activities plan is a treatment procedure for occupational therapy, as well as a physiotherapy rehabilitation program. According to the participants’ view, the rehabilitation program executed a daily living activities plan in various phases of life. Hötting et al. (2012), indicated that physiotherapy constructs everyday daily routine activities, creates strategic plans, and analyses everyday life schedules. Rehabilitation acts as a guideline for how people manage their time at home and in the workplace effectively and successfully during their stressful lives. Nevertheless, (Spencer et al., 2017) in a previous literature review explained that occupational therapy is an evidence-based practice of rehabilitation programs but is not useful in terms of people with stress-related disorders. In contrast to this statement, the opposite opinion emerged in primary data. Therefore, without the usefulness of occupational therapy programs, how do people manage their tasks effectively and in a timely manner? Occupational therapy redesigns daily activities to improve individual skills. This category is designed for stressful clients in various environments in Estonia, who are in homes or workplaces. Therefore, it is necessary to have a good activity plan for workers to mitigate substantial days off from the workplace, hence, if this can be prevented, organisational productivity will be enriched. One of the indispensable statements was delivered by one participant regarding the contribution of the rehabilitation program. As such, it provides the right direction for various activities, but the rest of us have to do it ourselves. This does not help if we do not contribute. This statement indicates that the rehabilitation program itself cannot provide the right direction unless other health professionals are involved. This statement is consistent with the research problem. As such, if a patient is not referred to receive rehabilitation by other medical services, then the rehabilitation program itself is not able to make the referral, and it requires collective efforts. Conversely, one distinctive comment came from another participant not see any major change in her condition because of not carried out exercise regularly. This means that if someone does not carry out home exercises regularly, she or he is not able to see any changes in his condition, but we cannot say that the rehabilitation program is not useful.\n\nSelf-control or self-mystery is a psychotherapy well-being therapeutic rehabilitation program. After analysing the participant’s comments, it was found that the rehabilitation program was useful for the self-control of individuals during various activities. The psychotherapy rehabilitation program helps people learn more about how to control themselves. The Author brought up a comparison study of rehabilitation programs and hospital services. By receiving rehabilitation services, people think that they are not isolated, can control their emotions, and are fully connected with interim service providers and service users. In contrast, hospital services are based on medication, where there is no management of how to control emotions, no connections from service providers to service users, or even no motivational support from the services. Accordingly, a rehabilitation program ensures that every individual can enjoy their day-to-day life efficiently with positive control, whereas hospital-based services are not able to provide any of them. Self-control or Self-mystery is a salient factor in relieving stress, which is highly demanding in terms of various psychological factors (Åhrberg et al., 2010, 167-77), and imposed well-being therapy is a more effective intervention in reducing symptoms than Treatment as Usual (TAU) (Fava et al., 2017, 801–808). However, according to Ruotsalainen et al. (2015), previous studies indicated that psychotherapy has low effects on people’s stress due to the low methodological quality of research, and a small number of participants recovered compared to the administered Treatment as Usual (TAU) procedure. However, this research found that a psychotherapy rehabilitation program is a useful method of intervention for the self-control of every individual during various activities and encourages people empowerment, which is not possible with any hospital-based intervention or even Treatment as Usual (TAU).\n\nMany participants stated that a rehabilitation program was a substantial tool for recovery from the initial phase to the recovery stage. Thus, the participant could complete the tasks in an effective time frame through the rehabilitation program. A rehabilitation program provides various interventions that help patients recover early, as it is a scientific-based therapeutic program that assists in being more accurate. Accordingly, a medium-progressed client receiving a rehabilitation program can still hope to recover even though her rehabilitation program has not yet finished. This means that rehabilitation is a useful and recovery-oriented treatment method in which clients benefit from the initial assessment to further follow-up procedures. When all clients have positive comments regarding the recovery of the rehabilitation process, there is no denying that the rehabilitation program is a useful method to relieve stress. The author found that there were no negative comments from any of the participants about the recovery sections. Conversely, the literature review stated, that many health practitioners, including psychiatric doctors, prescribe only anti-depressive medication to relieve stress rather than referring to the psychotherapy rehabilitation program because ignoring or thinking of psychological rehabilitation programs is not useful for relieving stress. In summary, a rehabilitation program is a useful method of treatment, if the symptoms remain mild further progress is possible.\n\nAttention and concentration are a cognitive-based interventions and physiotherapy methods used in rehabilitation programs. A greater number of participants perceived that rehabilitation programs focused on individual tasks and enhanced physical, mental, and cognitive functions. Previous studies have shown that cognitive interventions have insignificant effects on reducing stress symptoms compared to Treatment as Usual (TAU) (Perski et al., 2017, 551-561). However, concerning the practical observation of primary data on clients’ opinions, positive results were ascertained from the participants’ comments. However, one negative perception emerges from one individual, the rehabilitation program creates more attention on tasks but not a major change in her stress condition. This statement does not imply that the rehabilitation program is not useful, as the client has obtained significant results with attention to tasks but has not progressed adequately on stress due to probably not attending regularly or revealed that progress in delay depends on person to person. Cognitive-based rehabilitation programs are the most effective intervention for stress disorders. On the other hand, another participant commented, that she had not seen significant change through the rehabilitation program at home, but when she was at work, was told by her friends that her attention to activities had refined and, in the end, she realized why the rehabilitation program was required for people under stress conditions. Moreover, according to the last client’s perception of no comments about the rehabilitation program, either it brings positive or negative changes in relieving stress. This is due to some conceptual overlapping interventions interrelated with Treatment as Usual (TAU) and cognitive rehabilitation programs, such as executive function, memory training, and attention and processing speed (Cohen, J. D, 2017) where sometimes the outcome would not appear when all interventions were applied together.\n\nCoping skills are rehabilitation interventions in psychotherapy and physiotherapy programs. According to one participant’s impression, the rehabilitation program enhanced coping skills to get closer to the family members. Another participant’s perception was that as soon as she started the rehabilitation program, she managed to adapt to new things, new ways to exercise, new ways to see various situations and overcome stress symptoms. According to Stevens-Watkins et al. (2014) in the previous article from the literature review, psychological resilience is an intervention of psychotherapy that describes the ability to cope mentally or emotionally with a crisis or to return to pre-status instantly. The resilience psychotherapy program is defined as the ability to adapt and apply to obtain better outcomes for employees, people, and family stressors for people with stress (Muzzio, T, 2004). Another important point of resilience is allowing people to share their feelings and exchange their ideas, concepts, and skills with others in a positive way, where they can enjoy their lives purposefully (Leahy, Chan & Saunders, 2002, 68-81). Moreover, according to Gerber et al. (2012), a higher level of physical ability indicates higher resilience and lower stress when applying various settings of physical activity programs. On the other hand, one participant’s conception was that the rehabilitation program does not affect her significantly, sometimes the effectiveness depends on the environment and social circumstances, and then again, she stated that she had only completed a few sessions, not even completing a total of the rehabilitation program. This means that the participants did not disagree about the usefulness of the rehabilitation program regarding coping ability. However, there are some disputed opinions in the literature review due to limited laboratory findings, little-known knowledge about the efficacy of rehabilitation programs, and low methodological research. As a result, the actual outcome of rehabilitation programs was not visible. Eventually, it was devised from primary data rehabilitation programs as a useful intervention method to enhance coping skills.\n\nThe purpose of collecting additional data in a qualitative study was to maintain the standards of the research findings. The author formulated this additional category to identify and analyse participants’ perceptions of how Treatment as Usual, especially medication, contributes to individual clients in everyday life. Accordingly, the author devised concrete outcomes from primary data findings; however, secondary data have various opinions about Treatment as Usual (TAU) regarding relieving stress. According to the participants’ impressions, medication is not a useful intervention method that has various side effects compared to the rehabilitation program. Accordingly, participants also raised comments about the hospital and free health services where patients did not receive appropriate treatment facilities and the treatment was based only on medication. Practitioners did not deal with actual patient problems, not even referring to appropriate rehabilitation services, unless they produced any significant outcomes from the medication process and, in many cases, services overlapped by the practitioners in some cases. However, few clients receive rehabilitation services by chance when they have long queues for medical services. In other cases, the patient was referred to a green forest as a traditional method of intervention, which is not even a structural method of treatment while maintaining some rules or regulations. This is due to ignoring rehabilitation programs as an effective method of intervention or prioritizing pharmacological practice. Other participants commented when patients recovered from rehabilitation programs, they never came across receiving any further hospital services or even taking medication. On the other hand, one participant’s perceptions about the management systems of ‘Parnu’ Hospital were very impressive but did not refer patients to rehabilitation services. Grossi and Santell (2009), Brouwers et al. (2009) and Heiden et al. (2007), De vente et al. (2008), stated in a previous study that no or only marginal differences between various rehabilitation strategies and Treatment as Usual (TAU). However, it explored from the primary date that Treatment as Usual (TAU), especially medicine, can only change the symptoms; therefore, patients are not motivated by medicine due to not contributing individuals changing their life and dividing activities plans or assisting in adjusting various environments and even creating a balanced life in society.\n\nThe lack of understanding and knowledge of the participants about the usefulness of rehabilitation programs during the interview could have affected the quality of the responses. Due to inadequate rehabilitation centers in Estonia, clients have to be discharged before completing the full program; consequently, short interventions may have little or no effect on rehabilitation programs. In other words, as an author, it can be suggested to generate a larger sample size in future research, where articles will be formulated with adequate comparison along with an appropriate design and tool. Due to limited time and resources, a large sample selection would not have been taken where there was feasibility to get more ideas and concepts, the way to make research more reliable, valuable, and more scientific. Some participants could not speak English, therefore, the translation from Estonian to English and vice versa may have missed some context from the full interpretation.\n\n\nConclusion\n\nThe conclusion of this study summarizes the aims and answers to the research question. This study aims to determine the usefulness of rehabilitation programs for people with stress-related disorders. The discussion and findings of this study highlight the positive impact of rehabilitation programs on people with stress disorders. Rehabilitation programs are useful tools for enhancing many aspects of people’s lives. This study devised a rehabilitation program that plays a useful role in relieving stress disorders and helping individuals’ lives by identifying several positive aspects. After analysing the participants’ perceptions, the findings of the rehabilitation program are highlighted. All rehabilitation programs are useful for people with stress, such as psychotherapy, cognitive-based therapy, occupational therapy, and physiotherapy, and their excerpts come up in various forms, such as quality services, self-motivation, daily activities plan, self-control, recovery, attention and concentration, and coping skills. Rehabilitation programs provide effective guidelines for clients, such as how to perform daily activities, how to control emotions, how to cope with various working environments, demonstrate the best way to meet different people, teach how efficiently people can lead a good life, recovery from stress, self-motivation, etc. Rehabilitation programs provide good treatment procedures; therefore, a good treatment procedure ensures good quality service for an individual’s daily life. Motivation enhances healing to construct optimism and encourages the effective and efficient learning of new objects, which is only achievable through a rehabilitation program. Performing daily activities plan for individuals assisting functional tasks into simpler forms to finish accurately and in a timely manner. A redesigning daily activities plan evaluates individual tasks for an effective arrangement in an organization; as a result, organizational productivity is enriched. The rehabilitation program acts as a role model in making various useful forms to relieve stress, and Estonia has loads of stressed patients and requires adequate rehabilitation services. Another useful finding of the rehabilitation program was the self-control and coping skills. Rehabilitation programs help to control emotions and eliminate thinking about any external or unpleasant situations, thereby, encouraging individuals to be sociable. Through this rehabilitation program individuals can adapt to new things to overcome stress symptoms in various situations. Furthermore, the rehabilitation program refines cognitive skills for attention and concentration in specific tasks and enhances memory function during various executed activities. As a result, performance is ramped up in various activities in the home, outside, or even in any workplace. Another compelling finding of the rehabilitation program was the recovery. Rehabilitation programs accommodate initial patient assessment, and interventions until discharge and prepare participants to achieve a higher level of functioning activities with sufficient potentiality. Owing to recovery from the rehabilitation program, people can start to work early and meet the requirements of the deadline. If participants recovered from the rehabilitation program, they did not need any further interventions or medications to become healthy. A few comments suggested the necessity to have more rehabilitation programs in the context of Estonia, even though a few sessions were allocated on an individual basis, not enough for the following participants’ demands. Eventually, it was proven that a rehabilitation program is a useful intervention for people who want to get more sessions. Despite receiving some findings, there were no comments, and no effect was either positive or negative due to some overlapping procedures by Treatment as Usual (TAU) and prioritized medication; as a result, in a few cases, no visible outcome was empirically spotted through the rehabilitation program. The last category of this research study was devised to understand how Treatment as Usual (TAU) or medication impacts people’s lives as compared to rehabilitation programs. It has been discovered that Treatment as Usual (TAU) cannot change people’s lives; it can only reduce symptoms for a while. In comparison with primary and secondary data in this research, the author concluded that every rehabilitation program, such as psychotherapy, cognitive-based therapy, physiotherapy, and occupational therapy, performs a useful role for people under stress; however, the literature review did not support this view. Consequently, their opinion was that a combined rehabilitation program with medications may hold more promise for relieving stress. Every certified rehabilitation program is a useful method of intervention compared to the primary data. Accordingly, this conclusion is convincing and certifies that a rehabilitation program is a useful treatment method for people with stress. The author justified that the aim of this study was achieved from participants’ concrete statements that the rehabilitation program is useful for people with stress. In response to the main research question of this study, it is also achieved and convinced that the rehabilitation program is a useful method of intervention, which is apparent in the context of Estonia’s healthcare system when rehabilitation programs are devised as a quality services system, a motivational approach of interventions, its recovery skills, coping skills, self-control, can divide daily activities plans, improve cognitive skills, and so on. The usefulness of psychotherapy and physiotherapy rehabilitation programs has been worded many times in the primary data based on the participants’ opinions. In addition, cognitive-based therapy (CBT) and occupational therapy rehabilitation programs have many other useful methods that are displayed in primary data as well as in the literature review. Here, and are reciprocally connected. This study is essential for creating healthy organizations in various parts of Estonia. If the Estonian government creates a rehabilitation program as a useful method of intervention, people will benefit from being cured comfortably and can lead a happy life at home and in the workplace. Such information is rational for alleviating stress in people’s lives and performing tasks productively in the organization. The rehabilitation program is an inspirational treatment approach in which a client cannot be fortunate without receiving a rehabilitation plan; he or she can live with sufficient energy to recover early in the rehabilitation process. These findings are consistent with the literature and address the research aims and research questions. Every categorization carried out concrete client opinions, and each comment expressed that the rehabilitation program is a useful method of treatment. Further studies are needed to establish when rehabilitation programs are well established in Estonia and have sufficient aptitude to obtain a large sample size with adequate time and resources.\n\nParticipants do not want to receive treatment from free healthcare services and do not like to stay in hospitals where they are being neglected, overlooked, and feel isolated; therefore, they are required to organize and emphasize invigorating this sector. Most importantly, the Treatment as Usual (TAU) method should not only rely on medication that has several side effects and is unlikely, but people under stress do not take this due to the scare of giving up medicine and dependency; hence, they ought to maintain an appropriate referral system and establish an appropriate treatment protocol utilizing a client-centered approach in the workplace. This kind of research is useful not only in healthcare organizations but also in business organizations. Rehabilitation programs reduce costs associated with turnover rates to ensure that people are healthy enough to perform tasks regularly; thus, the productivity of the organization is enriched. Moreover, every individual requires a rehabilitation program once in their life; therefore, a business character is required to understand the usefulness of a rehabilitation program to improve productivity and how rehabilitation programs reduce turnover rates when people experience stress in the workplace. Simultaneously, they ought to know the impact of Treatment as Usual (TAU) when administering medicine to stressed clients. In summary, it can be stated that a rehabilitation program is a useful therapeutic intervention for people with stress because it helps to relieve stress via appropriate recovery, improves the quality of life, encourages self-control and self-motivation, adjusts to various environments at home or working place, and constructs attention and cognition, whereas Treatment as Usual (TAU), especially medication, might be acting on symptoms reduction but not appropriate to change people’s lives.\n\nEthical approval name: The Ethics Committee of Estonian Entrepreneurship University of Applied Sciences (EUAS).\n\nand the date - 06/05/2020.\n\nThe approval committee: Estonian Entrepreneurship University of Applied Sciences - regulation no 2.5.1-344.\n\nThe approval number: 350\n\nParticipants were informed verbally and with written consent according to their level of understanding of the aims of the research. They received a clear conception of the research study guidelines and provided informed consent in writing that their presence depended on their willingness, to participate as attendees. Participants were aware that their information might be published, but their names, ages, and addresses would not be published by any means of this research. Their data will be kept in a safe and secure place, and there is no chance of breaking confidentiality and anonymity. The notes, transcripts, and voice recorders were not shared or discussed with others. The Author provided consent from the organization manager where the interview took place and assured clients that the subjects of this study were completely voluntary and could deny any questions or withdraw at any time during the interview process. After obtaining consent from the clients, the author interviewed them.", "appendix": "Data availability statement\n\nThe data availability statement contains interview transcripts and the extended data - questionnaire.\n\nThe data that support the findings of this study are available to the public and from the corresponding author, upon reasonable request, therefore, the corresponding author name is Mohammad Delwar Hossain and the email address is mohammad.hossain16@nhs.net.\n\nThe data repository for Interview transcript: Figshare: The usefulness of rehabilitation program of people with stress-related disorders – A case from a rehabilitation center in Estonia. doi.org/10.6084/m9.figshare.26386195. (Hossain M, 2024b)\n\nDataset: Interview Transcript (January to March 2020), that describes each participant’s statement, opinions, and comments in line with the questionnaire.\n\nDate repository name for extended data; questionnaire; Figshare: The usefulness of rehabilitation program of people with stress-related disorder – A case from the rehabilitation center in Estonia. doi.org/10.6084/m9.figshare.26412901 (Hossain M, 2024a).\n\nDataset – questionnaire- every single question carries out the participant’s comments, statement, and so on.\n\nBoth of the dataset embodying the same license CCO - public domain dedication - databases are restricted by copyright or other rights. Databases may contain facts that, in and of themselves, are not protected by copyright law.\n\n\nReferences\n\nArends I, Bruinvels DJ, Rebergen DS, et al.: Interventions to facilitate return to work in adults with adjustment disorders. Cochrane Database Syst. Rev. 2012; 12: 1–15.\n\nÅhrberg Y, Landstad BJ, Bergroth A, et al.: Desire, longing and vanity: Emotions behind successful return to work for women on long-term sick leave. Work. 2010; 37: 167–177. PubMed Abstract \| Publisher Full Text\n\nBrouwers EP, Tiemens BG, Terluin B, et al.: Effectiveness of an intervention to reduce sickness absence in patients with emotional distress or minor mental disorders: a randomized controlled effectiveness trial. Gen. Hosp. Psychiatry. 2009; 28: 223–229.\n\nBall K, Berch DB, Helmers KF, et al.: Effects of cognitive training interventions with older adults: A randomized controlled trial. JAMA. 2002; 288 (18): 2271–2281. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBriand C, Durand M-J, St-Arnaud L, et al.: How well do return-to-work interventions for musculoskeletal conditions address the multicausality of work disability? J. Occup. Rehabil. 2008; 18(2): 207–217. PubMed Abstract \| Publisher Full Text\n\nBugarski Z, Medar M, van Ewijk JP , et al.: Uuring psüühilise erivajadusega inimestele suunatud erihoolekandesüsteemi ümberkorraldamiseks ja tõhustamiseks teiste riikide praktikate alusel. Lõppraport. 2016.\n\nBener A, Ghuloum S, Abou-Saleh MT: Prevalence, symptom patterns and comorbidity of anxiety and depressive disorders in primary care in Qatar. Soc. Psychiatry Psychiatr. Epidemiol. 2012; 47(3): 439–446. PubMed Abstract \| Publisher Full Text\n\nBorg V, Andersen Nexø M, Kolte IV, et al.: Hvidbog om mentalt helbred, sygefravær og tilbagevenden til arbejde [White paper on mental health, sickness absence and return to work]. København: Det Nationale Forskningscenter for Arbejdsmiljø; 2010.\n\nCohen JD: Cognitive control: Core constructs and current considerations.Egner T, editors. The Wiley handbook of cognitive control. West Sussex, UK: John Wiley & Sons; 2017; pp. 3–28.\n\nCorbière M, Samson E, Negrini A, et al.: Factors perceived by employees regarding their sick leave due to depression. Disabil. Rehabil. 2016; 38(6): 511–519. PubMed Abstract \| Publisher Full Text\n\nDeligkaris P, Panagopoulou E, Montgomery AJ, et al.: Job burnout and cognitive functioning: A systematic review. Work Stress. 2014; 28(2): 107–123. Publisher Full Text\n\nDe Vente W, Kamphuis JH, Emmelkamp PM, et al.: Individual and group cognitive-behavioral treatment for work-related stress complaints and sickness absence: a randomized controlled trial. J. Occup. Health Psychol. 2008; 13: 214–231. PubMed Abstract \| Publisher Full Text\n\nDiCicco-Bloom B, Crabtree BF: The qualitative research interview. Med. Educ. 2006; 40(4): 314–321. Publisher Full Text\n\nEuropean P: Rehabilitation Medicine Bodies A: White Book on Physical and Rehabilitation Medicine (PRM) in Europe. Chapter 1. Definitions and concepts of PRM. Eur. J. Phys. Rehabil. Med. 2018; 54: 156–165.\n\nEstonia Language Facts & Stats: 2019. Reference Source\n\nFava GA, Cosci F, Guidi J, et al.: Well-being therapy in depression: New insights into the role of psychological well-being in the clinical process. Depress. Anxiety. 2017; 34: 801–808. PubMed Abstract \| Publisher Full Text\n\nGill P, Stewart K, Treasure E, et al.: Methods of data collection in qualitative research: interviews and focus groups. Br. Dent. J. 2008; 204(6): 291–295. Publisher Full Text\n\nGustavsson A, Svensson M, Jacobi F, et al.: Cost of disorders of the brain in Europe 2010. Eur. Neuropsychopharmacol. 2011; 21: 718–779. Publisher Full Text\n\nGlise K, Ahlborg G Jr, Jonsdottir IH: Course of mental symptoms in patients with stress-related exhaustion: Does sex or age make a difference?. BMC Psychiatry. 2012; 12: 18. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGerber M, Kalak N, Lemola S, et al.: Adolescents’ exercise and physical activity are associated with mental toughness. Ment. Health Phys. Act. 2012; 5: 35–42. Publisher Full Text\n\nGrossi G, Santell B: A quasi-experimental evaluation of a stress management program for female county and municipal employees on long-term sick leave due to work-related psychological complaints. J. Rehabil. Med. 2009; 41: 632–638. PubMed Abstract \| Publisher Full Text\n\nHenderson M, Glozier N, Holland EK: Long-term sickness absence. BMJ. 200 Apr 9; 330(7495): 802–3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHealth and Safety Executive (HSE): Self-Reported Work-Related Illness and Workplace Injuries in 2006/07 Results from the Labour Force Survey Caerphilly. HSE; 2008.\n\nHoefsmit N, Houkes I, Nijhuis FJN: Intervention characteristics that facilitate return to work after sickness absence: a systematic literature review. J. Occup. Rehabil. 2012; 22(4): 462–477. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHötting K, Schauenburg G, Röder B: Long-term effects of physical exercise on verbal learning and memory in middle-aged adults. Results of a one-year follow-up study. Brain Sci. 2012; 2: 332–346. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHüning L, Radstaak M, Lamers S, et al.: Well-being as a predictor and outcome in PTSD treatment: An explorative study. Manuscript submitted for publication.2020.\n\nHeiden M, Lyskov E, Nakata M, et al.: Evaluation of cognitive-behavioral training and physical activity for patients with stress-related illness: a randomized controlled study. J. Rehabil. Med. 2007; 39: 366–373. PubMed Abstract \| Publisher Full Text\n\nHossain M: The usefulness of a rehabilitation program for people with stress-related disorders - A Case Study from a rehabilitation center in Estonia. Figshare. 2024a. Questionnaire. Publisher Full Text\n\nHossain M: The usefulness of a rehabilitation program for people with stress-related disorders - A Case Study from a rehabilitation center in Estonia. Figshare. 2024b. Interview Transcript. Publisher Full Text\n\nKoerner M: Mental strain among staff at medical rehabilitation clinics in Germany. Psychosoc Med. 2011; 8: 45–67.\n\nKlaperski S, von Dawans B , Heinrichs M, et al.: Does the level of physical exercise affect physiological and psychological responses to psychosocial stress in women? Psychol. Sport Exerc. 2013; 14: 266–274. Publisher Full Text\n\nKirschbaum C, Hellhammer DH: Salivary cortisol.Fink G, editor. Encyclopedia of stress. San Diego, CA: Academic Press; 2000; Vol. 3. : 379–384.\n\nKreitner, Robert dan Kinicki Angelo: PerilakuOrganisasi. Jakarta: SalembaEmpat; 2014.\n\nKosciulek J: Predicting family adaptation through resilience. J. Appl. Rehabil. Couns. 2011; 36: 8–12.\n\nKuuse R, Toros K: Estonian social policy: from soviet heritage to understanding the principles of deinstitutionalization. Eur. J. Soc. Work. 2017; 22: 388–399. Publisher Full Text\n\nKarlson B, Jönsson P, Pålsson B, et al.: Return to work after a workplace-oriented intervention for patients on sick leave for burnout – a prospective controlled study. BMC Public Health. 2010; Vol 2(10): 301. [about 10 pp]. Accessed 2010 Nov 19. Reference Source\n\nLindenberger U, Wenger E, Lövden M: Towards a stronger science of human plasticity. Nat. Rev. Neurosci. 2017; 18: 261–262. PubMed Abstract \| Publisher Full Text\n\nLopez A: Posttraumatic stress disorder and occupational performance: building resilience and fostering occupational adaptation. Work. 2011; 38(1): 33–38. PubMed Abstract \| Publisher Full Text\n\nLeahy MJ, Chan F, Saunders JL: Job functions and knowledge requirements of certified rehabilitation counselors in the 21st century. Rehabil. Couns. Bull. 2002; 46: 66–81.\n\nLeiner DJ: Convenience Samples and Respondent Pools.2014; 1–36.\n\nLejtzen N, Sundquist J, Sundquist K, et al.: Depression and anxiety in Swedish primary health care: Prevalence, incidence, and risk factors. Eur. Arch. Psychiatry Clin. Neurosci. 2013 July 5; 264: 235–245. PubMed Abstract \| Publisher Full Text\n\nLamers SM, Westerhof GJ, Glas CA, et al.: The bidirectional relation between positive mental health and psychopathology in a longitudinal representative panel study. J. Posit. Psychol. 2015; 10: 553–560. Publisher Full Text\n\nMangkunegara AP: Manajemen Sumber Daya Manusia Perusahaan. Bandung: PT RemajaRosdakarya; 2013.\n\nMuzzio T: RSA training update. Paper presented at the National Training Conference on Rehabilitation Education. Washington D.C.: 2004.\n\nPerski O, Grossi G, Perski A, et al.: A systematic review and meta-analysis of tertiary interventions in clinical burnout. Scand. J. Psychol. 2017; 58(6): 551–561. PubMed Abstract \| Publisher Full Text\n\nPearson A, Wiechula R, Court A, et al.: The JBI model of evidence-based healthcare. Int. J. Evid. Based Healthc. 2005; 3(8): 207–215. PubMed Abstract \| Publisher Full Text\n\nRuotsalainen JH, Verbeek JH, Marine A, et al.: Preventing occupational stress in healthcare workers. Cochrane Database Syst. Rev. 2015; 2015: Cd002892. Publisher Full Text\n\nSalomonsson S, Hedman-Lagerlof E, Öst LG: Sickness absence: a systematic review and meta-analysis of psychological treatments for individuals on sick leave due to common mental disorders. Psycho Med. 2018; 48: 1954–1965. PubMed Abstract \| Publisher Full Text\n\nSalomon JA, Wang H, Freeman MK, et al.: Healthy life expectancy for 187 countries, 1990–2010: A systematic analysis for the Global Burden Disease Study 2010. Lancelet. 2012; 380: 2144–2162.\n\nSchrank B, Brownell T, Tylee A, et al.: Positive psychology: An approach to Supportive Recovery in Mental Illness. East Asian Arch. Psychiatr. 2014; 24(3): 95–103. PubMed Abstract\n\nSpencer B, Sherman L, Nielsen S, et al.: Effectiveness of occupational therapy interventions for students with mental illness transitioning to higher education: A systematic review. Occup. Ther. Ment. Health. 2017; 34: 151–164. Publisher Full Text\n\nStevens-Watkins D, Sharma S, Knighton JS, et al.: Examining cultural correlates of active coping among African American female trauma survivors. Psychol. Trauma Theory Res. Pract. Policy. 2014; 6(4): 328–336. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThanh NC, Thanh TT: The interconnection between interpretivist paradigm and qualitative methods in education. Am. J. Educ. Stud. 2015; 1(2): 24–27.\n\nThomas RM: Blending Qualitative and Quantitative: Research methods in theses and dissertations. California: Sage; 2003.\n\nVos T, Flaxman AD, Naghavi M, et al.: Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010: A systematic analysis for the Global Burden of Disease Study 2010. Lancet. 2012; 380: 2163–2196. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan der Klink JJ, Blonk RW, Schene AH, et al.: The benefits of interventions for work-related stress. Am. J. Public Health. 2001 Feb; Vol. 91(2): 270–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWidodo SE: Manajemen Pengem bangan Sumber Daya Manusia. Yogyakarta: Pustaka Pelajar; 2015.\n\nWillis JW: Foundations of qualitative research: interpretive and critical approaches. London: Sage; 2007; p. 110.\n\nWittchen HU, Jacobi F, Rehm J, et al.: The size and burden of mental disorders and other disorders of the brain in Europe. Eur. Neuropsychopharmacology. 2010; 21: 655–679.\n\nWhat is Occupational Therapy: Canadian Association of Occupational Therapists\|Association Canadienne des aerotherapeutics. Retrieved 2017-05-24.\n\nYunus: Vulnerability and adaptation to climate change in Bangladesh: Processes, assessment and effects. Springer; 2014; p. 41. Reference Source" }	[ { "id": "337243", "date": "29 Nov 2024", "name": "Lena-Karin Erlandsson", "expertise": [ "Reviewer Expertise Occupational therapy", "evaluation of rehabilitation programmes", "rehabilitation for people that need to make revisions in their everyday life", "stress-related ill health", "qualitative method", "ethics", "health care ..." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReview regarding; The usefulness of a rehabilitation programme for people with stress-related disorders - A case from a rehabilitation center in Estonia. This manuscript reports a study aimed to determine the usefulness of rehabilitation programs for individual people with stress-related disorders, in Estonia. The background suggests that there is an urgent need for research and development of programs to reduce stress. The study applies a qualitative method, and 10 individuals have been interviewed. According to the reported result rehabilitation programs contribute to quality services, self-motivation, daily activities plan, self-control, recovery, attention and concentration, and coping skills. It is also commented that traditional treatment may reduce symptoms but not change people’s lifestyles. The author concludes that rehabilitation programs are useful for individuals with stress disorders in the context of the Estonian healthcare system.\nUnfortunately, I do not consider the manuscript to meet the standards of scientific reporting. The Introduction is quite superficial, with a variety of concepts mentioned to define the concept of stress-related ill health. There is a lack of a coherent definition of the concept. A variety of different references from different contexts are used to describe and define the concept. It is hard to see how these different expressions, and perspectives leads to a justification of the concept used (stress related disorders) in the aim. The aim of the study is overly broad given the methodology employed. To investigate “how useful the rehabilitation program is for people with stress-related disorders” seems vague. To evaluate/investigate any usefulness of an intervention usually demands more complex designs. Furthermore, it is unclear what rehabilitation program is referred to here. This is a general question that remains unanswered throughout the manuscript i.e. what the “rehabilitation program” is, as referred to in the aim, result and the discussion. The following \"literature review\" appears to lack rigor and depth. It claims to present four evidence-based “rehabilitation programmes”. However, since no rehabilitation programme is defined it is not unexpected that no evidence was found. To me it seems more like four different professions are presented but no specific rehabilitation programmes carried out by any of these professions is identified. The conclusions drawn from the references mentioned are not evident. A number of these are in addition, incomplete and erroneous. Today, there are indeed defined rehabilitation programmes provided by all the professions mentioned and references that confirms evidence for these exists, to a varying degree. As mentioned above it is unclear how the methodology applied aligns with the stated aim. The methodology section appears to describe parts of the research process, yet no reference is made to the method employed. The sample selection is peculiar, diffuse, and a rationale for this is lacking. The methodology employed for data collection lacks clarity and fails to elucidate even the most fundamental steps and considerations. An ethical approval seems to have been provided by the university. I would expect more reasoning around this especially considering the targeted group. The result commences with a further delineation of the methodology, yet the result itself remains very unclear. Thereby, the absence of a clear result that connects to the aim is evident. The following discussion section is similarly confusing. The discussion of methodologies also appears peculiar and lacks coherence. The conclusion spans at least 1.5 pages and is disproportionate to any conclusions that can be drawn from the presented result. To conclude, this paper needs major revisions and cannot be accepted with its current design and method. Unfortunately, I see such major problems throughout the manuscript, in the introduction, the aim, the methodology section, results, and discussion that I doubt that it can be improved by revision.\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?\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? No", "responses": [] } ]	1	https://f1000research.com/articles/13-1217
https://f1000research.com/articles/13-1215/v1	11 Oct 24	{ "type": "Research Article", "title": "Covid-19 mortality risk factors: Survival analysis of the hospitalized cohort in Sahloul university hospital in Tunisia", "authors": [ "ARWA NEFFATI", "Hela Ghali", "Rania Bannour", "Sana bhiri", "Habiba Ben hamada", "Balsam Kacem", "Mohamed Ben Rejeb", "Asma Ben Cheikh", "Mohamed Kahloul", "Walid Naija", "Halim Trabelsi", "Houyem Said Laatiri", "Hela Ghali", "Rania Bannour", "Sana bhiri", "Habiba Ben hamada", "Balsam Kacem", "Mohamed Ben Rejeb", "Asma Ben Cheikh", "Mohamed Kahloul", "Walid Naija", "Halim Trabelsi", "Houyem Said Laatiri" ], "abstract": "Background Tunisia was one of the most affected nations with COVID-19 disease. The clinical features of this illness range from asymptomatic illness to death.\n\nAim To analyse the survival of patients admitted to a Tunisian tertiary care center (Sahloul University Hospital) and identify independent predictive factors for hospital COVID-19 mortality.\n\nMethods A longitudinal study was conducted among confirmed COVID-19 patients hospitalized in Sahloul University Hospital between September 2020 and September 2022. Cox univariate regression was used to calculate the Hazard Ratio (HR) of death for patient characteristics regarding the time at risk. Risk factors with a p value of 0.2 or less in the univariate analysis were initially included in the multivariate Cox regression models.\n\nResults During the study at Sahloul Hospital, 1978 patients were hospitalized, averaging 55.65 years in age (± 21.39). Among them, 417 deaths occurred, with a median survival of 30 days (± 3.11) [23.904-36.096]. Factors significantly affecting the survival curve were: Age, male gender, comorbidities, diabetes, hypertension, endocrine diseases, obesity, intubation, and ICU admission Multilevel survival analyses revealed that hypertension (aHR 1.24; CI [1.02-1.52]; p=0.028), ICU admission (aHR 12.20- CI [9.56-15.57]; p<10-3), and male gender (HR 1.19; CI [0.98-1.46]; p=0.076) were independent factors associated with COVID-19 mortality.\n\nConclusion Our study concluded the importance of the early identification of high-risk COVID-19 patients to decrease this virus mortality. A good understanding of the possible clinical factors associated with COVID-19 severity is helpful for clinicians in identifying patients who are at high risk and require prioritized treatment to minimize death.", "keywords": [ "COVID-19", "Mortality", "predictive factors", "Survival analysis" ], "content": "Introduction\n\nThe coronavirus disease SARS-CoV-2 (COVID-19) was reported for the first time in China (Wuhan) in December 2019. After a few months, it became a global emergency, as more than 245 million positive cases were affected and 45 million deaths were caused worldwide, with a mortality rate of approximately 2%.1 This disease was classified as a pandemic by the World Health Organization (WHO) in March 2020.\n\nTunisia is one of the most affected countries with a high rate of patients with acute respiratory syndrome coronavirus. In fact, 1145686 cases and 29249 deaths were reported as of September 2022.2\n\nThe clinical features of COVID-19 range from asymptomatic to critical illness and death. Some cases may experience respiratory failure that requires mechanical ventilation and organ failure requiring admission to the intensive care unit (ICU). A literature review in 2020 showed that clinical predictors of disease severity ranged from demographic factors (such as ‘older age’), comorbidities (such as cardiovascular disease, chronic kidney disease, chronic lung diseases (particularly COPD), diabetes mellitus, hypertension, immunosuppression and obesity) and severe hypoxemia.3 A good understanding of these possible clinical factors associated with COVID-19 severity is helpful for clinicians in identifying patients who are at high risk and require prioritized treatment to prevent disease progression and adverse outcomes.\n\nThus, this study was conducted to identify independent predictive factors for hospital mortality of COVID-19 patients in a Tunisian tertiary care center from September 2020 to September 2022.\n\n\nMethods\n\nA longitudinal exhaustive study was conducted among COVID-19 patients in a tertiary care center (Sahloul University Hospital) from September 2020 to September 2022.\n\nSahloul University Hospital is a 690-bed tertiary care hospital in Sousse-Tunisia according to 2020 data. It is composed of seven medical departments, eight surgical departments, seven intensive care units, a developed technical platform, and an emergency department. It also includes radiology, nuclear medicine, prevention and safety of care department and medical analysis laboratories (hematology, anatomopathological-labs, biochemistry, and microbiology).\n\nSince the declaration of the first case of SARS-Cov2 infection in Tunisia, on March 4th, 2020, a COVID-19 cell was created in Sahloul University Hospital to undertake anticipatory measures. Many activities were implemented, including an organization of the COVID-19 circuit including installation of an outdoor presorting station near the emergency room and at the hospital entrance, setting up a COVID-19 unit in the emergency room, opening the transplant unit for the hospitalization of COVID-19 patients and the definition of the inpatient circuit. The second activity included programming theoretical and practical training sessions to master and respect the rules of hospital hygiene and the measures of protection against the risk of contamination by SARS-COV2. Indeed, the Prevention and Safety of Care Department organized training sessions on good hand hygiene practices; standard precautions; prevention of transmission of COVID-19 infection; dressing and undressing practices; and biological cleaning of COVID-19 patient isolation units.\n\nOther important activities were implemented during the pandemic, such as the drafting of guides, procedures and protocols, and audits and assessments of diverse activities among health workers.\n\nContinuous daily monitoring of the epidemiological status of COVID-19 patients was performed using a preestablished grid. Monthly reports were written and distributed to the medical committee describing the epidemic.\n\nThere was regular feedback to the medical committee and the regional health department.\n\nTo optimize management of the covid-19 pandemic in our hospital, hospitalization services have been reorganized into three main structures, each adapted to a particular level of severity:\n\n1- Conventional hospitalization units: these units have simple oxygen therapy facilities providing a maximum flow rate of < 15 l/min for patients with parenchymal damage < 75%.\n\n2- Intermediate structures: these structures correspond to conventional hospitalization services, reinforced by respiratory assistance supports such as CPAP, and Optiflow. These facilities care for patients with less than 75% parenchymal involvement, and whose needs correspond to a FiO2< 60% and a PEEP < 6.\n\n3- Intensive care units: these units admit patients with parenchymal damage > 75%; or high oxygen requirements (FiO2>60% or PEEP > 6), or an associated complication (stroke, acute myocardial ischemia, myocarditis, acute renal failure requiring bypass surgery, pulmonary embolism).\n\nOur study population included confirmed COVID-19 patients hospitalized in Sahloul University Hospital from September 2020 to September 2022.\n\nNon inclusion criteria: Non hospitalized patients in Sahloul University Hospital during the study period.\n\nA database including COVID-19 monitoring cases since the hospitalization of the first confirmed COVID-19 case in September 2020 has been regularly updated in the ‘Prevention and Safety of Care Department’ of Sahloul University Hospital of Sousse, Tunisia. All new cases of COVID_19 hospitalized in the various units have been registered. Daily monitoring of the evolution of the patients’ conditions was provided by the hygienist technicians of the department.\n\nThe data included information on age, genre, governorate, delegation, comorbidities, computed tomography data (CT), polymerase chain reaction (PCR), rapid diagnostic tests (RDT), oxygen source, tracheotomy, noninvasive ventilation (NIV), intubation, entry date, evolution, date of evolution, length of stay, exit location, discharge service, vaccination, dates of the different doses of vaccination, date of onset of symptoms, and vaccine type.\n\nCOVID-19 vaccination data were collected as a 5-category variable: Registered; Not registered; Vaccinated 1 shot; Vaccinated 2 shots; and Vaccinated 3 shots and were dichotomized into vaccinated and not vaccinated.\n\n\n\n- A confirmed COVID-19 case was defined as a patient with laboratory confirmation of COVID-19 infection, irrespective of clinical signs and symptoms.\n\n- Compatible clinical symptoms, an epidemiological link and radiological proof when having a nonreactive serological test for COVID-19. The result of tomography chest scanning was classified by radiologists as being compatible with COVID-19, uncertain, showing a noninfectious pattern or a normal pattern.\n\n- Length of stay: The period between the date of admission and the exit date (calculated in days).\n\n- Patients were admitted to the ICU if they presented an acute respiratory distress syndrome defined as hypoxemia secondary to a rapid onset of noncardiogenic pulmonary edema with hypoxemia with a PaO2/FiO2 ratio of less than 300 mg on positive end-expiratory pressure (PEP) or continuous positive airway pressure.4\n\n- Critical COVID-19 illness was defined as Vital distress, shock, sepsis and/or organ failure and/or the need for invasive or non-invasive respiratory assistance.5\n\n- Chronic kidney disease was defined as “abnormalities of kidney function or structure present for more than 3 months or an estimated glomerular filtration rate (eGFR) of less than 60 ml/min/1.73 m2 on at least 2 occasions 90 days apart (with or without markers of kidney damage).6\n\n- Cardiovascular diseases are all conditions affecting the heart or blood vessels, including strokes, coronary heart disease, peripheral arterial diseases, heart valve disease, and aortic disease.7\n\n- Endocrine diseases include all disorders related to the endocrine glands of the body, such as dysthyroid, acromegaly, Addison’s disease, and Cushing’s syndrome.8\n\n- Neurological disabilities include a wide range of disorders, such as epilepsy, learning disabilities, neuromuscular disorders, ADD, brain tumor, cerebral palsy …9\n\n- Obesity was defined as a body mass index (BMI)≥30 kg/m2.10\n\nSeveral types of COVID-19 vaccines have been developed, including inactivated or weakened virus vaccines (Sinopharm COVID-19 vaccine: May 7, 2021; and Sinovac-CoronaVac vaccine: June 1, 2021), protein-based vaccines (The Bharat Biotech BBV152 COVAXIN vaccine: November 3, 2021; The Covovax (NVX-CoV2373) vaccine: December 17, 2021), DNA vaccines (AstraZeneca/Oxford: February 16, 2021, Johnson vaccine March 12, 2021) and (Sputnik V), nucleic acid (mRNA) vaccines: Pfizer/BioNTech (December 31, 2020) and Moderna April 30, 2021.11\n\nAll statistical analyses were performed using the Statistical Package for Social Sciences SPSS (version 23, SPSS Inc., Chicago, USA).\n\nNormality of quantitative variables was assessed using Kolmogrov Smirnov test.\n\nNormally distributed variables were described using means and standard deviation and non normal variables were presented using the median and the interquartile range (IQR) [25th percentile-75th percentile].\n\nCategorial variables were described using the number of cases and percentages.\n\nSurvival function was graphically represented by Kaplan-Meier curve.\n\nCox univariate regression was used to calculate the Hazard Ratio (HR) of death for patient characteristics regarding the time at risk. Risk factors with a p value of 0.2 or less in the univariate analysis were initially included in the multivariate Cox regression models.\n\nFor all statistical tests, statistical significance was defined as p<0.05.\n\nThe present Study was reviewed and approved by the ‘ethics and research committee of Sahloul University Hospital and registered under the IRB approval number HS 58-2020 on 9th July 2020. The committee is an academic body responsible for ensuring the ethical integrity of research conducted within the institution.\n\nThis study was conducted with respect of the principles of the research ethics including patients’ anonymity and data confidentiality. Data was collected entirely from patient records, approval was obtained from the records holder to access and use the data. This ensures that all data used in the study complies with ethical standards and respects patient confidentiality and autonomy. The consent from participants was waived by the ethical approval committee.\n\n\nResults\n\nOverall, we included 1978 confirmed COVID-19 cases from 26 September 2020 to 30 September 2022 with a sex ratio (H/F) of 1.2. The mean age and the median length of stay were 55.65±21.39 years [1 – 94] and 8 days,4–9,11–14 respectively.\n\nThe most common comorbidity among the population was hypertension (42.7%).\n\nThe different characteristics of hospitalized patients are summarized in Table 1.\n\nConfirmed COVID-19 cases were hospitalized in different departments of the hospital. The transplant unit covered the most important percentage of hospitalized patients (n=909; 32.72%), followed by the medical departments (n=903; 32.4%). The different percentages are detailed in Table 2.\n\nDuring the study period, 417 patients died due to COVID-19 (21.1%).\n\nThe highest mortality rate was reported in the reanimation departments (60.7%) and the highe percent of discharges was reported in the medical departments (76.0%). The different outcomes are represented in the Table 3.\n\nThe deceased patients were males (60.4%) and had a mean age of 63.8 ±16.25 years. The median length of stay was 9 days.5–16 The most frequent comorbidity was hypertension (55.7%).\n\nThe trend of death prevalence increased from 9.7% in November 2021 to 23.3% in June 2021. The curve drops to 15.6% in July 2021 to level off between 22.1% in August 2022 and 23.3% in January 2022 (Figure 1).\n\n\nFactors associated with mortality among COVID-19 patients in Sahloul University Hospital from September 2020 until September 2022\n\nDuring the study period, the overall survival of hospitalized COVID-19 patients in Sahloul University Hospital was 78.9%, and a total of 417 deaths were reported. The median survival was 30±3.11 days (95% CI [23.90-36.09]).\n\nThe survival function is shown in Figure 2.\n\nWhen examining the survival rates of several factors, it becomes evident that patients aged 65 years and above have a notably lower estimated survival rate, with a higher percentage of mortality (52.8% compared to 47.2%). Similarly, among the sexes, males exhibited a higher mortality rate (60.4% versus 39.6%).\n\nOther factors significantly affecting the survival curve were comorbidities, diabetes, hypertension, endocrine diseases, obesity, intubation, and ICU admission. These varied factors are summarized in Table 4.\n\nThe multilevel analysis showed the following independent factors associated with mortality: the presence of hypertension and ICU admission. Male gender is a Forced factor always found in the literature. More details are shown in Table 5.\n\n\nDiscussion\n\nThis study represents one of the first large case studies with confirmed COVID-19 cases at a regional level and provides the most relevant novelty about the region of Sousse.\n\nIn the present work, data from hospitalized COVID-19-positive patients in a Tunisian university hospital were analyzed from the first case hospitalization.\n\nThis study discusses independent predictive factors for hospital mortality of COVID-19 patients in a Tunisian tertiary care center since September 2020. Many studies were conducted in the same context, but the study period is different, as the majority analyzed data of some months or a maximum of one year, while our study included a longest period.12–14\n\nTo identify the main predictive factors affecting the survival probability for COVID-19, survival analysis methods were used. Such analytic models can work with specific problems, with a data type that waits for the event to occur. In our study, the event mentioned was ‘death.’ We used Cox regression, which is the most appropriate method to analyze survival.\n\nData extracted from methods with survival analysis are robust.15\n\nThese data are helpful for making the right decision about each patient’s case according to the available treatment and medical instruments. Thus, this work will contribute at different levels, such as finding the survival probability for each patient, finding the effect of each feature on survival probability by calculating p value for each feature, and finally enhancing the COVID-19 system.10\n\nMany other works have studied clinical characteristics, outcomes, and predictive factors for mortality in hospitalized patients with COVID-19,16–19 but few of them used survival analysis.\n\nMoreover, our study focuses on the positive effect of vaccination against death and length of stay. Thus, the insights gained from this study have the potential to enhance people’s reassurance, thereby addressing vaccine hesitancy and dispelling conspiracy beliefs.\n\nOn the other hand, this study involved a large sample size that is needed to conflict with valid studies and representative results.\n\nOne of the major strengths of our work was the exhaustivity of our data. Patients were enrolled and registered upon their hospitalization, and all their information was directly collected. This significantly minimized, or even eliminated, the bias of loss to follow-up in our study.\n\nFrom the first COVID-19 hospitalization in September 2020 until September 2022, 1978, hospitalizations due to COVID-19 were followed with a sex ratio of 1.2. The mean age and the median length of stay were 55.65± 21.39 years and 8 days, respectively. The most common comorbidity among the population was hypertension (42.7%).\n\nA similar study during 2020 in Sofia Bulgaria included 138 hospitalized COVID-19 patients. The mean age was 52.9 years, and males were the dominant sex (sex ratio: = 1.6). The mean age was significantly different compared to other studies.20\n\nAnother study in early 2020 showed a higher mean age (65.5 years).21\n\nIn other studies, the mean age was 70.5 (±15.7, 30–101) years.\n\nThis difference can be related to the study population or the specific populations on which the research was conducted. Some studies have focused on a specific comorbidity in hospitalized COVID-19 patients, such as the characteristics of COVID-19 among hospitalized patients suffering from diabetes.22\n\nThe current findings regarding the sex ratio align with emerging research that indicates a higher susceptibility for severe outcomes, including death, in men with COVID-19 compared to women.23\n\nHypertension as the most frequent comorbidity was similar to the findings of many previous studies24\n\nIn our study, the reported death rate varied from 9.7% in November 2020 to 21.1% in September 2022, which is close to the fatality rate found in a study in Mexico and the United States (12%).25,26 However, this rate was lower than the reported death rate in an Italian hospital (33.3%).27 This can be justified, as Italy has registered the most important mortality rates in the world, especially in the first period of the disease. It can also be justified due to differences in thresholds for hospitalization. A third possible explanation for variation in country/regional-specific case-fatality rates is the different strategies used for COVID-19 PCR testing.28 Additionally, mortality rate differences can relate to the types of hospitals (public or private hospitals), and this can be explained by the difference in socioeconomic profiles.29\n\nIn our study, the median survival time was 30 days (95% CI [23.9; 36.1]). At the end of the follow-up, 417 deaths were recorded. These findings came online with the results of a similar study.\n\nThe median survival time was 12 days (95% CI 11.82–12.18). At the end of the follow-up, 21 408 deaths were recorded.30\n\nThe overall survival rate in our study (78.9%) was higher than that in a study by Bonfada et al., which analyzed the survival of elderly patients hospitalized in the ICU (66.64%).31\n\nThe median survival time was close to that reported in Brazil (19 days) and higher than that reported in Ethiopia (9 days), the USA (10 days) and Mexico (9 days).30,32,33\n\nWhen searching for the different predictive factors in the ‘Cox’ model, we found similar studies using the survival multilevel analysis conducted in Brazil, India, South India, Sweden and China.30,33–38\n\nOur study identified three statistically significant covariates sex, hypertension, and ICU admission - in our Cox proportional hazards model, all of which were separately identified in previous studies. Notably, gender’s significance in our model aligns with the study from Sweden, hypertension’s relevance matches findings from the study in Wuhan, and ICU admission’s impact mirrors conclusions drawn in the Brazilian study. These consistent results across different studies underscore the importance of these covariates in predicting the risk of death in our research context.\n\nConcerning sex-related factors, our analysis has confirmed a higher risk for male patients compared to females. The different prevalence of infection among patients according to sex was mentioned in other studies.26\n\nThe reduced susceptibility of females to viral infections may be attributed to their inherent protection from factors associated with the X chromosome and sex hormones, both of which play crucial roles in both innate and adaptive immunity.39 Notably, SARS-CoV-2, the virus responsible for COVID-19, utilizes ACE2 receptors located on pulmonary endothelial cells for entry, and it is worth noting that the ACE2 gene is situated on the X chromosome.40 This genetic aspect could explain the higher prevalence of COVID-19 in men than in women. Additionally, in premenopausal women, the ovaries produce estradiol. However, after menopause, the ovaries significantly decrease estradiol production, equating with men.\n\nICU admission emerged as a crucial factor strongly associated with 80.1% of deaths among confirmed cases of COVID-19.\n\nThese results were in line with other studies that concluded that the ICU was a risk factor for disease severity, especially among men, as men admitted to the ICU were 5.42 and 1.39 times more likely to die, respectively, than those who did not enter these units.41\n\nOther covariates that demonstrated statistical significance in various separate studies were also found to be statistically significant in our univariate survival analysis. These covariates include age,42 comorbidities,43 diabetes, endocrine diseases, obesity, and the need for invasive ventilatory support. The present study confirmed that age above 65 years was significantly associated with death in patients with COVID-19 in univariate survival analysis (52.8% vs 47.2%; p<10-3).\n\nIn a similar study using survival analysis, it was found that the hazard ratio increased with increasing age. For instance, in the group aged above 65 years, the patient is at 39.3 times higher risk of dying overall than a patient in a younger age group.44\n\nThe significant comorbidities associated with mortality in our univariate analysis were hypertension, diabetes, endocrine diseases, and obesity. Similarly, comorbidities found in a Mexican study were hypertension, diabetes and obesity in COVID-19–positive patients.25\n\nOur findings can be explained by the high prevalence of diabetes, hypertension, and obesity in Tunisia. On the other hand, comorbidities are the main risk factor for hospitalization. Thus, the highest prevalence of these hospitalized patients already suffers from a comorbidity, and more importantly, the prevalence of hypertension in positive patients was higher than the population mean.45\n\nThis observation could be elucidated by considering the detrimental impacts of comorbidities on the body’s autoimmune response and its capacity to manage metabolic stress, which are characteristic features of systemic diseases. Comorbidities, such as diabetes, hypertension, and cardiovascular diseases, often introduce a state of chronic inflammation and metabolic dysfunction within the body. These conditions can compromise the immune system’s ability to mount an effective defense against pathogenic agents, including viruses such as SARS-CoV-2. In essence, the presence of comorbidities not only weakens the body’s innate and adaptive immune responses but also creates an environment that is more conducive to the replication and spread of pathogens, potentially contributing to the increased susceptibility and severity of diseases such as COVID-19 in individuals with underlying health conditions.46\n\nEven studies that did not use survival analysis showed that older patients, men, and those with preexisting comorbidities such as hypertension, diabetes, cardiac diseases, renal diseases, respiratory diseases, neurological diseases and other health problems were the highly prevalent characteristics in our study. This comes in line with previous records in the literature, where these characteristics were associated with higher mortality rates and greater risk of negative health outcomes.10,15,16\n\n\nConclusions\n\nTunisia was one of the most affected countries with COVID-19 disease until vaccination became a potential resolution of the threat.\n\nOur study aimed to analyze the survival of patients admitted to a Tunisian tertiary care center (Sahloul University Hospital) to identify independent predictive factors for hospital COVID-19 mortality.\n\nThis work is the first large case study with confirmed COVID-19 cases at a regional level and provides the most relevant novelty about the region of Sousse.\n\nThe survival analysis made this work unique thanks to the robust results that it produces. This analysis showed three independent predictive factors associated with higher COVID-19 mortality: ICU hospitalization, hypertension, and sex.\n\nThe present Study was reviewed and approved by the ‘: ethics and research committee of Sahloul University Hospital and registered under the IRB approval number HS 58-2020 on 9th July 2020. The committee is an academic body responsible for ensuring the ethical integrity of research conducted within the institution.\n\nThis study was conducted with respect of the principles of the research ethics including patients’ anonymity and data confidentiality. Data was collected entirely from patient records, approval was obtained from the records holder to access and use the data. This ensures that all data used in the study complies with ethical standards and respects patient confidentiality and autonomy. The consent from participants was waived by the ethical approval committee.\n\n\nAuthor contributions\n\nThe corresponding author attests that all listed authors meet the journals authorship criteria and that no others meeting the criteria have been omitted.\n\nConceptualization, A. N, H.G; Methodology, H. G and A.N.; Software, H. G, A.N., and R.B.; Validation, H.S.L, and M.B.R; Formal Analysis, A.N.; Investigation A. N, H.G and R.B.; Data Curation A. N, R.B. and H.G. Writing—Original Draft Preparation, A.N.; Writing—Review and Editing, H. G, B. R, M.B.R and H.S.L.; Visualization B. S, H.B.H, B. K and A.B.C; Supervision M. K, H.G, W. N, H.T; Project Administration H. T, H.S.L, W. N and M.K. All authors approve the final manuscript submitted and agree to be personally accountable for the work.", "appendix": "Data availability statement\n\nThe prevention and safety of care department, Sahloul University Hospital-Sousse (Tunisia), as well as the corresponding author, have full access to all data. The data that support the findings of this study are not publicly available due to confidentiality concerns. The dataset includes exhaustive data of all hospitalized patients with COVID-19 at Sahloul University Hospital, as well as internal hospital information that cannot be shared in order to protect patient privacy and comply with institutional policies. Access to the data is restricted, and it is not available for sharing or publication. Anyone seeking access to the data should contact the corresponding author (arwaneffati@gmail.com), who will then consult with the other authors to determine whether the data can be shared.\n\nThe reader or reviewer who seeks for access to data should provide this information: Age, grade, institution, country, the reason to apply for access to the data, The data must be requested for legitimate research purposes, such as public health studies, academic research, or healthcare improvement projects.\n\nApplicants must submit a research proposal detailing the objectives, methods, and intended use of the data, Applicants must be affiliated with a recognized institution such as a university, research institute, or healthcare organization. Independent researchers may apply but must submit dditional documentation of their qualifications, the applicant must provide proof of ethical approval from their institution or a recognized ethics review board, and must confirm the Non-ommercial Use.\n\n\nAcknowledgments\n\nNo acknowledgements.\n\n\nReferences\n\nHuang YZ, Kuan CC: Vaccination to reduce severe COVID-19 and mortality in COVID-19 patients: a systematic review and meta-analysis. Eur. Rev. Med. Pharmacol. Sci. 2022; 26(5): 1770–1776. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Tunisia: WHO Coronavirus Disease (COVID-19) Dashboard With Vaccination Data.2023 [cited 2023 Jan 30]. Reference Source\n\nGallo Marin B, Aghagoli G, Lavine K, et al.: Predictors of COVID-19 severity: a literature review. Rev. Med. Virol. 2021; 31(1): 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nClark SB, Soos MP: Noncardiogenic Pulmonary Edema. StatPearls. Treasure Island (FL): StatPearls Publishing; 2022 [cited 2023 Jan 31]. Reference Source\n\nGao YD, Ding M, Dong X, et al.: Risk factors for severe and critically ill COVID-19 patients: a review. Allergy. 2021; 76(2): 428–455. PubMed Abstract \| Publisher Full Text\n\nUK Kidney Association: CKD Stages.2023 [cited 2023 Jan 31]. Reference Source\n\nCleveland Clinic: Cardiovascular Disease: Types, Causes & Symptoms. 2023 [cited 2023 Jan 31]. Reference Source\n\nLisco G, Tullio AD, Stragapede A, et al.: COVID-19 and the endocrine system: a comprehensive review on the theme. J. Clin. Med. 2021 Jul [cited 2023 Jan 31]; 10(13). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMontana Department of Public Health and Human Services. Neurological disorders. 2023 [cited 2023 Jan 31]. Reference Source\n\nAtlam M, Torkey H, El-Fishawy N, et al.: Coronavirus disease 2019 (COVID-19): survival analysis using deep learning and Cox regression model. Pattern. Anal. Applic. 2021 Aug 1; 24(3): 993–1005. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Obesity.2023 [cited 2023 Jan 31]. Reference Source\n\nGavin W, Campbell E, Zaidi SA, et al.: Clinical characteristics, outcomes and prognosticators in adult patients hospitalized with COVID-19. Am. J. Infect. Control. 2021 Feb 1; 49(2): 158–165. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAkter F, Mannan A, Mehedi HMH, et al.: Clinical characteristics and short term outcomes after recovery from COVID-19 in patients with and without diabetes in Bangladesh. Diabetes Metab. Syndr. 2020 Nov; 14(6): 2031–2038. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMughal MS, Kaur IP, Wang C, et al.: Variation in clinical characteristics, outcomes, and mortality of hospitalized patients with COVID-19 during the second wave of the pandemic: a single-center experience. J. Investig. Med. 2021 Dec 1; 69(8): 1479–1482. PubMed Abstract \| Publisher Full Text\n\nTableman M, Kim JS: Survival Analysis Using S: Analysis of Time-to-Event Data. CRC Press; 2003; p. 277.\n\nPoliseno M, Drago EP, Poli MA, et al.: Clinical characteristics, outcomes, and risk factors of patients hospitalized for COVID-19 across the latest pandemic waves: has something changed? Biomed. 2023 Jun; 3(2): 272–281. Publisher Full Text\n\nLee LY, Cazier JB, Angelis V, et al.: COVID-19 mortality in patients with cancer on chemotherapy or other anticancer treatments: a prospective cohort study. Lancet. 2020 Jun 20; 395(10241): 1919–1926. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee LY, Cazier JB, Angelis V, et al.: Clinical characteristics, outcomes, and risk factors for mortality in hospitalized patients with COVID-19 and cancer history: a propensity score-matched study. Infect Agents Cancer. 2020 Dec 18; 15: 69. Publisher Full Text\n\nAbohamr SI, Abazid RM, Aldossari MA, et al.: Clinical characteristics and in-hospital mortality of COVID-19 adult patients in Saudi Arabia. Saudi Med. J. 2020 Nov; 41(11): 1217–1226. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPopov GT, Baymakova M, Vaseva V, et al.: Clinical Characteristics of Hospitalized Patients with COVID-19 in Sofia, Bulgaria. Vector Borne Zoonotic Dis. 2020; 20(12): 910–915. PubMed Abstract \| Publisher Full Text\n\nAggarwal S, Garcia-Telles N, Aggarwal G, et al.: Clinical features, laboratory characteristics, and outcomes of patients hospitalized with coronavirus disease 2019 (COVID-19): Early report from the United States. Diagnosis. 2020; 7(2): 91–96. PubMed Abstract \| Publisher Full Text\n\nAkter F, Mannan A, Mehedi HMH, et al.: Clinical characteristics and short term outcomes after recovery from COVID-19 in patients with and without diabetes in Bangladesh. Diabetes Metab. Syndr. 2020; 14(6): 2031–2038. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTeich VD, Klajner S, de Almeida FAS , et al.: Epidemiologic and clinical features of patients with COVID-19 in Brazil. Einstein (São Paulo). 2020; 18: 18. Publisher Full Text\n\nCasas-Rojo JM, Anton-Santos JM, Millan-Nunez-Cortes J, et al.: Clinical characteristics of patients hospitalized with COVID-19 in Spain: results from the SEMI-COVID-19 registry. Rev. Clin. Esp (Engl Ed). 2020 Nov 1; 220(8): 480–494. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nParra-Bracamonte GM, Lopez-Villalobos N, Parra-Bracamonte FE: Clinical characteristics and risk factors for mortality of patients with COVID-19 in a large data set from Mexico. Ann. Epidemiol. 2020; 52: 93–98.e2. Publisher Full Text\n\nKim L, Garg S, O’Halloran A, et al.: Risk Factors for Intensive Care Unit Admission and In-hospital Mortality Among Hospitalized Adults Identified through the US Coronavirus Disease 2019 (COVID-19)-Associated Hospitalization Surveillance Network (COVID-NET). Clin. Infect. Dis. 2021; 72(9): e206–e214. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamos-Rincon JM, Buonaiuto V, Ricci M, et al.: Clinical characteristics and risk factors for mortality in very old patients hospitalized with COVID-19 in Spain. J. Gerontol. A Biol. Sci. Med. Sci. 2021; 76(3): e28–e37. Publisher Full Text\n\nOnder G, Rezza G, Brusaferro S: Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy. JAMA. 2020; 323(18): 1775–1776. PubMed Abstract \| Publisher Full Text\n\nMarcolino MS, Ziegelmann PK, Souza-Silva MVR, et al.: Clinical characteristics and outcomes of patients hospitalized with COVID-19 in Brazil: Results from the Brazilian COVID-19 registry. Int. J. Infect. Dis. 2021; 107: 300–310. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSantos MM, Lucena EES, Lima KC, et al.: Survival and predictors of deaths of patients hospitalised due to COVID-19 from a retrospective and multicentre cohort study in Brazil. Epidemiol. Infect. 2020; 148.\n\nBonfada D, dos Santos MM , Lima KC, et al.: Survival analysis of elderly patients in Intensive Care Units. Rev. Bras. Geriatr. Gerontol. 2017 Apr; 20: 197–205. Publisher Full Text\n\nKaso AW, Agero G, Hurissa Z, et al.: Survival analysis of COVID-19 patients in Ethiopia: A hospital-based study. PLoS One. 2022 May 9; 17(5): e0268280. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAltonen BL, Arreglado TM, Leroux O, et al.: Characteristics, comorbidities and survival analysis of young adults hospitalized with COVID-19 in New York City. PLoS One. 2020 Dec 14; 15(12). Publisher Full Text\n\nSousa GJB, Garces TS, Cestari VRF, et al.: Mortality and survival of COVID-19. Epidemiol. Infect. 2020 Jan; 148. Publisher Full Text\n\nLi X, Xu S, Yu M, et al.: Risk factors for severity and mortality in adult COVID-19 inpatients in Wuhan. J. Allergy Clin. Immunol. 2020 Jul 1; 146(1): 110–118. Publisher Full Text\n\nDrefahl S, Wallace M, Mussino E, et al.: A population-based cohort study of socio-demographic risk factors for COVID-19 deaths in Sweden. Nat. Commun. 2020 Oct 9; 11(1): 5097. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDas D, Saikia H, Bora D, et al.: A survival analysis approach for identifying the risk factors in time to recovery of COVID-19 patients using Cox proportional hazard model. Decis. Anal. J. 2022 Dec 1; 5: 100137. Publisher Full Text\n\nThiruvengadam G, Lakshmi M, Ramanujam R: A study of factors affecting the length of hospital stay of COVID-19 patients by Cox-proportional hazard model in a South Indian tertiary care hospital. J. Prim. Care Community Health. 2021 Jan 1; 12: 215013272110002. Publisher Full Text\n\nJaillon S, Berthenet K, Garlanda C: Sexual dimorphism in innate immunity. Clin. Rev. Allergy Immunol. 2019; 56(3): 308–321. Publisher Full Text\n\nPatel SK, Velkoska E, Freeman M, et al.: From gene to protein—experimental and clinical studies of ACE2 in blood pressure control and arterial hypertension. Front. Physiol. 2014 [cited 2023 Sep 1]; 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSalinas-Escudero G, Carrillo-Vega MF, Granados-García V, et al.: A survival analysis of COVID-19 in the Mexican population. BMC Public Health. 2020 Oct 27; 20(1): 1616. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSong J, Park DW, Cha JH, et al.: Clinical course and risk factors of fatal adverse outcomes in COVID-19 patients in Korea: a nationwide retrospective cohort study. Sci. Rep. 2021; 11(1): 10066. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurillo-Zamora E, Hernandez-Suarez CM: Survival in adult inpatients with COVID-19. Public Health. 2021; 190: 1–3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKundu S, Chauhan K, Mandal D: Survival Analysis of Patients With COVID-19 in India by Demographic Factors: Quantitative Study. JMIR Form. Res. 2021; 5(5): e23251. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFlores-Kanter PE, Medrano LA: Núcleo básico en el análisis de datos cualitativos: pasos, técnicas de identificación de temas y formas de presentación de resultados. Interdisciplinaria. 2019; 36(2): 203–215. Publisher Full Text\n\nDi Castelnuovo A, Bonaccio M, Costanzo S, et al.: Common cardiovascular risk factors and in-hospital mortality in 3,894 patients with COVID-19: survival analysis and machine learning-based findings from the multicentre Italian CORIST Study. Nutr. Metab. Cardiovasc. Dis. 2020; 30(11): 1899–1913. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "353775", "date": "21 Jan 2025", "name": "Md Momin Islam", "expertise": [ "Reviewer Expertise Meta-analysis", "Infectious disease", "maternal and Child health", "NCD" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 opportunity. The overall presentation of the manuscript is appropriate, but some revisions are required. After incorporating the revisions, this manuscript could be accepted for possible publication in F1000Research.\nThe author mentions that factors significantly affecting the survival curve include age, comorbidities, diabetes, hypertension, etc. It’s suggested that the author either only mention \"comorbidities\" or exclude specific conditions like diabetes and hypertension to avoid redundancy. The author should include current statistics on COVID-19 cases and fatalities, particularly the present situation in Tunisia. Please provide an update on the current state of COVID-19 in Tunisia. The introduction is too brief. The author should expand this section with more recent research and context. While the study objectives are clearly stated in the last paragraph, the introduction needs to better explain the motivation behind the study. Why was Cox regression chosen for this analysis? How does it compare to other regression models like Weibull, Log-logistic, or Log-normal regression? Please explain why Cox regression is the most suitable option. The total number of patients is listed as 2778, but the author mentions 1978 patients. Were any patients admitted to multiple departments simultaneously? Clarify this discrepancy. The author claims that patients aged 65 years and above have a significantly lower survival rate, with a higher mortality percentage (52.8% compared to 47.2%). However, age is presented as a continuous variable with a mean and standard deviation. If the age was categorized (65 or above vs. below 65), please provide a reference for this categorization. The discussion part is excellent, the author may consider comparing several risk factors with the study referenced below. https://doi.org/10.1007/s10900-020-00920-x In the discussion section, it could be better to include some findings that are dissimilar to your findings. Cross-check all references in the list and text, and also check reference styling.\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? Partly", "responses": [ { "c_id": "13194", "date": "23 Jan 2025", "name": "ARWA NEFFATI", "role": "Author Response", "response": "Subject: Response to Reviewer Comments – Manuscript [Covid-19 mortality risk factors: Survival analysis of the hospitalized cohort in Sahloul university hospital in Tunisia] Dear Prof. Md Momin Islam, We sincerely thank you and the reviewers for the thoughtful and constructive comments on our manuscript titled \" Covid-19 mortality risk factors: Survival analysis of the hospitalized cohort in Sahloul university hospital in Tunisia.\" We have carefully addressed each point raised and made the necessary revisions to improve the manuscript. Please find below our detailed responses to your comments and a description of the changes made in the revised manuscript. Reviewer 's Comments: Comment 1: The author mentions that factors significantly affecting the survival curve include age, comorbidities, diabetes, hypertension, etc. It’s suggested that the author either only mention \"comorbidities\" or exclude specific conditions like diabetes and hypertension to avoid redundancy. Response: \"We will clarify this point in the 'Results' section. We will delete the item ‘comorbidities’\". Comment 2: The author should include current statistics on COVID-19 cases and fatalities, particularly the present situation in Tunisia. Please provide an update on the current state of COVID-19 in Tunisia Response: Thank you for this comment. As our study included the patients hospitalized between ‘September 2020 and September 2022’; we focused, in the ‘introduction part, on the situation of Covid-19 in Tunisia during that period(2020-2022) .” Tunisia is one of the most affected countries with a high rate of patients with acute respiratory syndrome coronavirus. In fact, 1145686 cases and 29249 deaths were reported as of September 2022” Comment 3: The introduction is too brief. The author should expand this section with more recent research and context. While the study objectives are clearly stated in the last paragraph, the introduction needs to better explain the motivation behind the study. Response: Yes of course. We will add more recent researches and more details in the introduction part. Comment 4: Why was Cox regression chosen for this analysis? How does it compare to other regression models like Weibull, Log-logistic, or Log-normal regression? Please explain why Cox regression is the most suitable option. Response: This is a very important question. We responded to this point in the ‘discussion part’ and put as reference an interesting article showing why ‘Cox regression is a robust method’. And here is another explanation: “Cox regression is often chosen for survival analysis because of its flexibility compared to other parametric regression models like Weibull, Log-logistic, or Log-normal regression. 1. Assumption of Proportional Hazards Cox regression assumes that the hazard ratios between groups are constant over time (the proportional hazards assumption). This assumption simplifies the model and focuses on the relative risk of the event occurring rather than estimating the baseline hazard function directly. 2. Semi-Parametric Nature Unlike Weibull, Log-logistic, or Log-normal models, which require specifying a distribution for the survival times, Cox regression does not make assumptions about the shape of the baseline hazard function. This makes Cox regression more robust and flexible for analyzing survival data with unknown or complex baseline hazard distributions. 3. Handling of Censored Data Cox regression effectively handles right-censored data (common in survival analysis) and provides unbiased estimates of the effect of covariates, even when not all events are observed. 5. Focus on Covariates The primary goal of Cox regression is to assess the effect of covariates on the hazard rate. This aligns well with studies aiming to understand relative risks or the influence of predictors, rather than estimating the exact survival probabilities. 6. Interpretation Cox regression provides hazard ratios, which are easily interpretable as the relative risk of an event occurring in one group compared to another. This simplicity in interpretation often makes it a preferred choice.” Comment 5: The total number of patients is listed as 2778, but the author mentions 1978 patients. Were any patients admitted to multiple departments simultaneously? Clarify this discrepancy. Response: Thank you for this valuable comment. Yes, we put a ‘’ in front of the total number to clarify this point. We will add it in the manuscript under the table: ‘: The difference existing between the population size and the total is due to the readmission of the patient in different departments which includes counting the same patient many times.’ Comment 6: The author claims that patients aged 65 years and above have a significantly lower survival rate, with a higher mortality percentage (52.8% compared to 47.2%). However, age is presented as a continuous variable with a mean and standard deviation. If the age was categorized (65 or above vs. below 65), please provide a reference for this categorization. Response: We will clarify this point in the ‘methods’ section, and we will put a reference. Comment 7: The discussion part is excellent; the author may consider comparing several risk factors with the study referenced below. https://doi.org/10.1007/s10900-020-00920-x. Response: Thank you very much: We will consider this article and include it as part of our references. Comment 8: In the discussion section, it could be better to include some findings that are dissimilar to your findings. Response: Yes of course. We will add this part as soon as we are able to publish a modified version of our article. Comment 9: Cross-check all references in the list and text and check reference styling. Response: Thank you very much. We will check and modify the inappropriate references. Changes Made: We will incorporate all the changes based on the reviewers' comments into the revised version of our article, which will be updated as soon as it is published. We believe that these revisions have significantly improved the clarity and quality of our manuscript. We are grateful for the reviewers’ valuable insights and suggestions, which have helped us refine our work. Please do not hesitate to contact us if further clarification or additional revisions are required. Thank you for considering our revised manuscript. Sincerely, Arwa NEFFATI" } ] } ]	1	https://f1000research.com/articles/13-1215
https://f1000research.com/articles/13-1213/v1	11 Oct 24	{ "type": "Research Article", "title": "Preterm birth: associated risk factors in the tertiary care center", "authors": [ "Sweety Jousline Fernandes", "Tessy Treesa Jose", "Judith Angelitta Noronha", "Sushmitha Karkada", "Sweety Jousline Fernandes", "Judith Angelitta Noronha", "Sushmitha Karkada" ], "abstract": "The study aimed at identifying the prevalence of preterm labor and the associated risk factors.\nDesign A quantitative approach using a retrospective case-control study.\n\nSetting Tertiary care hospital of Udupi district Karnataka.\n\nPopulation or Sample Women delivered in tertiary care Hospital of Udupi district, Karnataka, were the sample; among them, the cases (250) were the records of the women who had delivered before 37 weeks of gestation, and controls (500) were the records of women who delivered after 37 weeks of gestation and without any complications.\n\nMethod The study was conducted using a retrospective case-control design by reviewing the case records of women who had delivered in a tertiary care hospital.\n\nMain Outcome Measures Women delivered in tertiary care Hospital of Udupi district, Karnataka, and their inpatient records were assessed for risk factors during the antenatal and delivery periods.\n\nResults The study revealed that the prevalence of preterm labor was 356 (14.86%) Out of 2402 deliveries. Among them, only 250 were assessed. It was significantly correlated with age, place of residence, degree of education, occupation, marital status, gravid para, number of deliveries, type of deliveries, gap between births, blood type, and religion. Pregnant women who had been exposed or had a risk for preterm labor included those who had been diagnosed with pregnancy-induced hypertension, medication during pregnancy, history of abortion, intense physical labor, and conception dates older than 30 years.\n\nConclusion The preterm labor prevalence can be minimized if the modifiable risk factors are in control. Non-modifiable risk factors require keen supervision. Thus, health professionals must be alert to all modifiable and non-modifiable risk factors.", "keywords": [ "preterm labor", "prevalence", "risk factors" ], "content": "Introduction\n\nA neonate born after 37 weeks requires significant attention and care as they transition into a new environment post-birth. The morbidity associated with preterm labor can persist into later life, leading to physical, psychological, and economic costs. Globally, one in 10 babies is born preterm, and approximately one million babies die annually due to complications from preterm births. Preterm labor is an obstetric emergency and poses a threat to population health, contributing to 75% of infant mortality31 (https://www.who.int).\n\nPreterm labor not only imposes financial and emotional distress on families but can also result in permanent disabilities (physical or neural) in infants. Surviving babies often exhibit periodic disabilities such as learning, visual, and hearing difficulties. The preterm birth rate ranges from 5% to 7% of live births in developed countries compared to developing countries. Despite an increased understanding of potential risk factors and their pathological mechanisms, the preterm birth rate has remained unchanged or even increased in most countries over the past two decades.15,16\n\nThe pathway to preterm labor remains unclear, whether it results from the interaction of multiple pathways or an independent pathway. Factors commonly affecting preterm labor include the health condition of the mother or fetus, genetic causes, environmental exposure, infertility treatments, habits, socioeconomic factors, and iatrogenic factors. Preterm birth was the second leading cause of death in children under five years old in 2010. Of the approximately 3.1 million newborn deaths that year, a quarter occurred within the first 24 hours after birth14American College of Obstetricians and Gynecologists (2020).\n\nIn India, out of 27 million neonates born each year, 3.5 million are delivered prematurely. The antenatal period, labor process, and postnatal period are critical for infant and maternal survival. Preterm labor is unpredictable, but cues can be identified, and preventive measures can be taken. Physicians strive to delay delivery to allow the baby to grow as much as possible. Therefore, pregnant women should not omit any essential health details during regular visits to the obstetrics clinic. They should provide a detailed history of their lifestyle, past pregnancies, and any health issues they have experienced and clarify any doubts—Centers for Disease Control and Prevention (2019).4\n\nThe statistics presented above and the supporting data assist obstetric care providers in designing appropriate studies and planning measures to decrease delivery rates before 37 weeks of gestation and improve the health status of women who have delivered. This will help reduce and fill the gaps between study areas, serving as baseline information for other countries. The present study was conducted to identify preventive measures to determine the risk factors of preterm labor. Early identification and extra precautions for risk factors, such as medication intake during pregnancy and previous abortion, can prevent preterm labor. Moderate risk factors like hard physical work and conception age above 30 years can prevent preterm labor if managed.\n\n* Significance at the level of 0.05.\n\n* Significant at the level of .005.\n\n\nMethods\n\nThis retrospective case-control study aimed to identify the prevalence and risk factors for preterm labor by examining the case records of women who delivered in tertiary care hospitals in the Udupi district. The cases were women who delivered before 37 weeks of gestation, and the controls were women who delivered after 37 weeks of gestation without any complications. As per the sample size calculation, a purposive sampling technique was employed to select the records of 250 out of 356 women.\n\nThe tools used included a maternal socio-demographic proforma and a structured Risk Assessment tool for preterm labor. This tool classified items into modifiable and non-modifiable risk factors, with the former further subdivided into social, economic, and environmental factors and the latter into medical, obstetrical, and fetal conditions.\n\nThe study received permission from various authorities related to the data and ethical clearance (IEC 30/2018), and it was registered with the Clinical Trial Registry of India (CTRI/2018/05/014078). Data were analyzed using SPSS version 16, employing descriptive and inferential statistics.\n\nThe study identified that the prevalence of preterm labor was 14.82% (356 out of 2402 deliveries). The background characteristics of the cases and controls varied, with the majority residing in rural areas and being homemakers. The mean height and age among the cases were 154.32cm and 27.44 years, respectively, and the average total weight gain during pregnancy was 7.67 kg.\n\nUnivariate analysis was initially computed, followed by the computation of the adjusted odds ratio to obtain an accurate result. The data showed that risk factors like pregnancy-induced Hypertension Hypertension (p=.001), medication intake (p=.001), and conception age at 30 or above (p=.005) are associated with preterm labor, which is significant at the 0.005 level. Previous abortion (p=.001) and hard physical work (p=.001) are statistically preventive factors but are not clinically preventive risk factors. Most women in both the case and control groups were administered medications such as Tibolone (a steroid) and Ceftriaxone (an antibiotic). Statistically, these medications were associated with an increased likelihood of preterm labor. However, from a clinical perspective, these steroids and antibiotics are typically administered as a prophylactic measure for cases that progress into labor before 37 weeks of gestation.\n\n\nDiscussion\n\nThe data from this study revealed that 14.82% (356 out of 2406) of deliveries were preterm. This finding aligns with a cross-sectional study conducted on the prevalence of preterm labor among young parturient women aged 15 – 24 years attending public hospitals in Brazil, which found a high prevalence of preterm labor (86.3% out of 2400 parturient women).\n\nSimilarly, a retrospective study in Jordan identified the existence and reasons associated with preterm delivery, showing that all the preterm deliveries were approximately 647. Most neonates were female (54.9% Vs. 45.1%), and most (75.6%) were the second child. The women who delivered preterm were predominantly between 25 and 35.\n\nThis study found associations between preterm labor and several factors, including age, residence, education level, occupation, marital status, gravida, number of deliveries, type of delivery, birth interval, blood group, and religion. However, no association was found between preterm labor and height or weight gain during pregnancy.\n\nThese findings are supported by a retrospective cross-sectional study on the prevalence of preterm labor in a Labor room, which identified risk factors for early labor such as active relationships during the previous week of labor, multiple pregnancies, small birth intervals between two conceptions, PIH, fetal anomaly, premature rupture of membrane, and Hypertension.\n\nA case-control study by Barbara Luke et al. in the United States on the relation between occupational factors and preterm delivery among nurses found that risk factors related to preterm delivery included working hours per week, different duty timings, standing hours, noisy areas, physical stress, and work-related stress.\n\nThe results of this study and similar ones suggest that eliminating risk factors and reinforcing protective factors could help decrease the rate of preterm labor and its human and social burden. However, further studies with better design, such as cohort prospective studies with a proper follow-up period and large study population, are needed to determine these factors accurately. As the Hospital studied is a referral center for these patients, it represents the general population of the country to a great extent.\n\n\nConclusion\n\nThe study concludes that preterm labor is commonly seen in pregnant women who are exposed to non-modifiable and modifiable risk factors. Modifiable risk factors can be avoided and thus allow the pregnancy to continue till term. Non-modifiable risk factors need to be supervised very keenly so that there is no risk to the life of the mother and the fetus. It even states that the prevalence of preterm is higher among homemakers. Thus, these women need to be released from the level of stress to which they are exposed. All in all, the study concludes that these risk factors are different for each woman, which will lead to preterm labor, but they need to be identified at the earliest and treated adequately.\n\nMore information can be found on our data guidelines page. Data is available in the OSF web application: Contributors: Sweety Jousline Fernandes Identifier: https://osf.io/wp8xu/?view_only=da380485c7c74b20befc1e58f95fe431\n\nRepository: Strobe checklist for ‘Prevalence and Risk factors associated with Preterm Labour’, https://doi.org/10.17605/OSF.IO/RBHXJ\n\n\nEthical statement: Ethical consideration\n\nThe data collection for the study commenced only after obtaining prior ethical clearance from the departments, which are as listed below:\n\nAdministrative permission from Dean Manipal College of Manipal, to conduct the study.\n\nPermission from IRC of Manipal College of Nursing Manipal for conducting the study (IRC148/2017)\n\nPermission from IEC of Kasturba Hospital Manipal on 10/1/2018 (IEC 30/2018)\n\nCTRI registration (CTRI/2018/05/014078) (its not a clinical trial but during this study duration it was insisted to register under clinical trial)\n\nPermission from the OBG Department of Kasturba Hospital Manipal was obtained for the selection and utilizing the samples Records\n\nPermission from the Medical Superintendent of the Kasturba Hospital Manipal, was obtained to have access to the Medical Record\n\nConsent to participate written consent was obtained from the hospital authority and the MRD section to view the records. Based on the hospital numbers selected every day fifteen records were issued for the study assessment.\n\n\nAuthor contributions\n\nPrincipal Investigator: Mrs. Sweety J Fernandes (role: Recruitment, data collection, rater, intervention provider, concept analysis, training provider, and manuscript)\n\nGuide: Dr Tessy Treesa Jose (Role: Intellectual inputs, mentoring)\n\nCo–guide: Dr Judith A Noronha (Role: Intellectual, mentoring)\n\nCo-investigator: Dr Sushmitha R Karkada (Role: Intellectual analysis)", "appendix": "Data availability\n\nData is available in the OSF web application: Contributors: Sweety Jousline Fernandes Identifier: https://osf.io/wp8xu/?view_only=da380485c7c74b20befc1e58f95fe431, https://doi.org/10.17605/OSF.IO/RBHXJ. 10\n\nLicense: CC-By Attribution 4.0 International\n\n\nAcknowledgment\n\nI am grateful to the Hospital for permitting me to get access to the records and thankful to the co-investigators for their constant support and intellectual inputs.\n\n\nReferences\n\nArreola, et al.: Health and working conditions of pregnant women working inside and outside the home in Mexico City. BMC Public Health. 2007; 7: 25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeck, et al.: The worldwide incidence of preterm birth: a systematic review of maternal mortality and morbidity. National Institute of Health. 2009; 88(1): 31–38.\n\nBritannica.com: Case definition epidemiology.n.d. Reference Source\n\nCenters for Disease Control and Prevention: Preterm birth information.2019. Reference Source\n\nCunningham, et al.: Pregnancy Overview, Organization, and Diagnosis. Williams Obstetrics. 1997; 13–35.\n\nDerakshi, Esmailnasab, Ghaderi, et al.: The risk factor of preterm labor in the west of Iran: A case-control study. Iranian Journal of Public Health. 2014; 43(4): 499–506.\n\nHalder, Vijayselvi, Jose: Changing perspectives of infectious causes of maternal mortality. Turkish–German Gynecological Education and Research Foundation. 2015; 16: 208–213. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHalimi, et al.: Epidemiology and Related Risk Factors of Preterm Labor as an Obstetrics Emergency. Emerg. 2015; 5(1): 2017. Free Full Text\n\nDerakshi, Esmailnasab, Ghaderi, et al.: The risk factor of preterm labor in the west of Iran: A case-control study. Iranian Journal of Public Health. 2014; 43(4): 499–506.\n\nFernandes SJ: Prevalence and risk factors for preterm labour.2024, August 27. Iyengar, Martines, Dashora, & Deora. (2008). Childbirth practices in rural Rajasthan, India: Implications for neonatal health and survival. Journal of Perinatology, 28, S23-S30. 10.1038/jp.2008.174. Publisher Full Text\n\nIshikawa: Fishbone diagram. American Society for Quality, Fishbone diagram; 1987. Reference Source\n\nKuppusamy, Vidhyadevi: Prevalence of Preterm Admissions and the Risk Factors of Preterm Labor in Rural Medical College Hospital. International Journal of Scientific Study. 2016; 4(9): 124–128.\n\nKate: Case-Control Study: Definition.2008. Reference Source\n\nLawther: Ishwak model of conceptual framework.2012. Reference Source\n\nLuke: The association between occupational factors and preterm birth: a United States nurses’ study. American Journal of Obstetrics & Gynecology. 1995; 173(3 Pt 1): 849–862. PubMed Abstract \| Publisher Full Text\n\nMarch of Dimes: Report card on preterm birth.2019. Reference Source\n\nMiranda, Szwarcwald: Prevalence and correlates of preterm labor among young parturient women attending public hospitals in Brazil. American Journal of Public Health. 2009; 32(5): 330–334.\n\nNakai, Taniuchi, Miyake, et al.: Increased level of granulocyte elastase in cervical secretion is an independent predictive factor for preterm delivery. Gynecologic and Obstetric Investigation. 2005; 60(2): 87–91. PubMed Abstract \| Publisher Full Text\n\nPark: Park’s Textbook of Preventive and Social Medicine. 23rd edition.Jabalpur, India: Banarsidas Bhanot Publishers; 2015.\n\nPolit, Beck: Nursing research: Generating and assessing evidence for nursing practice. Philadelphia: Lippincott Williams & Wilkins; 2008.\n\nPompeii, Savitz, Evenson, et al.: Physical exertion at work and the risk of preterm delivery and small-for-gestational-age birth. Obstetric and Gynecology Journal. 2005; 106(6): 1279–1288.\n\nQuinn: Preterm birth: Case definition & guidelines for data collection, analysis, and presentation of immunization safety data. Vaccine. 2012; 34(49): 6047–6056. Publisher Full Text\n\nRobinson: Preterm birth risk factors. and maternal prognosis search preterm & source search result& selected.2018. Reference Source\n\nRao: A Case-Control Study on Risk Factors for Preterm Deliveries in a Secondary Care Hospital, Southern India. ISRN Obstetrics and Gynecology. 2014; 2014: 1–5. Article ID 935982. Publisher Full Text\n\nShah: Incidence and risk factors of preterm birth in a rural Bangladeshi cohort. BMC Pediatrics. 2014; 14: 2–11. Publisher Full Text\n\nSharma: Nursing Research and Statistics. 2nd ed.India: Elsevier; 2014.\n\nSuarez: Risk of infection and adverse outcomes among pregnant working women in selected occupational groups: A study in the Danish National Birth Cohort. BMC Journal. 2010; 9: 70. Publisher Full Text\n\nSaurel-Cubizolles: Employment, working conditions, and preterm birth: results from the Euro-pop case-control survey. Epidemiology Community Health Journal. 2004; 58(5): 395–401. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTemu: Maternal and obstetric risk factors associated with preterm delivery at a referral hospital in northern-eastern Tanzania. Asian Pacific Journal of Reproduction. 2016; 5(5): 365–370. Publisher Full Text\n\nTheresia: Maternal and obstetric risk factors associated with preterm delivery at a referral hospital in northern-eastern Tanzania. Asia Pacific Journal of Reproduction. 2016; 5(5): 365–370. Publisher Full Text\n\nOza, Lawn, Hogan, Mathers, Cousens: Neonatal cause-of-death estimates for the early and late neonatal periods for 194 countries. Bulletin of the World Health Organization. 2013, 2015; 93(1): 19–28.\n\nVakilian, Ranjbaran, Khorsandi, et al.: Prevalence of preterm labor in Iran: A systematic review and meta-analysis. International Journal Reproductive Biomedicine. 2015; 13(12): 743–748. Publisher Full Text\n\nWorld Health Organization: Preterm birth: Global report on preterm birth and stillbirth.2018. Reference Source\n\nZhang: Risk Factors for Preterm Birth in Five Maternal and Child Health Hospitals in Beijing.2012. Publisher Full Text" }	[ { "id": "341100", "date": "04 Dec 2024", "name": "Dr Nalini D.S.J", "expertise": [ "Reviewer Expertise Women's health. Neonatology", "Teaching methodologies" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 authors for taking efforts to conduct and present the study results. The STROBE guidelines has been used for reporting the results. Wish to recommend these points for consideration. Consistency in the term used Preterm birth or Preterm labour. In the key words only preterm labour is mentioned and not preterm birth.\nIn the abstract, the concepts of design, setting, population, sample, etc., can be placed under the main heading of methods. Recent statistics of preterm birth can be provided.\nFollow the style of citation suggested by the journal. The citation numbers are not sequential. The discussion part does not project any citations. The introduction projects about the preterm statistics. With many published studies existing on factors associated with preterm birth, the researchers can justify the gap that their study tries to fill. The lines projected to justify the need for early identification in Page1 seems to be like assumption predicted after viewing the study results. They can be general statements on modifiable / non modifiable risk factors or reviews from other studies be added with citation.\n\nThe methods section needs to be strengthened. In retrospective studies, it is important to mention the timelines (dates/ months) of reviewed records, the criteria set for considering the record for the study, number of records excluded with missed data and also project a flowchart for inclusions of record in the study. Include the criteria for gestational age determination. On what basis was the samples for cases and control determined, the ratio used for cases: controls. Was the tool used a standardized one or was it prepared by researcher and further validated? . The plan for data analysis has to be detailed.\nIn the results part, in table 1,the gravidae of women can be categorized as prime / multi or as one, two, three, etc.. Hence, a combination of both can be avoided. The researchers mention that the women had a regular follow up and took the supplements as prescribed. Being retrospective, we cannot establish whether the prescribed drugs were actually taken by subjects. Why was religion considered as a factor influencing preterm birth? Is there any supportive evidence existing? The concept of clinically preventive and statistically preventive risk factors is not clear. Steroids coverage for preterm labour cannot be ideally considered as a risk factor for PTL. The statement that medications had an increased likelihood of resulting in preterm labour seems to be contradictory. Analysis shows unadjusted estimates and, confounder-adjusted estimates and their precision (eg, 95% confidence interval). Provide clarity on which confounders were adjusted for and why they were included.\nThe discussion part looks superficial and weak. In the discussion part, while projecting the prevalence of preterm births from existing literature, percentage can be used than numbers for better understanding. The potential confounders and their effects have to be discussed. Discuss the limitations of the study, taking into account sources of potential bias or imprecision. Discuss the generalisability of the study results too. Why the researchers did not consider any fetal factors namely, IUGR or abnormal presentation as a risk factor for preterm birth.\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/13-1213
https://f1000research.com/articles/13-1212/v1	11 Oct 24	{ "type": "Research Article", "title": "Molecular docking, synthesis and preliminary evaluation of hybrid molecules of benzothiazole cross-linked with hydroxamic acid by certain linkers as HDAC inhibitors", "authors": [ "Yazen Abdul-Hameed", "Shakir Mahmood Alwan", "Ashour Humood Dawood", "Yazen Abdul-Hameed", "Ashour Humood Dawood" ], "abstract": "Background Molecular hybridization in drug design is proved to be very successful approach to provide new chemical entities with potential activities and desirable physicochemical properties. Histone deacetylases (HDACs) are involved in controlling the behavior and acetylation of histone and non-histone proteins and their inhibition causes block of cell growth, differentiation, changes in gene expression, and death. Consequently, HDAC inhibitors may lead to anticytotoxic activity. An approach of synthesizing hybrid molecules of benzothiazole cross-linked with hydroxamic acid via an amino acid or aminoalkanoic acid was considered. This approach is expected to optimize the anticytotoxic activity of the proposed compounds.\n\nMethods Hybrid molecules of benzothiazole cross-linked with hydroxamic acid (2A-E) were synthesized and their chemical structures were confirmed by spectral analyses (FT-IR, 1H-NMR and 13C-NMR). These were subjected to molecular docking on HDAC8 (PDB ID: 1T69). Computational methods were employed using the SwissADME server to predict the ADME parameters and other physicochemical properties. The cytotoxicity evaluation was performed using MTT colorimetric assay.\n\nResults Hybrids (2A-E) recorded lower ΔG (-6.322 to - 9.46) than Vorinostat (SAHA, -5.375). ΔG is an affinity scoring function (kcal/mol) and is employed to rank the candidate poses as the sum of the electrostatic and Van der Waals energies. Benzothiazole cross-linked with hydroxamic acid by a p-aminobenzoic acid (2E) has recorded the lowest docking score of -9.460 and this may refer to the possibility of high inhibitory activity. The hybrids showed no violation from Lipinski’s rule and complied with parameters with low possible passive oral absorption and no penetration into BBB. Hybrid molecules of benzothiazole recorded very interesting results, particularly, 2D and 2E which showed significant and remarkable activity.\n\nConclusions Hybrid molecules of benzothiazole cross-linked with hydroxamic acid recorded very interesting results, particularly, compounds 2D and 2E which showed significant and remarkable activity on lung cancer cell line type A549.", "keywords": [ "Hydroxamic acid", "Molecular hybridization", "Benzothiazole", "HDACs inhibitors" ], "content": "Introduction\n\nBenzothiazole (BZT) is a fused rings of benzene and thiazole and has been intensively studied, as one of the privileged pharmacophores in medicinal chemistry.1 BZT has emerged as a core structure for diversified therapeutic applications, such as, antioxidant, anticancer, antiviral anti-proliferative, anti-diabetic, analgesic, anti-malarial, anti-fungal, anti-histamine and anti-convulsant.2 BZT scaffolds showed a crucial role in the inhibition of the tumor-associated metalloenzyme carbonic anhydrase and consequently, serve as anticancer agents.3 Research has revealed that inhibition of histone deacetylases (HDACs) causes inhibition of cell growth, differentiation, changes in gene expression and death.4,5 HDACs inhibitors have relatively low toxicity toward normal cells, while, inhibiting tumor cells from proliferation and survival. The first FDA-Approved HDACs inhibitor was the hydroxamate, Vorinostat (SAHA), which is used for treating cutaneous T-cell lymphoma.6 When HDACs activity is inhibited, the balance between the conflicting activities of HATs (histone acetylates) and HDACs shifts towards the predominance of HAT activity, leading to the induction of acetylation of both histone and non-histone proteins. As a result, certain genes that influence gene expression will be influenced by the induction or silencing of transcription factor expression as well as certain proliferative and/or apoptotic genes.7 As a result, HDACIs may activate pathways that lead to apoptosis, DNA replication is hindered, the cell cycle is inhibited, proliferation is stimulated, angiogenesis is decreased and DNA fragmentation is promoted. All of which can result in the death of cancer cells.8,9 The development of hybrid multifunctional inhibitors has generated a lot of interest in the search for new medicines. Hybrid molecules have the potential to simultaneously act on two or more cancer-relevant targets, such as, metallo-proteinase, ATP binding cassette subfamily G member 2, human mitochondrial peptide deformylase, nuclear factor kappa light-chain-enhancer of activated B cells, P-glycoprotein, tubulin and vascular endothelial growth factor.10–12 Various hybrid molecules of hydroxamic acid have anti-proliferative and anticancer activities and certain hybrids possess great potency against both drug-sensitive and drug-resistant cancers.13 2-Aminobenzothiazole derivatives containing hydroxamic acid were reported to have potent histone deacetylase inhibitory and antitumor activities.14 Hydroxamic acid derivatives prepared by the reaction of 2-aminobenzo-thiazole with adipic acid have exhibited good anticancer activities against five different cell lines such MCF-7, AsPC-1, SW620, PC3 and NCI-H460.15 Due to their reduced risk of adverse drug-drug interactions than multicomponent medications, hybrid molecules can also counteract the recognized side effects associated with various hybrid elements. As a result, one of the most popular contemporary methods for preparing new anticancer drugs is hybridization.16\n\nIn view of the previous findings, a new approach of synthesizing hybrid molecules of BZT cross-linked with hydroxamic acid via an amino acid or aminoalkanoic acid, as the linkers, was considered. 2-Mercapto-benzothiazole is to be reacted with 2-bromoacetic acid to afford BZT-carboxylate. This is to be covalently linked with either of the linkers and further reaction with hydroxylamine to form new hybrid molecules through amide bond using the mixed anhydride method. This approach is expected to optimize the pharmacological activities of the proposed compounds, particularly, the antitumor activity.\n\n\nExperimental methods\n\n2-Mercaptobenzothiazole, p-aminobenzoic acid, 3-aminopropionic acid, 6-aminohexanoic acid were purchased from Hyperchem/China. Ethyl chloroformate (ECF, CAS ID: 541-41-3), Hydroxylamine. HCl (CAS ID: 5470-11-1), Vorinostat (suberoylanilide hydroxamic acid, SAHA, CAS ID: 149647-78-9), L-Alanine (CAS ID: 56-41-7), L-Cysteine (CAS ID: 52-90-4), aminopropionic acid (CAS ID: 107-95-9), aminohexanoic acid (CAS ID: 60-32-2) and p-amino- benzoic acid (CAS ID: 150-13-0) were purchased from sigma/Aldrich (Germany). For cell culture studies all the investigated compounds were dissolved in dimethyl sulfoxide (DMSO, 10 ml stocks) and were stored in a deep freezer at -20 °C. Experimentally, stock solutions were diluted in cell culture medium. The hybrid molecules were synthesized as described in details in the following section.\n\nPreparation of the investigated hybrid molecules\n\nHybrid molecules of benzothiazole cross-linked with hydroxamic acid through certain linkers, such as, L-alanine, L-cysteine, 3-aminopropionic acid, 6-aminohexanoic acid or p-aminobenzoic acid were proposed. These hybrid molecules were synthesized starting from 2-mercaptobenzothiazole, which is S-alkylated with bromoacetic acid leading to the formation of benzothiazole containing a side chain with a sulfide and a carboxyl group, as called the intermediate (2-(benzo- [d]thiazol-2-yl-thio) acetic acid). The chemical structures of the new hybrids (Scheme 1) and their SMILES (Simplified Molecular-Input Line-Entry Systems) notations were constructed using Chemdraw ultra 10.0. Vorinostat (SAHA) was used as the reference ligand.\n\nMolecular docking\n\nMolecular docking was performed using the Maestro software (Schrödinger, version 2023-1) and the ΔG (kcal/mol) values, as the docking scores function representing the energy required for binding to receptor, were calculated. The chemical structure of HDAC8 type 1T69 was retrieved from protein data bank, PDB, website (https://www.rcsb.org) and imported to Maestro software program. They were processed and their energy were minimized by the protein preparation workflow module. Through this process, unnecessary metals (except Zn+2 ions), ligands (except SAHA, which is the reference ligand), enzyme chains (except chain A), and the water molecules were deleted. The Grid was generated by the Receptor Grid Generator module, during which the binding site was defined by SAHA. The lowest docking scores, as ΔG (kcal/mol), for the investigated compounds and their images, which showed the interaction of each compound with Zn2+ ions and the amino acid residues in the binding site. Docking scores and visualization images of ligand-receptor complexes were shown on Table 1 and Figure 1. These hybrids were treated as successful candidates that have the highest binding affinities based on the lowest docking scores (∆G, kcal/mole).\n\nGeneral methods\n\nMelting points were determined (uncorrected) using electrical melting point apparatus, Electro-thermal 9300, USA. The infrared spectra were recorded in KBr disc by FT-IR spectrophotometer (Shimadzu) 1H-NMR and 13C-NMR spectra were recorded using NMR Bruker 500 MHz-Avance III spectrometer and the chemical shifts were recorded in parts per million (ppm). Tetramethylsilane was used as the reference.\n\nChemical synthesis of the intermediate (2-(benzo [d]thiazol-2-yl-thio) acetic acid)\n\nThis compound is synthesized through S-alkylation reaction of 2-mercaptobenzothiazole with α-bromoacetic acid, and as follows;\n\nTo a stirred aqueous solution of α-bromoacetic acid (10 mmol, 1.389 g) in sodium hydroxide solution (10%, 10 mL), 2-mercaptobenzothiazole (10 mmol, 1.6725 g) in an aqueous solution of sodium hydroxide (10%, 10 mL) was added drop wise with continuous stirring. The mixture was refluxed for 3hrs and was then cooled and acidified with diluted hydrochloric acid to obtain a precipitate, which was filtered, washed excessively with distilled water and crystallized from ethanol to afford a yield of 90%, as white powder, m.p. 152-153 °C, as depicted on Figure 1.\n\nFT-IR spectra recorded the following bands; 3110-2513 (str. vib. of OH of COOH), 3074 (str. vib. of C-H aromatic ring), 2956-2896 (str. vib. of C-H aliph. (asym and sym), 1714 (str. vib. of C=O of COOH), 1602-1581-1498 (str. vib. of C=C aromatic ring), 1315 (str. vib. of C=O of COOH).\n\nGeneral procedure for the synthesis of BZT-Linker (1A-E)\n\nThese compounds were prepared using the mixed anhydride method,17 as depicted in Figure 1 and as follows;\n\nThe intermediate (2-(benzo [d]thiazol-2-yl-thio) acetic acid) (10 mmol) was suspended in dry chloroform (40 ml) containing triethylamine (TEA, 10 mmol) and the mixture was cooled to (-5 to -8 °C) in an ice bath. Ethyl chloroformate (10 mmol) was added dropwise during 15 min and the mixture was stirred for further 15 min. The linker (10 mmol) was dissolved in a cold distilled water containing TEA (10 mmol) and was added immediately all at once with vigorous stirring for 1hr in an ice bath and for further 3 hrs at room temperature. A two-layered yellowish-orange solution was obtained, which was separated using a separatory funnel and the aqueous layer was removed. The chloroform layer was washed with distilled water (3 × 20 ml) and was dried with anhydrous magnesium sulfate, filtered and evaporated under reduced pressure in a rotary evaporator to obtain yellowish-orange residues. The residues were washed with diethyl ether or petroleum ether few times to afford crystalline powder representing the resultant products (1A-E). These compounds were collected as follows:\n\nBZT-Linker-Ala (1A) {(2-(benzo [d]thiazol-2-yl-thio) acetyl) alanine (C12H12O3N2S2, 296.36 g/mole)} was synthesized starting from the intermediate (2-(benzo [d]thiazol-2-yl-thio) acetic acid) and L-Alanine (10 mmol, 1.6 g), as red crystalline powder, m.p. 165-167 °C with 79% yield. FT-IR spectra (ʋ, cm−1) recorded the following characterized bands; 3461 (str. vib. of OH-COOH), 3419 (str. vib. of NH-amide), 2954-2905 (str. vib. of C-H aliph. (asym and sym), 1712 (str. vib. of C=O of COOH), 1668 (str. vib. of C=O of amide), 1589-1573-1479 (str. vib. of C=C aromatic ring).\n\nBZT-Linker-Cys (1B) {(2-(benzo [d]thiazol-2-yl-thio) acetyl) cysteine (C12H12O3N2S3, 328.42 g/mole)} was prepared using L-Cysteine (10 mmol, 1.2 g) and collected as yellow crystalline powder, m.p. 175-177 °C with 85% yield. FT-IR spectra recorded the following bands; 3461 (str. vib. of OH-COOH), 3288 (str. vib. of NH-amide), 3062 (str. vib. of C-H aromatic ring), 2912-2871 (str. vib. of C-H aliph. (asym and sym), 1714 (str. vib. of C=O of COOH), 1641 (str. vib. of C=O of amide), 1600-1545 (str. vib. of C=C aromatic ring).\n\nCompound 1C {3-(2-(benzo [d]thiazol-2-yl- thio) acetamido) propionic acid (C12H12O3N2S2, 296.36) was prepared by reacting the intermediate with 3-Aminopropionic acid (10 mmol, 1.6 g) and collected as orange powder, m.p. 210-212 °C with 76% yield. FT-IR spectra recorded the following bands; 3442(str. vib. of OH-COOH), 3225 (str. vib. of NH amide), 3050 (str. vib. of CH arom), 2987-2858 (str. vib. of C-H aliph. (asym and sym), 1724 (str. vib. of C=O of COOH), 1631 (str. vib. of C=O of amide), 1600-1514 (str. vib. of C=C arom).\n\nBZT-Linker-Aminohexanoic acid (1D) {6-(2-(benzo [d]thiazol-2-yl-thio) acetamido) hexanoic acid (C15H18O3N2S2, 338 g/mole)} was prepared starting from the intermediate and 6-Aminohexanoic acid (10 mmol, 1.31 g) and collected as orange powder, m.p. 225-227 °C with 90% yield. FT-IR spectra recorded the following bands; 3427 (str. vib. of OH-COOH), 3271(str. vib. of NH of amide), 3075 (str. vib. of C-H arom), 2983-2873 (str. vib. of C-H aliph. (asym and sym), 1737 (str. vib. of C=O of COOH),1629 (str. vib. of C=O of amid),1612-1581 (str. vib. of C=C arom).\n\nBZT-Linker-p-Aminobenzoic acid (1E) {4-(2-(benzo [d]thiazol-2-yl-thio) acetamido) benzoic acid (C16H12O3N2S2, 344.4 g/mole)} was prepared from the intermediate and p-Amino-benzoic acid (10 mmol, 1.37g) and collected as purple powder, m.p. 180-182 °C with 70% yield. FT-IR spectra recorded the following bands; 3430 (str. vib. of OH-COOH), 3330 (str. vib. of NH of amide), 3026 (str. vib. of C-H arom), 2981-2937 (str. vib. of C-H arom), 1703 (str. vib. of C=O of COOH), 1641(str. vib. of C=O of amide), 1598-1558-1479 (str. vib. of C=C arom).\n\nGeneral procedure for preparing the hybrid molecules (2A-E)\n\nThe target hybrid molecules were prepared starting with compounds 1A-E and reacted with hydroxylamine to afford compounds 2A-E, as depicted in scheme 1. This reaction was performed using the mixed anhydride method (17), as previously described. Compounds 1A-E (10 mmol) in dry chloroform containing TEA (10 mmol) was reacted with ECF (10 mmol) and was then reacted with hydroxylamine. HCl (10 mmol) in an aqueous solution (10 ml) containing TEA (10 mmol).\n\nBZT-Linker-Ala Hydroxamate (2A) {2-(2-(benzo- [d]thiazol-2-yl-thio) acetamido)-N-Hydroxy-propanamide (C12H13O3N3S2, 311.37 g/mole) was synthesized using compound 1A (10 mmol, 2.964 g) and was collected as yellow powder, m.p. 253-255 °C with 80% yield. FT-IR spectra recorded the following bands; 3452 (OH str. vib. of oxime), 3257 (NH str. vib. of oxime), 3200 (NH str. vib. of amide), 3058 (str. vib. of C-H arom), 2983-2852 (str. vib. of C-H aliph, asym and sym), 1699 (str. vib. of C=O of oxime),1616 (str. vib. of C=O of amide), 1610-1569 (str. vib. of C=C arom). 1H-NMR spectra recorded the followings signals (ppm); 1.28 (doublet, 3H, CH3), 4.25 (quartet,1H, CH), 4.92 (singlet, 2H, CH2), 7.40-8.35 (multiplate, 4H, represent phenyl), 8.85 (singlet 1H, NH of amide group), 9.20 (singlet 1H, NH of oxime group), 10.96 (singlet, 1H, OH group). 13C-NMR spectra recorded the followings signals; 13.67 (CH3), 34.59 (CH), 61.50 (CH2), 111.91-125.83 (arom. CH), 152.58 (C=N of benzothiazole), 164.54 (C=O of amide), 168.08 (C=O of oxime).\n\nBZT-Linker-Cys Hydroxamate (2B) {2-(2-(benzo [d]thiazol-2-yl-thio) acetamido)-N-hydroxy-3-mercapto propanamide (C12H13O3N3S3, 343.43 g/mole) was synthesized starting from compound 1B (10 mmol, 3.284 g) and was collected as paige-colored powder, m.p. 235-237 °C with 77% yield. FT-IR spectra recorded the following characteristic bands; 3431 (str. vib. of OH-oxime), 3290 (NH str. vib. of oxime), 3114 (str. vib. of NH-amide), 3078 (str. vib. of C-H aromatic ring), 2964-2894 (str. vib. of C-H aliph. (asym and sym), 1699 (str. vib. of C=O of oxime), 1639 (str. vib. of C=O of amide), 1596-1554-1496 (str. vib. of C=C arom.). 1H-NMR spectra recorded the following signals; 3.48 (singlet, 1H, SH), 4.50 (triplet, 1H, CH), 4.13 (doublet, 2H, CH2), 4.88 (singlet, 2H, CH2), 7.37-8.10 (multiplate, 4H, phenyl), 8.27 (singlet, 1H, NH of amide group), 8.82 (singlet, 1H, NH of oxime group), 10.81 (singlet, 1H, OH group).\n\n13C-NMR spectra recorded the following signals; 39.66 (CH2-SH), 40.78 (CH), 41.23 (CH2), 124,86-135.25 (CH arom), 153.32 (C=N of benzothiazole), 158.61 (C=O of amide), 167.27 (C=O of oxime).\n\nBZT-Linker-Aminopropionic acid (2C) {3-(2-(benzo [d]thiazol-2-yl-thio) acetamido)-N-hydroxypropanamide (C12H13O3N3S2, 311.37 g/mole)} was prepared starting from compound 1C (10 mmol, 2.964 g) and was collected as dark brown powder, m.p. 219-221 °C with 88% yield. FT-IR spectra recorded the following bands; 3315 (OH str. vib. of oxime), 3188 (NH str. vib. of oxime), 3112 (NH str. vib. of amide), 3053 (str. vib. of C-H arom.), 2981-2837 (str. vib. of C-H aliph. (asym and sym), 1704 (str. vib. of C=O of oxime), 1679 (str. vib. of C=O of amide), 1600-1531-1500 (str. vib. of C=C arom.). 1H-NMR spectra recorded the following signals; 2.16 (triplet, 2H, CH2-C=O), 3.58 (triplet, 2H, CH2-N), 4.32(singlet, 2H, CH2-S), 7.32-8.20 (multiplate, 4H, phenyl, 8.90 (singlet, 1H, NH of amide), 8.94 (singlet, 1H, NH of oxime), 9.86 (singlet, 1H, OH).\n\n13C-NMR spectra recorded the following signals; 19.05 (CH2-C=O), 38.30 (CH2-N), 56.53 (CH2-S), 119.31-129.34 (CH arom), 152.97 (C=N of benzothiazole), 166.37 (C=O of amide), 166.59 (C=O of oxime).\n\nBZT-Linker-Aminohexanoic acid (2D) {6-(2-(benzo [d]thiazol-2-yl-thio) acetamido)-N-hydroxyhexanamide (C15H19O3N3S2, 353.45 g/mol) was synthesized from compound 1D (10 mmol, 3.38 g) and was collected as chocolate-color powder, m.p. 269-271 °C with 85% yield. FT-IR spectra recorded the following bands; 34446 (str. vib. of OH-oxime), 3359 (str. vib. of NH-oxime), 3184 (NH str. vib. of amide), 3060 (str. vib. of C-H arom.), 2985-2918 (str. vib. of C-H aliph. (asym and sym), 1704 (str. vib. of C=O of oxime), 1649 (str. vib. of C=O of amide), 1599-1583(str. vib. of C=C arom.). 1H-NMR spectra recorded the following signals; 1.25-2.11(Multiplate, 6H, 3(CH2), 4.14 (triplet, 2H, CH2-C=O), 4.19 (triplet, 2H, CH2-N), 4.87 (singlet, 2H, CH2-S),7.35-8.05 (multiplate, 4H, phenyl), 8.32(singlet, 1H, NH of amide), 8.86 (singlet, 1H, NH of oxime), 10.20 (singlet, 1H, OH). 13C-NMR spectra recorded the followings; 13.78 (CH2), 18.25 (CH2), 20.89 (CH2), 24.60 (CH2 C=O), 35.86 (CH2-N), 55.86 (CH2-S), 111.86-134.90 (CH arom), 151.03 (C=N of benzothiazole), 158.84 (C=O of amide), 162.32 (C=O of oxime).\n\nBZT-Linker-p-Aminobenzoic acid Hydroxamate (2E) {4-(2-(benzo [d]thiazol-2-yl-thio) acetamido)-N-Hydroxy benzamide (C16H13O3N3S2, 359.42 g/mole) was prepared starting from compound 1E (10 mmol, 3.44 g) and was collected as white powder, m.p. 280-282 °C with 90% yield. FT-IR spectra recorded the following bands; 3444 (OH str. vib. of oxime), 3404 (NH str. vib. of oxime), 3295 (NH str. vib. of oxime), 3022 (str. vib. of C-H arom), 2972-2925 (str. vib. of C-H aliph. (asym and sym), 1685 (str. vib. of C=O of oxime), 1625 (str. vib. of C=O of amide), 1597-1546 (str. vib. of C=C arom). 1H-NMR spectra recorded the following signals; 4.12 (singlet, 2H, CH2-S), 7.28-7.30 (doublet, 2H, CH far C=O), 7.31-7.82 (multiplate, 4H, CH of benzothiazole),7.91-7.94 (doublet, 2H, CH near C=O), 8.35 (singlet, 1H, NH of amide group), 9.35 (singlet, 1H, NH of oxime), 10.78 (singlet, 1H, OH). 13C-NMR spectra recorded the following signals; 41.12 (CH2-S), 116.28-137.12 (CH arom), 153.61 (C=N of benzothiazole), 158.62 (C=O of amide), 167.22 (C=O of oxime).\n\nCell culture\n\nDetailed information as well as culture and MTT seeding conditions for used cell lines are provided. All cells were grown under standard cell culture conditions and regularly checked for mycoplasma contamination. The medium was supplemented with 10% fetal bovine calf serum.\n\nCell viability assays\n\nCells were plated (depending on the cell model 2–7x 103 cells/well) in 96-well plates and allowed to recover for 24 h, 48 h and 72 h. Subsequently, the indicated drugs or their combinations were added. After 72 h exposure, the proportion of viable cells was determined by MTT assay.18 Cytotoxicity was expressed as IC50 (μg/ml) values calculated from full dose-response curves using Graph Pad Prism 8 software. The new hybrid molecules (2A-E) were tested for their anticancer activities using a colorimetric assay on the A549 human lung cancer cell.18 MTT stock solution was added and the mixture was stored to generate purple formazan crystals for 2-4 h at 37°C. MTT solution was correctly disposed, formazan crystal was mixed in DMSO (100 μl) containing SDS (10%) and acetic acid (1%). To completely dissolve the formazan crystals, the plates were agitated on the top of a shaker for 10 min. The procedure was done in 96-well flat plates at different concentrations (500-0.97 μM) of the investigated compounds and the IC50 values were calculated after treating the cells with the compounds for 24, 48 and 72 hrs. Cell culture medium was carefully removed after being treated with the hybrids. The optical density was obtained at 570 nm and a Safire 2 Microplate reader were used to calculate the concentrations. The experiments were carried out in triplicate independently. The results are presented on Table 4. The dose-response curves were done by Prism Pad 9 using nonlinear regression analysis for the synthesized molecules using A549 cells are shown on Figure 3.\n\n\nResults\n\nAll the investigated compounds (2A-E) have shown very interesting results of interaction pattern with the amino acids of HDAC8 (PDB ID: 1T69). These compounds have recorded high binding affinities, as indicated from the low docking scores, expressed as ΔG (Kcal/mol) than SAHA (Table 1). Moreover, compound 2E (BZT linked to hydroxamic acid by p-aminobenzoic acid, recorded the lowest docking score -9.460). This may indicate that this compound has the highest HDAC8 inhibitory activity. The interaction of compound 2E with the target HDAC8 type 1T69 was shown on Figure 2, and revealed the amino acids that were involved in this interaction. This compound recorded the best binding score that has been obtained in comparison with other compounds.\n\nThe SwissADME server was employed for the prediction of the physicochemical and ADME properties of the investigated compounds in comparison with SAHA. The pharmacokinetic parameters of these target compounds have shown variation in properties according to chemical structures, as illustrated on Tables 2 and 3. The predicted results have indicated that there was no violation of Lipinski’s rule19 and all the investigated compounds complied with all parameters. However, the results have predicted low passive oral absorption and no penetration into the blood brain barrier (BBB), as shown on Table 3. This may be due to the violation of other rules such as Veber, Egan, and Muegge. All target compounds have violated these rules because their total polar surface area (TPSA) is >131.6 for Egan, and >140 for Veber. Additionally, compound 2B has violated Muegge rule because it has a TPSA of >150 (Table 2).\n\nThe predicted low oral bioavailability of the target compounds may suggest that the potent compounds could be used through other route of administration. Compounds 2B and 2D may be considered as P-gp substrates. However, compounds 2A, 2C and 2D may exhibit a lower incidence of cellular resistance. SAHA did not show a predictive inhibitory activity to any of the CYP enzymes used in this study. While, compounds 2B, 2D and 2E have shown possible predictive inhibitory activities (Table 3). It is worth mentioning that the cap group and the linker of the presently investigated compounds are considered more versatile due to the presence of more hydrogen bond acceptors and donors. Besides, the optimal length, which is favorable for the interaction with the target enzyme, as indicated by the well-confirmed structure-activity relationships of HDACs inhibitors.20,21\n\nThe interaction of the investigated compounds and SAHA with HDAC8 type 1T69 were comparable to a large extent showing that these target compounds bound to the target enzyme on approximately the same amino acids (Table 1). This may indicate that these compounds may have certain inhibitory activity resembling that of SAHA. However, compound 2E has recorded a remarkable result of binding affinity (docking score) of –9.460, and hence, is expected to have a much higher activity than SAHA. Moreover, this hybrid molecule has interacted to the target enzyme in a much similar way in comparison with SAHA (Figure 2). SAHA has interacted on Asp101, His142, Tyr306, Zinc378 of the target enzyme. While, compound 2E has interacted with His142, Tyr306, Zinc 378 with a very high docking score than SAHA (Table 1).\n\nThe determination of the half-maximal inhibitory concentrations (IC50) of the hybrid molecules has revealed that compounds 2B, 2D and 2E have showed significant and remarkable activity on lung cancer cell line type A549, potent than SAHA results, particularly after 72 hrs incubation time (Table 4).\n\nMoreover, dose-response curves were constructed to evaluate the relationship between the percent inhibition of the cell line activity of A549 by the synthesized compounds in comparison with SAHA (Figure 3). The results revealed that there is a great similarity in the pattern of the relationship. This is an expected result due to the great similarity in chemical structures of this series of compounds and SAHA.\n\n\nDiscussion\n\nThe highest predicted activity of compound 2E may be due to the rigidity of the aromatic ring which enforces the molecule to take a specific pose directed toward Zinc ions, forming a stronger interaction, as shown in Figure 2. Moreover, this compound may form a π- π interaction (π-π stacking) with the aromatic amino acid residues (such as L-Tyrosine, L-Phenylalanine and L-Histidine) lining the hydrophobic tunnel of the active site near the Zinc ions, as previously reported.22 The significance of the aromatic linker has been evident in developing several HDACs inhibitors, such as, tubastatin A, belinostat and quisinostat.23\n\nThe predicted results of low passive oral absorption and no penetration into the blood-brain barrier (BBB) may be due to the violation of other rules such as Veber, Egan and Muegge. All the target compounds (2A-E) have violated these rules because their total polar surface area (TPSA) is >131.6 for Egan, and >140 for Veber. Moreover, compound 2B has violated Muegge rule because of the high TPSA of >150 (Table 2). Results have indicated that SAHA did not show a predictive inhibitory activity to any of the CYP enzymes, while, compounds 2B, 2D and 2E have shown possible predictive inhibitory activities. These results may be due to the presence of versatile groups, such as, -SH of L-Cysteine in compound 2B, (-CH2 -)4 present in compound 2D and p-aminobenzoic acid present in compound 2E, which added more hydrogen bond acceptors and donors. Interestingly, the aromatic ring in the hybrid molecule 2E contributed to binding affinity to target enzyme to record better docking score and also to activity against lung cancer cell line type A549. Contribution of an aromatic moiety to binding affinity and actual in vitro antibacterial activities has also been noticed in previous findings.24,25\n\nBesides, the long chain of (-CH2-)4 provides hydrophobicity that is favorable for perfect binding or interaction with target enzyme. A similar case was noticed with the FDA-Approved drug, Panobinostat as powerful HDAC inhibitor.26 This situation is highly indicated by the well-confirmed structure-activity relationships of HDACs inhibitors.27 It was reported that the presence of 6-aminohexanoic hydroxamate, prominently induced the differentiation of mouse neuroblastoma cells at sub-millimolar concentrations.28 A similar case was noticed with compound 2D, which include benzothiazole-linked to aminohexanoic hydroxamate and afforded significant activity on lung cancer cell line A549 (Table 4). Previously, a reported work stated that new benzothiazole analogues containing aliphatic side chain and based on SAHA exhibited potent HDAC inhibition and cytotoxicity against five cancer cell lines, namely colon cancer SW620, breast cancer MCF-7, prostate cancer PC-3, pancreatic cancer AsPC-1 and lung cancer NCI-H460.29\n\n\nConclusions\n\nNew hybrid molecules of Benzothiazole cross-linked with hydroxamic acid through an amino acid or aminoalkanoic acid linkers were successfully prepared and their binding affinities to HDAC8 (PDB ID: 1T69) were higher than the reference ligand, SAHA. Moreover, the aromatic linker in compound 2E has contributed to much better binding and causes the highest docking score than SAHA and the other hybrid molecules. Compounds 2A, 2C and 2D were not shown to be P-gp substrates. Therefore, this work may introduce new hybrid molecules 2B, 2D and 2E with significant anticancer activity when compared with SAHA. Moreover, compound 2E is a promising and potential successful candidate.", "appendix": "Data availability\n\nZenodo: Cytotoxicity Evaluation, https://doi.org/10.5281/zenodo.11190227. 30\n\nZenodo: Spectral Analyses, https://doi.org/10.5281/zenodo.11190182. 31\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 gratefully acknowledge Dr. Wrood Salim Al-khfajy for performing the in vitro cytotoxicity evaluation.\n\n\nReferences\n\nChander Sharma P, Sharma D, Sharma A, et al.: New horizons in Benzothiazole scaffold for cancer therapy: Advances in bioactivity, functionality and chemistry. Appl. Mater. Today. 2020; 20: 100783. Publisher Full Text\n\nAli SA: Synthesis and Preliminary Antibacterial Study of New 2-Mercapto-1, 3- Benzothiazole Derivatives with Expected Biological Activity. Al Mustansiriyah J. Pharm. Sci. 2013, 1; 13(1): 119–124. Publisher Full Text\n\nQiu X, Xiao X, Li N, et al.: Histone deacetylases inhibitors (HDACsI) as novel therapeutic application in various clinical diseases. Prog. Neuro-Psychopharmacol. Biol. Psychiatry. 2017; 72: 60–72. PubMed Abstract \| Publisher Full Text\n\nShah RR: Safety and Tolerability of Histone Deacetylase (HDAC) Inhibitors in Oncology. Drug Saf. 2019, 16; 42(2): 235–245. Publisher Full Text\n\nEckschlager T, Plch J, Stiborova M, et al.: Histone Deacetylase Inhibitors as Anticancer Drugs. Int. J. Mol. Sci. 2017 Jul 1; 18(7): 1414. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDuvic M, Vu J: Vorinostat: a new oral histone deacetylase inhibitor approved for cutaneous T-cell lymphoma. Expert Opin. Investig. Drugs. 2007, 26; 16(7): 1111–1120. PubMed Abstract \| Publisher Full Text\n\nEckschlager T, Plch J, Stiborova M, et al.: Histone Deacetylase Inhibitors as Anticancer Drugs. Int. J. Mol. Sci. 2017, 1; 18(7): 1414. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi G, Tian Y, Zhu WG: The Roles of Histone Deacetylases and Their Inhibitors in Cancer Therapy. Front. Cell Dev. Biol. 2020; 8: 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeng B, Luo Q, Halim A, et al.: The Anti-Angiogenesis Role of Histone Deacetylase Inhibitors: Their Potential Application to Tumor Therapy and Tissue Repair. DNA Cell Biol. 2020, 1; 39(2): 167–176. PubMed Abstract \| Publisher Full Text\n\nShaveta MS, Singh P: Hybrid molecules: The privileged scaffolds for various pharmaceuticals. Eur. J. Med. Chem. 2016; 124: 500–536. PubMed Abstract \| Publisher Full Text\n\nSzumilak M, Wiktorowska-Owczarek A, Stanczak A: Hybrid Drugs—A Strategy for Overcoming Anticancer Drug Resistance? Molecules. 2021, 29; 26(9): 2601. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeng L, Xu Z, Chang L, et al.: Hybrid molecules with potential in vitro anti-plasmodial and in vivo antimalarial activity against drug-resistant Plasmodium falciparum. Med. Res. Rev. 2020 May 6; 40(3): 931–971. PubMed Abstract \| Publisher Full Text\n\nKerru N, Singh P, Koorbanally N, et al.: Recent advances (2015–2016) in anticancer hybrids. Eur. J. Med. Chem. 2017; 142: 179–212. PubMed Abstract \| Publisher Full Text\n\nTung T, Kim Oanh D, Phuong Dung P, et al.: New Benzothiazole/thiazole-Containing Hydroxamic Acids as Potent Histone Deacetylase Inhibitors and Antitumor Agents. Med. Chem. (Los Angeles). 2013 Oct 1; 9(8): 1051–1057. PubMed Abstract \| Publisher Full Text\n\nTung T, Kim Oanh D, Phuong Dung P, et al.: New benzothiazole/thiazole-containing hydroxamic acids as potent histone deacetylase inhibitors and antitumor agents. Med. Chem. 2013; 9(8): 1051–1057. Publisher Full Text , PMID: PubMed Abstract \|\n\nHu L, Cai X, Dong S, et al.: Synthesis and Anticancer Activity of Novel Actinonin Derivatives as HsPDF Inhibitors. J. Med. Chem. 2020, 9; 63(13): 6959–6978. PubMed Abstract \| Publisher Full Text\n\nNaguchi T, Sekine M, Yokoo Y, et al.: Convenient preparation of primary amides via activation of carboxylic acids with ethylchloroformate and triethylamine under mild conditions. Chem. Lett. 2013; 42(6): 580–582. Publisher Full Text\n\nChang J, Ren H, Zhao M, et al.: Development of a series of novel 4-anilinoquinazline skeleton. Design, synthesis, EGFR kinase inhibitory efficacy and evaluation of anticancer activities in vitro. Eur. J. Med. Chem. 2017; 138(38): 669–688. PubMed Abstract \| Publisher Full Text\n\nLipinski CA, Lombardo F, Dominy BW, et al.: Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 2012; 64: 4–17. Publisher Full Text\n\nSandrone G, Cukier CD, Zrubek K, et al.: Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors. ACS Med. Chem. Lett. 2021, 11 [cited 2023 Jun 3]; 12(11): 1810–1817. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReßing N, Schliehe-Diecks J, Watson PR, et al.: Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia. J. Med. Chem. 2022; 65(22): 15457–15472. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRajak H, Singh A, Raghuwanshi K, et al.: A Structural Insight into Hydroxamic Acid Based Histone Deacetylase Inhibitors for the Presence of Anticancer Activity. Curr. Med. Chem. 2013, 23; 21(23): 2642–2664. PubMed Abstract \| Publisher Full Text\n\nMohammed Manal MJN, Chandrasekhar JG, Priya MJN: Inhibitors of histone deacetylase as antitumor agents: A critical review. Bioorg. Chem. 2016 August; 67: 18–42. Publisher Full Text\n\nAlwan SM, Jawad Al-Mudhafar MM, Abdul-Wahab A-HH: Synthesis, Preliminary Antimicrobial Evaluation and Molecular Docking of new Schiff bases of Ceftizoxime. J. Pharm. Sci. Res. 2017; 9(5): 588–592.\n\nMuhsin YF, Khan AK, Alwan SM: Design, Molecular Docking, Synthesis and Preliminary Evaluation of the Antimicrobial Activity and Stability against β-lactamases of Dipeptides Linked to Cephalexin. Int. J. Drug Delivery Technol. 2021. Publisher Full Text\n\nBailey H, Stenehjem DD, Sharma S: Panobinostat or the treatment of multiple myeloma: the evidence to date. J. Blood Med. 2015; 6: 269–276. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFabian BK, Han M, Felix F, et al.: Photocaged Histone Deacetylase Inhibitors as Prodrugs in Targeted Cancer Therapy. Pharmaceuticals. 2023; 16: 356. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZong JL, Chen P, Yan YP, et al.: Aminohexanoic hydroxamate is a potent inducer of the differentiation of mouse neuroblastoma cells. Cancer Lett. 2000; 160: 59–66. PubMed Abstract \| Publisher Full Text\n\nOanh DTK, Hai HV, Hue VTM, et al.: Benzothiazole containing hydroxamic acids as histone deacetylase inhibitors and antitumor agents. Bioorg. Med. Chem. Lett. 2011; 21: 7509–7512. PubMed Abstract \| Publisher Full Text\n\nAlwan SM: Cytotoxicity Evaluation. Zenodo. 2024. Publisher Full Text\n\nAlwan SM: Spectral Analyses. Zenodo. 2024. Publisher Full Text" }	[ { "id": "352917", "date": "08 Jan 2025", "name": "Sandip Kr Baidya", "expertise": [ "Reviewer Expertise Drug design", "synthesis", "QSAR" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 “Molecular docking, synthesis and preliminary evaluation of hybrid molecules of benzothiazole cross-linked with hydroxamic acid by certain linkers as HDAC inhibitors” is a research work which encompass a series of molecules of benzothiazole linked with hydroxamic acid were designed and synthesized as potential HDAC inhibitors. Among these molecules studied, 2D and 2E exhibited significant cytotoxic activity against the A549 lung cancer cell line, with 2E showing the strongest binding affinity (ΔG = -9.460 kcal/mol). Also, these compounds adhered to drug-likeness rules and hold promise for further anticancer therapeutic development. However here are some few comments that may help refine and improve the work:\nWhile the background is thorough, emphasize the novelty of your proposed hybrid molecules and how they differ from previously studied compounds. Authors should highlight what makes your approach unique and innovative. In the Introduction section explicitly state the gaps in current HDAC inhibitor or benzothiazole research that your work aims to address. This strengthens the justification for your study. Include a description of how the docking methodology was validated. For instance, re-docking the reference ligand (SAHA) into the HDAC8 binding site to reproduce the experimental binding pose. The text mentions \"high binding affinities, as indicated from the low docking scores,\" but it would be helpful to explicitly state that lower docking scores correlate with stronger binding. Authors should add a brief explanation of ΔG in the context of docking which can clarify for readers unfamiliar with the term. While the docking scores are mentioned, adding a comparative percentage improvement of compound 2E over SAHA could help highlight the significance of the findings. Provide a brief explanation of Veber, Egan, and Muegge rules for readers who may not be familiar with them. Why do these rules matter for drug development? Elaborate on the significance of the shared binding sites between compound 2E and SAHA (e.g., His142, Tyr306, Zinc378). Why are these residues crucial for HDAC8 inhibition? For binding mode of analysis authors may consult: refer 1 to 3\n8. Although your writing is great overall, focusing on these points will help it become clearer and more logical. The content will be easier to understand if complicated sentences are simplified and grammatical consistency is maintained.\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\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "352914", "date": "11 Jan 2025", "name": "Abhijit Debnath", "expertise": [ "Reviewer Expertise Computer-Aided Drug Design", "Molecular Docking", "MD Simulation", "Cancer 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\n1. Title is not correct HDAC is not a single protein it is a class of enzymes.\n\n2. Authors worked on PDB id: 1T69 which is HDAC8.\n3. There are huge number of amino acid residues are missing with 1T69. Few of such Incomplete or Invalid Residues are: A:LEU14 , A:GLU23 , A:LYS60 A:GLU65, A:THR69, A:GLN84 A:ASP92, A:GLU95, A:GLU106 A:TYR111, A:LYS221, A:GLN253 A:GLU358, A:HIS360, A:LYS370, A:VAL377\nBut authors did not mentioned how they fixed those residues before docking!\n4. Writing the predicted ΔG in abstract is not a good practice. I suggest authors should perform wet lab experiment to validate the ΔG or omit it; as predicted ΔG usually differs form experimental values!\n\n5. That's interesting that 2E showing better IC50 than others. How authors are sure that 2E is specifically binding with HDAC8 and not interacting with others?\n6. SwissADME predicts more ADME parameters than the parameters mentioned in Table3. I am surprised why authors did not mentioned about important parameters such as Solubility and Permeability!\n\n7. Performing Docking with one software is not sufficient in modern times. I suggest the authors should conduct docking with at least 3 software.\n8. I suggest to conduct at least 300-500 MD simulation data and incorporate the MD results so that the Protein-Ligand interaction could be understood.\n\n9. Improve the discussion section with more detail.\n10. Compare the findings with existing literature to prove the novelty of the paper.\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?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/13-1212
https://f1000research.com/articles/12-446/v1	26 Apr 23	{ "type": "Research Article", "title": "An Insight into developmental changes in reasoning skills among Indian Preschoolers: A cross-sectional study using a story-based approach", "authors": [ "Aparna Prasanna", "Gagan Bajaj", "Malavika Anakkathil Anil", "Jayashree S Bhat", "Aparna Prasanna", "Malavika Anakkathil Anil", "Jayashree S Bhat" ], "abstract": "Background: Considering the importance of exploring the development of reasoning skills during preschool period and the suitability of using a culturally linguistically relevant story-based approach for the same, the present research intended to profile the reasoning skills in typically developing Indian preschool children between 36 and 72 months using a story-based approach. The specific objectives were to develop explanation, prediction, and inference based reasoning tasks around a story and assess the reasoning skills in typically developing Indian preschool children using the same. Method: Reasoning tasks across explanation, prediction, and inference domains were developed based on a story and evaluated for its psychometric properties. The developed tasks were then administered to 63 typically developing Indian preschool children attending English medium schools in Mangalore. The preschoolers were equally divided into three age groups, and the responses obtained across the age groups were analyzed quantitatively and qualitatively. Results: The developed tasks were confirmed to have good psychometric properties like content validity and reliability. The age comparisons of reasoning abilities using one-way ANOVA suggested an increase in reasoning abilities with age during the preschool period. The qualitative analysis further suggested that with increasing age, the nature of reasoning changed from content-based reasoning to reasoning based on prior knowledge which was integrated with the story content. Conclusion: The study describes reasoning skill development using a story-based task in Indian preschoolers. The study findings further provide clinical and educational implications to assess and foster reasoning abilities among preschoolers.", "keywords": [ "explanation", "prediction", "inference", "reasoning", "development", "story", "preschoolers", "India" ], "content": "Introduction\n\nReasoning is a cognitive process of making inferences, drawing conclusions, or evaluating a proposed conclusion (Andrews, 2020). Reasoning skills enable individuals to understand and learn about the physical and social environment on a daily basis (Khemlani, 2018). The ability to appropriately reason across different life situations is essential for a successful professional and everyday life (Bronkhorst et al., 2020). It was long believed that reasoning skills do not develop until adolescence (Piaget, 1952). Although preschoolers are known as ‘little scientists’ with abundant curiosity and an innate drive to know the world (Alvarez & Booth, 2014; Piaget, 1952), reasoning skills are considered to be a higher-level cognitive skill that is beyond the reach of preschoolers (Whittaker & McMullen, 2014). Thinking abilities among preschoolers have often been described as “egocentric, pre-logical, affective, undifferentiated, pre-causal, personal, vague and unanalysed” (Piaget, 1952). However, some recent researchers indicate that the development of reasoning skills begins during the preschool years and continues through adolescence (Amsterlaw, 2006; Gopnik et al., 2004; Legare et al., 2010; Säre, Luik & Fisher, 2016a; Whittaker & McMullen, 2014).\n\nIt is essential to explore the development of reasoning skills during the preschool age, as it significantly influences the development of other critical skills like language and literacy (Bauer & Booth, 2019; Nussipzhanova et al., 2018). Understanding reasoning skills during preschool years is vital for several critical decisions, such as the timely preparation of children to perceive and understand real-life scenarios, the right time for school entry, and laying the foundation for academic achievement and success (Niklas et al., 2018; Pasnak et al., 2015).\n\nThe existing literature suggests that reasoning abilities among preschoolers have been explored in domains like reasoning associated with improbable and less logical events like growing money on a tree, going back in time (Shtulman & Carey, 2007), counterfactual events (Muller et al., 2007), judgments on human abilities (Heyman et al., 2003), temporal ordering of events (McCormack & Hoerl, 2005), teleological functions (Kelemen et al., 2003), consistent and inconsistent events (Legare et al., 2010), pre-energy reasoning (Koliopoulos et al., 2009), analogies (Simms et al., 2018), and causal reasoning concerning scientific literacy associated with space, structures, tools, etc. (Bauer & Booth, 2019). However, the findings from these studies remain inconclusive in understanding the general reasoning development in preschoolers that could be fostered through education during the preschool period (Säre, Luik, & Fisher, 2016a). These studies seem to focus less on how children verbally reason in a general living context and how education could be the mediator to foster reasoning among preschoolers in such contexts. We could find one such recent initiative by Säre, Luik, and Fisher (2016a), wherein a valid and reliable tool ‘Younger Children Verbal Reasoning Test’ was developed to aid educators in assessing the general verbal reasoning of older preschoolers between five and six years of age. The tool utilized scenarios related to a theme on ‘bravery’ with illustrations and prompted children to judge how brave the characters are in the given scenario based on their actions. However, the authors of the work highlighted the psychometric properties of the developed tool and provided limited description regarding application of their tool in understanding general reasoning skills development in preschoolers.\n\nThe stimuli used to assess the reasoning abilities among preschoolers is a significant aspect to consider while discussing the development of general reasoning skills in this age group. In this context, Kendeou et al. (2019) put forth an integrated theoretical framework, inferential Language Comprehension (iLC), guiding and recommending the effective use of static or dynamic visual narratives (Stories) as a stimulus for evaluating reasoning skills among younger children. The study recommended that reasoning skills, such as inferencing opportunities, could be increased using static or dynamic visual narrative with questioning techniques in younger children who are non-readers. The story-based materials are reported to aid in better representation of general reasoning abilities in everyday communication contexts as they are more relatable to the natural learning context for the children (Killick & Boffey, 2012; O’Reilly et al., 2022). Stories also seem to provide an opportunity for children to provide explanations, form predictions, and make inferences that would help them to form logical, causally sequenced plots (Paris & Paris, 2003). Since a long, stories are known to constitute an inevitable part of childhood education, as children are intrinsically drawn to stories, and stories facilitate the development of thinking and learning in children (Paley, 2013). Recent research by Dawes et al. (2019) advocates the potential and sensitivity of a story-based approach to obtain insight into preschoolers’ developmental changes for skills such as inferential comprehension. The application of story-based stimuli to assess reasoning skills during preschool years has ranged from asking questions in an open-ended format after a short story sequence with picture cards (Muller et al., 2007; Shtulman & Carey, 2007) or after short fragments of story scenarios depicted through illustrations and objects (Bauer & Booth, 2019; Heyman et al., 2003; McCormack & Hoerl, 2005; Simms et al., 2018). A recent review by O’Reilly et al. (2022) highlighted the effectiveness of stories in fostering critical thinking, such as reasoning and problem-solving among preschoolers, and advocated the utility of story-based approaches in the field of critical thinking for future researchers.\n\nCognitive assessments, in general, have been recommended to be culturally and linguistically relevant to the age and community of the participants for yielding accurate findings (Tanveer et al., 2022). Likewise, though stories offer significant potential in assessing reasoning abilities among preschool age children, it is important to note that stories should be culturally and linguistically relevant for getting a true insight into the developmental trends of reasoning abilities among preschoolers (Rao et al., 2021; Sternberg, 2004).\n\nSome other crucial aspects while exploring general reasoning skills among preschoolers, besides the stimuli, are the ways reasoning based responses are elicited with the children and the different tasks employed to assess their abilities. An interventional research on facilitating reasoning among preschoolers used undirected, shared picture book narration within a peer-group setting (Reed et al., 2015). The study qualitatively analyzed the narration discourse by preschoolers while they freely generated stories from picture books and observed the emergence of reasoning categories such as explanation, prediction, and inference. The findings of this research informed that spontaneously elicited reasoning categories in pre-schoolers without guidance could better represent the reasoning developmental changes in the preschool period. Regarding the tasks for assessing reasoning among preschoolers, different studies have employed tasks based on explanation, predictions, and inferencing. In the explanation-based reasoning tasks, participants are expected to explain the reason behind an outcome (Legare et al., 2010) whereas, in the prediction-based reasoning tasks, participants are required to predict the outcome of an event assuming a cause (Bonawitz et al., 2010). The inference-based reasoning task expects the participants to form a conclusion about a connection between an antecedent and an outcome with rational justification (Gopnik et al., 2004). Similar reasoning tasks based on explanation, prediction, and inference were utilized in preschoolers to explore reasoning skills related to the physical causality of objects by Blank et al. (1981). It seems most promising to incorporate explanation, prediction, and inference based reasoning tasks in a story-based approach while studying reasoning development during preschool years.\n\nWhile realizing the need to explore the developmental trends of reasoning among preschoolers and the potential of culturally-linguistically relevant story-based approach for the same, the present research aimed at profiling the reasoning skills in typically developing Indian preschool children between 36 and 72 months using a story-based approach. The specific objectives of the research were to develop explanation, prediction, and inference based reasoning tasks around a story and assess reasoning skills in typically developing Indian preschool children using the same. The study did not expect the developmental trends of the reasoning abilities to be gender specific based on the evidence from previous literature (Ardila et al., 2011).\n\n\nMethods\n\nThe study followed a cross-sectional research design following STROBE guidelines and commenced after obtaining Institutional Ethical Clearance from Kasturba Medical College, Mangalore, Manipal Academy of Higher Education (IEC KMC MLR 02-19/51). The data collection was conducted between June 2021 to January 2022 in Mangalore, India.\n\nSixty-three typically developing children aged 36 to 72 months attending English medium schools in Mangalore were selected as participants. Written informed consent was obtained from school authorities, and parents of all the participants before their inclusion in the study. The age and gender of the participants was confirmed based on parental report and the participants were equally divided into three groups according to age, i.e., Group I (Age range: 36–48 months, Mean age: 43 months, Standard deviation: 3.8 months, 10 Females and 11 Males), Group II (Age range: 49–60 months, Mean age: 54 months, Standard deviation: 3.8 months, 10 Females and 11 Males) and Group III (Age range: 61–72 months, Mean age: 65 months, Standard deviation: 3.2 months, 10 Females and 11 Males). Initially, 76 children were screened for typical sensorimotor, cognitive, and language development using the Ten Questions Screen (TQS) (Durkin et al., 1995) and Assessment of Language Development (ALD) (Lakkanna et al., 2021). Children who qualified across all the 10 items of the TQS and those who exhibited age-adequate receptive and expressive language skills according to ALD were recruited. Since socioeconomic status highly correlates with the cognitive development of young children (Greenfield & Moorman, 2019), only those participants who belonged to middle socioeconomic status according to the modified Kuppuswamy socioeconomic scale (Saleem, 2019) were included in this study. Only those children who had attended nursery before joining preschool were included in the study to ensure homogeneity concerning exposure to literacy skills. Likewise, 13 children were excluded from participation due to either history or complaint of deficits in sensory, motor, and/or language development. All the shortlisted children had English as their second language. Children with English language proficiency of seven or greater on a 10-point rating scale of the Child Language Experience and Proficiency Questionnaire (LEAP-Q-Child version) were included in the study (Marian et al., 2007; Rochanavibhata et al., 2019).\n\nA story-based assessment task for reasoning was developed based on the iLC framework proposed by Kendeou et al. (2019) for assessing the reasoning skills among preschoolers. This framework emphasized the utility of a static visual narrative and questioning technique for assessing reasoning abilities among preschoolers. Present research used a modified version of a story constructed in our previous work (Prasanna et al., 2022), wherein the effects of modality on a story-based recall task were assessed among the preschoolers. The story titled ‘A Day at Grandparents House’ (Prasanna et al., 2021b) with its six pictures (Prasanna et al., 2021a) was modified concerning its length and distribution of story elements across the modalities of presentation. The modified story, which did not differ with respect to the overall theme of the basic story, comprised three-story sections with two corresponding pictures under each section and 14 story elements per section delivered only through the auditory and auditory-visual modality. The researchers jointly validated the modified story to ensure that the story’s overall theme and linguistic elements, relevant to the preschool age, were retained. The story was designed in English to maintain uniformity among participants from different native languages.\n\nTo assess the reasoning abilities, explanation, prediction, and inference based reasoning tasks were formulated for each of the sections of the story. Considering the potential of questioning as a strategy to assess reasoning among young children (Kendeou et al., 2019; Säre, Luik, & Tulviste, 2016b), the tasks in the present research were designed in a question based format. The questions regarding explanation and prediction based reasoning abilities were framed in an open-ended format (Eg: Why did Virat get scared? [explanation], What would have happened if grandpa had not locked the dog in the cage? [prediction]), whereas the questions for the inference based reasoning comprised of a closed-ended polar question (Yes/No type) to elicit the inference followed by an open-ended question to prompt the justification for the same (Eg: Did Virat love grandparents? [inference] followed by What made you feel that way? [justification for the inference]).\n\nThe initial version of the tasks that comprised six explanation, six prediction, and nine inference questions were content validated for their relevance, demand posed on the child, linguistic appropriateness of the instructions, questions, and scoring, using a five-point Likert scale (1 - Highly inappropriate/Highly incomprehensible/Highly irrelevant, 2 - “Inappropriate/Incomprehensive/Irrelevant,” 3 - “Not sure,” 4 - Appropriate/Comprehensive/Relevant, and 5 - “Highly Appropriate/Highly comprehensive/Highly relevant”). Three Speech-Language Pathologists with more than five years of expertise in the field of cognitive communication and three preschool teachers with more than five years of teaching experience with preschoolers performed the content validation. The items with a content validity index greater than 0.78 were included in the assessment protocol (Almanasreh et al., 2019). Based on this criteria, three questions from the inference based reasoning task were excluded. Further, the feasibility of these tasks was ascertained through a pilot study among 15 typically developing children aged between 36 to 72 months. Since diverse answers could be possible for some of these reasoning tasks, especially among preschoolers, all the probable responses obtained during the pilot study were reviewed and discussed by the researchers to formulate an answer key. To obtain the test-retest reliability, the tasks were re-administered after two weeks among the 15 preschoolers (five from each age group). Since the present study is a preliminary step in tool development, which is planned to be commercially released in the future, the optimum representation of the story text and reasoning tasks has been provided in Table 2 of the Results section for the readers.\n\nThe data collection was carried out within the home premises, wherein the participants were seated in a well-lit, quiet room with only the researcher and the child present during the assessment. The evaluation was scheduled in the morning, considering the children’s active time according to the mother’s feedback. The researcher initially built rapport with the children and developed their interest in listening to the story through engaging in an active conversation about stories (For example: Do you like to listen to a story? Does your mother tell you stories? I am going to tell you a story. Would you like to know what happened in that story?). The researcher then instructed the child to carefully listen to the story and answer the questions, which was rewarded with reinforcement (stickers). The researcher also explained that if the child did not know the answer or wanted to think longer, they could freely say that. A practice trial was given to the child by listening to another short story (different from the story used in present assessment) and answering three reasoning-based questions based on the story to familiarise with the assessment procedure.\n\nAfter the practice trial, the story was presented using a laptop and headphones. The reasoning tasks were performed after the presentation of each story section to ensure that excessive recall load did not dilute the findings. The order of the presentation of the questions in each section was randomized for each participant using a random number generator. Children were encouraged to respond verbally to all the questions and were rewarded with reinforcement (stickers). The assessment took around 20 minutes per participant, including a one-minute rest after each story section and task.\n\nThe psychometric properties of the developed story-based reasoning tasks were evaluated using content validity and test-retest reliability measures. The Content Validity measure at the Item level (I-CVI) was computed by obtaining the ratio of experts who rated the items of the tasks as either 4 or 5 and the total number of experts involved in validation (Polit & Beck, 2006). Scale Content Validity Index (S-CVI/Ave) was also calculated by taking the average of I-CVI across each task. The test-retest reliability was established using the Intra class correlation coefficient (ICC) analysis at 95% confidence interval with absolute agreement using two-way mixed model.\n\nThe responses obtained from the assessment of reasoning skills using the three tasks were analyzed quantitatively and qualitatively. For the quantitative analysis, the responses across the explanation, prediction, and justification components of the inference tasks were scored based on their appropriateness. The appropriateness of the answers was determined based on the answer key prepared by the researchers, considering logic and rationality. Children received a score of ‘one’ for the appropriate reasons and ‘zero’ for the inappropriate or no reasons for all the tasks. For example, for an explanation based question, ‘Why did Virat get scared?’, if the child’s response was ‘because he saw the dog’ or ‘because the dog would bite,’ it was interpreted as appropriate and received a score of ‘one.’ Whereas if the child’s response to the same question was unrelated (such as ‘because he saw a ghost’ or ‘don’t’ know’), then such answers were considered inappropriate and scored ‘zero’ accordingly. The closed-end polar questions (Yes/No type) of the inference based reasoning task were scored as ‘one’ for the correct answers and ‘zero’ for the incorrect answers. A child could thus obtain a maximum score of ‘six’ for each reasoning task. To prevent bias in the scoring, two independent researchers who were blind to the participants’ demographic details scored the responses, and any disagreements were resolved by reaching a consensus through discussion with a third independent researcher. The scored data were subjected to one-way ANOVA with post hoc Tukey test using SPSS V.25 software to investigate the quantitative changes in reasoning skills with age during the preschool period. Receiver Operating Characteristic (ROC) analysis was also carried out to determine the cut-off values distinguishing the significant quantitative changes in reasoning skills revealed during ANOVA analysis. Gender wise analysis of the task scores was carried out using Independent t test.\n\nThe data was further analyzed qualitatively, exploring the manner in which children reason with increase in age to get an insight into the typical pattern of reasoning during the preschool years. Such an analysis was expected to serve as a guide for stimulating typical reasoning development in clinical and educational settings. A general inductive approach (Thomas, 2006), a systematic set of procedures for analyzing qualitative data that produce reliable and valid findings, was followed for qualitative analysis of the reasoning responses. Two independent researchers coded and categorized the responses for explanation, prediction, and justification of the inference tasks. The codes and categories obtained from the two researchers were compared and merged into a combined set to establish the extent of overlap. The agreement between the two coders was set at 95%, and disagreements were resolved through discussion with a third independent researcher. Based on this process and the consensus among the researchers, the responses of the participants were qualitatively categorized into ‘Appropriate reasoning with story content,’ ‘Appropriate reasoning integrating story content with prior knowledge,’ ‘Inappropriate reasoning with improper story content usage,’ and ‘Inappropriate reasoning with context associated with prior knowledge but improper to the story content’ and ‘No reason.’ An example of the qualitative analysis of one such response from the first section of the story is provided in Table 1. For more details of the associated data see underlying data (Prasanna et al., 2023a).\n\n\nResults\n\nThe story-based tasks for assessing reasoning skills in preschoolers were developed. The details regarding of finalized story and the tasks are shown in Table 2. The psychometric properties of the tasks were determined using content validity and test-retest reliability measures. The content validity measures indicated appropriate validity as all the items of the reasoning tasks obtained an I-CVI of 0.83 or higher and S-CVI of 0.98 (Almanasreh et al., 2019; Polit & Beck, 2006). The test-retest reliability measures computed using ICC at 95% confidence interval with absolute agreement using two-way mixed model revealed an ICC of 0.76, indicating moderate test-retest reliability.\n\nThe validated story-based tasks were then used to assess the reasoning abilities of 63 typically developing Indian preschool children. The responses obtained from the participants across the explanation, prediction, and inference based reasoning tasks were quantitatively and qualitatively analyzed. The mean and standard deviation of the total reasoning scores and the percentage of categories of responses for the explanation, prediction, and inference based reasoning tasks across the age groups are illustrated in Figure 1(a,b), Figure 2(a,b), and Figure 3(a-c) respectively.\n\nA comparison of the mean scores of the explanation based reasoning tasks revealed that the explanation based reasoning scores increased with age, F (2,60)=17.91, p<0.001, irrespective of the gender (t[61]=0.401,p=0.690). The post hoc pairwise comparison showed that the older groups (Groups II and III) performed significantly better (p<0.01) than the younger group (Group I); however, there was no statistically significant difference between the older groups (p=0.08). Receiver Operating Characteristic (ROC) analysis revealed a cut-off score of 2.5 discriminating between the younger (Group I) and older groups (Groups II and III) for explanation-based reasoning performance with 81% sensitivity, 62% specificity, and 0.8 Area under the curve (AUC) that is statistically significant (p<0.05).\n\nThe qualitative analysis using the percentage of categories of reasoning responses showed that with the increase in age, most children reasoned appropriately, integrating story content with prior knowledge. The codes identified under appropriate reasoning categories and their frequency across the age groups under the explanation task are presented in Table 3.\n\nThe comparison of the mean scores for the prediction based reasoning task also showed a significant increase with age F (2,60)=26.58, p<0.001, irrespective of the gender t (61)=0.564, p=0.575. Post hoc pairwise comparison revealed a significant difference in prediction scores between all three age groups (p<0.01). The ROC analysis revealed a cut-off prediction score of 4.5 discriminating between Group I and Group II with 52% sensitivity, 90% specificity, and 0.8 statistically significant AUC (p<0.001), and a cut-off prediction score of 5.5 discriminating Group II from Group III with 52% sensitivity, 86% specificity, and 0.7 AUC, that is statistically significant (p<0.05).\n\nThe qualitative analysis showed that similar to the explanation task, most children reasoned integrating story content with prior knowledge as their age increased. The codes identified under appropriate reasoning categories and their frequency across the age groups under the prediction task are presented in Table 4.\n\nFor the inference-based reasoning tasks, comparison of the mean score revealed that the inference scores remained almost similar across the age groups, F (2,60)=0.206, p=0.82, irrespective of the gender (t [61]=0.167, p=0.868). However, the scores pertaining to the justification for inference were found to increase with age, F (2,60)=6.04, p<0.05, without gender as a factor (t [61]=1.767, p=0.082). Post hoc pairwise comparison revealed significant differences in the inference justification performance between older groups (Groups II and III) and younger group (Group I) (p<0.05). There was no statistically significant difference between the older groups (Group II and III) (p=0.99). ROC analysis determined the cut-off score as 0.5, discriminating between the younger (Group I) and older groups (Groups II and III) for inference justification scores with 62% sensitivity, 86% specificity, and 0.7 statistically significant AUC (p<0.05).\n\nQualitative analysis showed that most of the responses belong to the ‘No reason’ category across the age groups and a smaller percentage of responses under ‘appropriate reasoning’ categories. Among the ‘appropriate categories,’ majority of the preschoolers reasoned under the category of ‘appropriate reasoning with story content.’ The codes identified under the smaller percentage of appropriate reasoning categories and their frequency across the age groups under the justification of inference task are presented in Table 5.\n\n\nDiscussion\n\nThe evaluation of psychometric properties of the story-based reasoning tasks revealed adequate content validity and test-retest reliability. The developed stimuli consisting of a story and reasoning tasks in a question format align with the theoretical framework proposed for exploring reasoning skills among preschoolers (Kendeou et al., 2019). The use of story as the assessment material is also consistent with the other research that supports the efficacy of story-based approaches among preschoolers (Dawes et al., 2019; O’Reilly et al., 2022). Besides adding culturally and linguistically relevant data on reasoning skills to the existing literature in this domain among preschoolers (Muller et al., 2007; Shtulman & Carey, 2007), the current study has offered additional depth by exploring the development of reasoning skills across explanation, prediction and inference domains using a single story. Moreover, the present format of these tasks, wherein domains of the reasoning abilities could be assessed on spontaneously emerged output of typically developing preschoolers, is aligned with the earlier perspectives in this regard (Reed et al., 2015). Further, the components of the story, such as the characters, sequences, objects, dress, pictures, vocabulary, and task formats, were designed to reflect the real-life Indian context, which could offer appropriate familiarity and suitability to Indian preschoolers and aid in accurate representation of their abilities (Rao et al., 2021; Sternberg, 2004).\n\nThe developed story-based tasks assessed the reasoning abilities of typically developing Indian preschool children. The comparison of mean reasoning scores across the age groups in the explanation, prediction, and justification of inference task revealed that the preschooler’s reasoning skills improved significantly with age. In most tasks (explanation and justification of inference), a significant change in performance was observed from Group I (36–48 months) to Group II (49–60 months) and III (61–72 months) than between Group II (49–60 months) and III (61–72 months), indicating the rapid development of reasoning skills during the initial phase of the preschool period. The results agree with the previous literature that younger preschoolers show a significant improvement in reasoning skills with age than older preschoolers (Hong et al., 2005). The results also imitate the age bands of thinking differences (Symbolic function substage: 2–4 years, Intuitive thought substage: 4 to 7 years) in Piaget’s preoperational stage of cognitive development (Piaget, 1952). However, the results obtained in the prediction task showed evidence for age-wise developmental changes than in age bands, with significant improvement in performance with age in years. The improved performance in reasoning skills with age across the tasks was not surprising as the preschool period is known to be critical for most of the developmental domains, including executive function skills (Garon et al., 2008).\n\nContrary to the expectation, the age-related difference in reasoning performance was not found in the inference task. More specifically, the findings from the inference task suggested that Group I (36–48 months) children performed like the Group II (49–60 months) and III (61–72 months) children. These results indicate that children as young as 36–48 months of age (Group I) can make inferences. Previous literature supports the findings attesting that preschoolers make logical inferences easily and earlier in development (Moshman, 2004). However, we could not exclude the fact that the inference task’s yes/no question nature might also have influenced the extent of this lack of age-related differences. In yes/no questions, researchers opine that younger preschoolers might show a yes/no bias (all yes responses, i.e., yes bias and vice versa) due to social pressure or difficulty inhibiting yes responses (Okanda & Itakura, 2010). Therefore, there is a chance that the younger participants in this study might have also undergone such yes/no bias in the inference task influencing the lack of age-related differences. Hence, it indicates that, though yes/no questions have been recommended for reasoning skills assessment (Säre et al., 2017), we need to be cautious regarding the chance of yes/no bias in younger preschoolers. However, despite the probability of yes/no bias in this study, the preschooler’s early inferential ability observed in the previous literature adds substantial weight to the conclusion of inferential ability in younger preschoolers.\n\nAnother interesting finding comparing mean reasoning scores was that the preschoolers performed poorly on the justification of inference task than on the other tasks. Though preschoolers could make inferences, the findings contend that they find it difficult to justify their inferences. This difficulty could be because the ability to justify the inferences is a higher quality of thinking requiring metacognition (Moshman, 2004). Though metacognition was not explicitly studied in this research, previous literature findings indicate that children require metacognitive awareness to justify their inferences (Whittaker & McMullen, 2014), which is beyond the preschool age in development (Veenman et al., 2006), lend support for the poorer performance in the current study. However, it is also noteworthy that a smaller percentage of older preschoolers (Group II, 49–60 months and Group III, 61–72 months) could provide appropriate responses (20%) in the justification of inference tasks using story content. Though it could be due to individual differences, it might also indicate the traces of metalogical development for reasoning from 4 years of age using the linguistic content, suggesting the scope of improvement in justification if provided with support.\n\nOn qualitative analysis, results from the explanation and prediction task revealed that among the appropriate reasons made by the preschoolers, younger preschoolers (Group I, 36–48 months) predominantly reason under the category of ‘reasoning with story content,’ and the older preschoolers (Group II, 49–60 months and Group III, 61–72 months) reason in the category of ‘reasoning integrating story content with prior knowledge.’ The results indicate that while younger preschoolers reason with reference to the inference based on the story content premise, older preschoolers undergo a higher thinking process of coordinating the logical inferences from the story and prior knowledge to conclude and reason. The results support the previous literature findings that preschoolers integrate inferences from linguistic context (Florit et al., 2011) and access prior knowledge while reasoning (Gopnik et al., 2004). The findings also align with the comprehension development process, which activates and integrates linguistic knowledge with background knowledge to connect the story contents and form a mental representation to comprehend (Kendeou et al., 2019).\n\nAnother interesting finding in qualitative analysis was with respect to the justification of the inference task. The results from the justification of inference task revealed that preschoolers depend on the source of knowledge from the linguistic contents to justify their inference. We have observed that older preschoolers tried to justify inference with respect to the source of knowledge from the story contents rather than the prior knowledge premise. It was also noted that most preschoolers provided empty reasons such as ‘I know’ for justification questions, claiming they had always known the inference. The findings are supported by the previous literature (Kuhn et al., 2004; Taylor et al., 1994) that children tend to give such responses when unsure or unaware of the answer. This could be because the metacognitive awareness of reasoning is in the emerging stage during the preschool period (Veenman et al., 2006). Based on the pattern of development observed in other tasks of reasoning, it could be expected that with increase in age over the preschool period, with the development of metacognitive awareness of reasoning, children might justify their inference majorly by integrating the story content with their prior knowledge and own interpretation, thereby following the similar pattern of reasoning development.\n\nAll the developmental changes in reasoning obtained in this study could be attributed to the biological maturational change of the brain and reconfiguration of frontoparietal networks (Andrews, 2020) and facilitated by the everyday interactional context (Niklas et al., 2018; Säre, Luik, & Tulviste, 2016b), working memory (Andrews, 2020), language (Richland & Burchinal, 2013) and theory of mind development (Taggart et al., 2005; Whittaker & McMullen, 2014). Consistent with existing literature gender wise differences were not found in all the reasoning tasks (Ardila et al., 2011). The study’s findings need to be cautiously generalized, as reasoning responses are dynamic.\n\nIn conclusion, the study describes the general reasoning skill development in typically developing Indian preschool children between 36 to 72 months of age using story-based tasks. The study put forth a valid and reliable story-based task for the purpose, and the assessment concluded that reasoning skills increase with age during preschool in a pattern of moving from reasoning based on story content to reasoning integrating the story content with prior knowledge. The study findings provide clinical and educational implications with insights on general reasoning development in preschoolers and the utility of age-appropriate story-based explanation, prediction, and inference question tasks to assess and foster reasoning responses in preschoolers. The findings also guide educators to scaffold reasoning in preschoolers, and the developed stimuli aid in early identification of reasoning deficits and guide planning intervention for Indian preschoolers with reasoning deficits. Though the study findings provide insight into general reasoning development in preschoolers, the role of contributing factors such as working memory, theory of mind, and social interaction was not explored, and it remains a limitation of the present study. Therefore, future studies considering such factors could provide an in-depth understanding of reasoning development to assess and foster reasoning during preschool years.", "appendix": "Data availability\n\nFigshare: ‘An Insight into developmental changes in reasoning skills among Indian Preschoolers - A Cross-Sectional Study using a story-based approach’, https://doi.org/10.6084/m9.figshare.22140617.v1 (Prasanna et al., 2023a).\n\nThis project contains the following underlying data:\n\n• Data file 1. (Quantitative and Qualitative data of Reasoning responses)\n\nFigshare: STROBE checklist for ‘An Insight into developmental changes in reasoning skills among Indian Preschoolers - A Cross-Sectional Study using a story-based approach’, https://doi.org/10.6084/m9.figshare.22140689.v2 (Prasanna et al., 2023b).\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 acknowledge all the participants in the study.\n\n\nReferences\n\nAlmanasreh E, Moles R, Chen TF: Evaluation of methods used for estimating content validity. Res. Soc. Adm. Pharm. 2019; 15(2): 214–221. Publisher Full Text\n\nAlvarez AL, Booth AE: Motivated by Meaning: Testing the Effect of Knowledge-Infused Rewards on Preschoolers’ Persistence. Child Dev. 2014; 85(2): 783–791. PubMed Abstract \| Publisher Full Text\n\nAmsterlaw J: Children’s beliefs about everyday reasoning. Child Dev. 2006; 77(2): 443–464. PubMed Abstract \| Publisher Full Text\n\nAndrews G: Reasoning and Problem Solving.Hupp S, Jewell JD, editors. The encyclopedia of child and adolescent development. John Wiley & Sons, Inc.; 2020; pp. 1–11. Publisher Full Text\n\nArdila A, Rosselli M, Matute E, et al.: Gender Differences in Cognitive Development. Dev. Psychol. 2011; 47(4): 984–990. Publisher Full Text\n\nBauer JR, Booth AE: Exploring potential cognitive foundations of scientific literacy in preschoolers: Causal reasoning and executive function. Early Child. Res. Q. 2019; 46(1): 275–284. Publisher Full Text\n\nBlank M, Rose SA, Berlin LJ: Reasoning and Problem Solving in Young Children.Friedman MP, Das JP, O’Connor N, editors. Intelligence and Learning (NATO) Confe. Boston, MA: Springer; 1981; pp. 231–236. Publisher Full Text\n\nBonawitz BE, Ferranti D, Saxe R, et al.: Just do it? Investigating the gap between prediction and action in toddlers’ causal inferences. Cognition. 2010; 115(1): 104–117. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBronkhorst H, Roorda G, Suhre C, et al.: Logical Reasoning in Formal and Everyday Reasoning Tasks. Int. J. Sci. Math. Educ. 2020; 18: 1673–1694. Publisher Full Text\n\nDawes E, Leitão S, Claessen M, et al.: Oral literal and inferential narrative comprehension in young typically developing children and children with developmental language disorder. Int. J. Speech Lang. Pathol. 2019; 21(3): 275–285. PubMed Abstract \| Publisher Full Text\n\nDurkin MS, Wang W, Shrout PE, et al.: Evaluating a ten questions screen for childhood disability: Reliability and internal structure in different cultures. J. Clin. Epidemiol. 1995; 48(5): 657–666. PubMed Abstract \| Publisher Full Text\n\nFlorit E, Roch M, Levorato MC: Listening Text Comprehension of Explicit and Implicit Information in Preschoolers: The Role of Verbal and Inferential Skills. Discourse Process. 2011; 48(2): 119–138. Publisher Full Text\n\nGaron N, Bryson SE, Smith IM: Executive Function in Preschoolers: A Review Using an Integrative Framework. Psychol. Bull. 2008; 134(1): 31–60. PubMed Abstract \| Publisher Full Text\n\nGopnik A, Sobel DM, Danks D, et al.: A Theory of Causal Learning in Children: Causal Maps and Bayes Nets. Psychol. Rev. 2004; 111(1): 3–32. PubMed Abstract \| Publisher Full Text\n\nGreenfield EA, Moorman SM: Childhood Socioeconomic Status and Later Life Cognition: Evidence From the Wisconsin Longitudinal Study. J. Aging Health. 2019; 31(9): 1589–1615. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHeyman GD, Gee CL, Giles JW: Preschool Children’s Reasoning about Ability. Child Dev. 2003; 74(2): 516–534. Publisher Full Text\n\nHong L, Chijun Z, Xuemei G, et al.: The influence of complexity and reasoning direction on children’s causal reasoning. Cogn. Dev. 2005; 20(1): 87–101. Publisher Full Text\n\nKelemen D, Widdowson D, Posner T, et al.: Teleo-functional constraints on preschool children’s reasoning about living things. Dev. Sci. 2003; 6(3): 329–345. Publisher Full Text\n\nKendeou P, McMaster KL, Butterfuss R, et al.: The Inferential Language Comprehension (iLC) Framework: Supporting Children’s Comprehension of Visual Narratives. Top. Cogn. Sci. 2019; 12(1): 256–273. PubMed Abstract \| Publisher Full Text\n\nKhemlani SS: Reasoning.Wixted JT, editor. Stevens’ Handbook of Experimental Psychology and Cognitive Neuroscience. 4th ed.John Wiley & Sons, Inc.; 2018; pp. 1–45. Publisher Full Text\n\nKillick S, Boffey M: Building Relationships through Storytelling A foster carer’s guide to attachment and stories. The Fostering Network. 2012; 2012.\n\nKoliopoulos D, Christidou V, Symidala I, et al.: Pre-energy reasoning in preschool children. Rev. Sci. Math. ICT Educ. 2009; 3(1): 123–140. Reference Source\n\nKuhn D, Katz JB, Dean D: Developing reason. Think. Reason. 2004; 10(2): 197–219. Publisher Full Text\n\nLakkanna S, Venkatesh K, Bhat JS, et al.: Assessment of Language Development A Manipal Manual. 1st ed.Manipal Universiy Press; 2021.\n\nLegare CH, Gelman SA, Wellman HM: Inconsistency with prior knowledge triggers children’s causal explanatory reasoning. Child Dev. 2010; 81(3): 929–944. Publisher Full Text\n\nMarian V, Blumenfeld HK, Kaushanskaya M: The Language Experience and Proficiency Questionnaire (LEAP-Q): Assessing Language Profiles in Bilinguals and Multilinguals. J. Speech Lang. Hear. Res. 2007; 50(August): 940–967. PubMed Abstract \| Publisher Full Text\n\nMcCormack T, Hoerl C: Children’s reasoning about the causal significance of the temporal order of events. Dev. Psychol. 2005; 41(1): 54–63. PubMed Abstract \| Publisher Full Text\n\nMoshman D: From inference to reasoning: The construction of rationality. Think. Reason. 2004; 10(2): 221–239. Publisher Full Text\n\nMuller UM, Miller M, Michalczyk K, et al.: False belief understanding The influence of person, grammatical mood, counterfactual reasoning and working memory. Br. J. Dev. Psychol. 2007; 25(4): 615–632. Publisher Full Text\n\nNiklas F, Cohrssen C, Tayler C: Making a difference to children’s reasoning skills before school-entry: The contribution of the home learning environment. Contemp. Educ. Psychol. 2018; 54(July): 79–88. Publisher Full Text\n\nNussipzhanova B, Berdibayeva S, Garber A, et al.: Cognitive development of pre-school children with language and speech disorders. The European Journal of Social and Behavioural Sciences. 2018; 21(1): 13–27. Publisher Full Text\n\nO’Reilly C, Devitt A, Hayes N: Critical thinking in the preschool classroom - A systematic literature review. Think. Skills Creat. 2022; 46(December): 101110. Publisher Full Text\n\nOkanda M, Itakura S: When do children exhibit a “yes” bias? Child Dev. 2010; 81(2): 568–580. PubMed Abstract \| Publisher Full Text\n\nPaley V: In their own words. Teacher Preparation as an Inspirational Practice: Building Capacities for Responsiveness. 1st ed.Routledge; 2013; p. 138.\n\nParis AH, Paris SG: Assessing Narrative compehension in young children. Read. Res. Q. 2003; 38(1): 36–76. Publisher Full Text\n\nPasnak R, Kidd JK, Gadzichowski KM, et al.: Abstracting sequences: Reasoning that is a key to academic achievement. J. Genet. Psychol. 2015; 176(3): 171–193. PubMed Abstract \| Publisher Full Text\n\nPiaget J: The origins of intelligence in children. 2nd ed.W W Norton & Co.; 1952. Publisher Full Text\n\nPolit DF, Beck CT: The Content Validity Index: Are You Sure You Know What’s Being Reported? Critique and Recommendations. Res. Nurs. Health. 2006; 29(5): 489–497. PubMed Abstract \| Publisher Full Text\n\nPrasanna A, Anakkathil Anil M, Bajaj G, et al.: Do preschool children have modality specific recall abilities? - A cross-sectional pilot study. Cogent Educ. 2022; 9(1). Publisher Full Text\n\nPrasanna A, Bajaj G, Anil MA, et al.: Reasoning Research Data among Indian Preschoolers. [Dataset]. figshare. 2023a. Publisher Full Text\n\nPrasanna A, Bajaj G, Anil MA, et al.: STROBE checklist for the article. [Dataset]. figshare. 2023b. Publisher Full Text\n\nPrasanna A, Bhat JS, Anil MA, et al.: A DAY AT GRANDPARENTS HOUSE- STORY PICTURES (Patent No. L-99255/2021). Copyright office, Government of India.2021a.\n\nPrasanna A, Bhat JS, Anil MA, et al.: A DAY AT GRANDPARENTS HOUSE (Patent No. L-98307/2021). Copyright office, Government of India.2021b.\n\nRao N, Chan SWY, Su Y, et al.: Measuring Being “Developmentally on Track”: Comparing Direct Assessment and Caregiver Report of Early Childhood Development in Bangladesh, China, India and Myanmar. Early Educ. Dev. 2021; 33(6): 1013–1035. Publisher Full Text\n\nReed HC, Hurks PPM, Kirschner PA, et al.: Preschoolers causal reasoning during shared picture book storytelling: A cross-case comparison descriptive study. J. Res. Child. Educ. 2015; 29(3): 367–389. Publisher Full Text\n\nRichland LE, Burchinal MR: Early Executive Function Predicts Reasoning Development. Psychol. Sci. 2013; 24(1): 87–92. PubMed Abstract \| Publisher Full Text\n\nRochanavibhata S, Kaushanskaya M, Marian V: Child Language Experience and Proficiency Questionnaire.2019.\n\nSaleem SM: Modified Kuppuswamy socioeconomic scale updated for the year 2019. Indian Journal of Forensic and Community Medicine. 2019; 6(1): 1–3. Publisher Full Text\n\nSäre E, Luik P, Fisher R: Supporting educational researchers and practitioners in their work in education: Assessing the verbal reasoning skills of five- to six-year-old children. Eur. Early Child. Educ. Res. J. 2016a; 24(5): 638–651. Publisher Full Text\n\nSäre E, Luik P, Tulviste T: Improving pre-schoolers’ reasoning skills using the philosophy for children programme. Trames. 2016b; 20(3): 273–295. Publisher Full Text\n\nSäre E, Tulviste T, Luik P: The function of questions in developing a preschooler’s verbal reasoning skills during philosophical group discussions. Early Child Dev. Care. 2017; 189(4): 555–568. Publisher Full Text\n\nShtulman A, Carey S: Improbable or Impossible ? How Children Reason About the Possibility of Extraordinary Events. Child Dev. 2007; 78(3): 1015–1032. Publisher Full Text\n\nSimms NK, Frausel RR, Richland LE: Working memory predicts children’s analogical reasoning. J. Exp. Child Psychol. 2018; 166: 160–177. PubMed Abstract \| Publisher Full Text\n\nSternberg RJ: Culture and intelligence. Am. Psychol. 2004; 59(5): 325–338. Publisher Full Text\n\nTaggart G, Ridley K, Rudd P, et al.: Thinking skills in the early years a literature review. The Mere, Upton Park Slough, Berkshire: National Foundation for Educational Research; 2005. Reference Source\n\nTanveer S, Croucher MJ, Porter R: Cultural modification of neuropsychiatric assessment: complexities to consider. BJPsych Open. 2022; 8(2): e68–e63. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTaylor M, Esbensen BM, Bennett RT: Children’s Understanding of Knowledge Acquisition: The Tendency for Children to Report That They Have Always Known What They Have Just Learned. Child Dev. 1994; 65(6): 1581–1604. PubMed Abstract \| Publisher Full Text\n\nThomas DR: A General Inductive Approach for Analyzing Qualitative Evaluation Data. Am. J. Eval. 2006; 27(2): 237–246. Publisher Full Text\n\nVeenman MVJ, Van Hout-Wolters BHAM, Afflerbach P: Metacognition and learning: Conceptual and methodological considerations. Metacogn. Learn. 2006; 1(1): 3–14. Publisher Full Text\n\nWhittaker JV, McMullen MB: Preschool: Good Thinking! Fostering Children’s Reasoning and Problem Solving. YC Young Children. JSTOR; 2014; (Vol. 69, Issue 3)." }	[ { "id": "170971", "date": "05 Jul 2023", "name": "Ramesh Kaipa", "expertise": [ "Reviewer Expertise Speech and Language Therapy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: This is a well-developed study. The authors have attempted to develop a stimulus that is culturally relevant to Indian children. The authors need to be appreciated for this line of work. I do have some comments that are mentioned below.\nIntroduction:\nThe rationale for this study is not developed appropriately. The authors need to justify how will the current line of research advance the empirical knowledge.\n\nIt would help if the authors could review prior literature pertaining to reasoning skills and language development in children.\nMethods:\n“What did the authors mean by “Children who qualified across all the ten items of the TQS”. Is there a cut-off score in TQS? The authors expand on this.\n\nCan authors present data on the participants’ language usage? Were they bilingual or multilingual? I believe this variable could skew the findings.\n\nThe authors mentioned that 13 children were excluded. Was it from the cohort of 63 children?\n\nCan I please have the authors present data on the reliability and validity of the assessment tool “A Day at the Grandparents House”?\n\nIf the story was designed in English, how did the authors make sure that the translated version was faithful to the original version? It would be helpful to compare the psychometric properties of the original version to the translated version.\n\nCan the authors present the findings of test-retest reliability for the pilot test on 15 children?\nResults\nThe results are well presented, along with visual illustrations.\nDiscussion\nThe authors make a case that the findings can be attributed to biological maturation. The authors need to discuss the specific neurophysiological substrates that are correlated with higher-order tasks such as the one used in the current study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "11916", "date": "28 Jun 2024", "name": "Gagan Bajaj", "role": "Author Response", "response": "1. Summary: This is a well-developed study. The authors have attempted to develop a stimulus that is culturally relevant to Indian children. The authors need to be appreciated for this line of work. I do have some comments that are mentioned below. Reply: We are grateful to the reviewer for the constructive feedback and suggestions. The authors have endeavoured to revise the manuscript according to these valuable suggestions and hope that the reviewer will find our efforts satisfactory. 2. Introduction 2a. The rationale for this study is not developed appropriately. The authors need to justify how will the current line of research advance the empirical knowledge. Reply: The rationale of the study has been revisited to ensure that it aligns with the research gaps illustrated in the introduction and justifies the potential of the present work in advancing empirical knowledge. 2b. It would help if the authors could review prior literature pertaining to reasoning skills and language development in children. Reply: The literature on reasoning skills and their significance in children's language development has been reviewed and updated within the manuscript. Consequently, the importance of the association between the two has been underscored in the rationale and discussion sections of the manuscript, respectively. 3. Methods 3a. What did the authors mean by “Children who qualified across all the ten items of the TQS.” Is there a cut-off score in TQS? The authors expand on this. Reply: Thank you for providing the opportunity to clarify. The TQS does not have any cut-off scoring; instead, it functions as a screening tool for the presence or absence of childhood disabilities. In the present study, the TQS was utilized to ensure that only participants who were found to have no disability across all ten items of the questionnaire were included. This statement has been rephrased in the manuscript to enhance clarity. 3b. Can authors present data on the participants’ language usage? Were they bilingual or multilingual? I believe this variable could skew the findings. Reply: The information regarding the number of languages known by the participants in the study has been updated in the manuscript. Although 89% of the participants were bilingual and the remaining 11% multilingual, all of them had English as their L2, with a linguistic proficiency score in English greater than 7 on LEAP-Q (child version). However, since the present study focused solely on the English language, we did not perform an analysis exploring performance differences in the children based on the nature of their L1. This has been noted as a limitation and a future direction in the manuscript. 3c. The authors mentioned that 13 children were excluded. Was it from the cohort of 63 children? Reply: Thank you for providing the opportunity to clarify. A total of 76 children were considered for the study, out of which 13 children were excluded based on the study selection criteria. This left us with 63 children, who were further subdivided into three age groups, each comprising 21 children. 3d. Can I please have the authors present data on the reliability and validity of the assessment tool “A Day at the Grandparents House”? Reply: Thank you for the opportunity to clarify. The tool used in the present research was developed in our previous work, where its content validity was established (Prasanna, Bajaj, et al., 2024). This information is referenced in the method section of the current study. Further evaluation of the tool's psychometric properties, specifically in terms of test-retest and inter-rater reliability, was conducted in the present research through a pilot study. The findings are detailed in the results section. The content has been updated accordingly to enhance clarity. 3e. If the story was designed in English, how did the authors make sure that the translated version was faithful to the original version? It would be helpful to compare the psychometric properties of the original version to the translated version. Reply: We apologize for the lack of clarity in our write-up, which led to this confusion. The present research employed the original English version of the tool, without any translations. Our study explored reasoning development among preschoolers using a story-based cognitive-communication assessment tool developed in our previous work (Prasanna, Bajaj, et al., 2024). The content validity of this tool was established in that prior research. In the current study, reliability measures for the reasoning tasks were established through a pilot study before assessing the reasoning abilities of the participants. The method section has been revised to avoid any confusion. 3f. Can the authors present the findings of test-retest reliability for the pilot test on 15 children? Reply: The test-retest reliability of the tool was established through the pilot testing on 15 children and the findings are presented in the results section. Results: The results are well presented, along with visual illustrations. Reply: Thank you for the kind feedback. Discussion 5a. The authors make a case that the findings can be attributed to biological maturation. The authors need to discuss the specific neurophysiological substrates that are correlated with higher-order tasks such as the one used in the current study. Reply: Thank you for the kind suggestion. The neurophysiological correlates of reasoning abilities among preschoolers, discussed in the present work, have been updated in the discussion section." } ] }, { "id": "206526", "date": "21 Nov 2023", "name": "Andreas Demetriou", "expertise": [ "Reviewer Expertise Cognitive development and individual differences in intelligence. Integration of cognitive developmental and psychometric theory." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is interesting and the paper well written. It has several limitations:\nThe number of children in each group is small. Power must be reported.\n\nNo specification of logical schemes is made.\n\nNo differentiation between changes in reasoning and language. No association with brain is justified.\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?\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": "11917", "date": "28 Jun 2024", "name": "Gagan Bajaj", "role": "Author Response", "response": "1. The study is interesting and the paper well written. It has several limitations. Reply: We are grateful to the reviewer for the constructive feedback and suggestions. The authors have endeavoured to revise the manuscript according to these valuable suggestions and hope that the reviewer will find our efforts satisfactory. 2. The number of children in each group is small. Power must be reported. Reply: The sample size of the study was determined using the formula n = Z1-α/22 SD 2 /d 2 at 95% confidence level, 20% absolute error, 80% power with an anticipated standard deviation of 0.789 based on pilot testing. The same has been reported in the method section. The present study was initiated as a preliminary investigation of a larger project aimed at exploring cognitive-communication skills within this population. Undoubtedly, given its preliminary nature, the study was constrained by a smaller sample size, a limitation that has been transparently acknowledged and addressed within the study's limitations section. 3. No specification of logical schemes is made. Reply: This research serves as a continuation of our previous work, which developed a tool specifically designed for assessing cognitive-communication skills among preschoolers in the Indian context, based on a story (Prasanna, Bajaj, et al., 2024). The current study represents the evaluation phase of this tool, focusing on the reasoning development among Indian preschoolers. The manuscript has been updated to clearly emphasize this aspect. Additionally, we have provided sub-headings in the method section to enhance the logical flow of the information. 4. No differentiation between changes in reasoning and language. Reply: Thank you for the kind feedback. We acknowledge that the present study exclusively included children with age-appropriate speech and language abilities, with their responses analysed for cognitive accuracy. While we recognize the potential for analysing responses in terms of various linguistic elements, such as syntactic and semantic depth, this aspect was beyond the scope of the present research. For example, in a task involving a reasoning question like \"Why did Virat get scared?\" responses such as \"Dog,\" \"When saw dog,\" and \"Because dog was there\" were all deemed correct reasoning responses, despite their linguistic differences in Mean Length of Utterance (MLU). We value the reviewer's suggestion to distinguish between cognitive and linguistic aspects, and we look forward to incorporating this consideration into our future research, particularly in the study of reasoning abilities among children with language disorders. Same has been updated under the future directions of the present study. 5. No association with brain is justified. Reply: Thank you for the kind suggestion. The neurophysiological correlates of reasoning abilities among preschoolers, discussed in the present work, have been updated in the discussion section." } ] } ]	1	https://f1000research.com/articles/12-446
https://f1000research.com/articles/13-868/v1	01 Aug 24	{ "type": "Research Article", "title": "Enhancing Academic Success: A mixed Study on the Influencing Factors among Pharmacy Students in Syrian Universities", "authors": [ "Mohab Qattan", "Mayssoon Dashash", "Zeina S. Malek", "Mayssoon Dashash", "Zeina S. Malek" ], "abstract": "Background Academic achievement is the result of both effort and perseverance exerted by the students. This mixed-methods study aims to investigate the factors affecting the academic achievement of pharmacy students in Syrian universities.\n\nMethods A convergent parallel mixed-methods study was utilized. In the quantitative phase, a cross-sectional study was conducted on 1008 students (773 females and 235 males) from 23 Syrian universities. A questionnaire consisting of 48 items was designed to be completed by pharmacy students using a 5-point Likert scale. In the qualitative phase, twelve questions were developed to interview thirty pharmacy students from five Syrian universities to obtain in-depth insights into the factors influencing their academic achievement.\n\nResults A significant number of students lacked effective time management skills, identified as a weakness among students. The majority of students faced challenges in maintaining a consistent study routine, averaging a score of (2.0). Motivation towards learning emerged as a crucial factor in enhancing academic performance. Lecturers in the pharmacy faculty employed traditional teaching methods (2.01), and the pharmacy curriculum was perceived as lacking modernity (1.92). Quantitative findings demonstrated that pharmacy students experienced exam-related anxiety (2.05), identified as a weakness in the qualitative phase. Factors associated with the Syrian crisis, like unreliable electricity (1.87) and transportation issues (1.83), could have an impact on academic achievement. Economic conditions were identified as challenging to students’ academic performance, negatively affecting the learning process (1.98).\n\nConclusion The results of the study demonstrate that personal factors, lecturers, educational environment, exams, and the Syrian crisis influence the academic achievement of pharmacy students in Syrian universities.", "keywords": [ "Academic Achievements", "Academic performance", "Pharmacy students", "Mixed-methods study", "Quantitative phase", "Qualitative phase." ], "content": "Introduction\n\nAcademic achievement serves as a measure of students’ attainment of their academic and educational objectives.\n\nThe enhancement of students’ academic achievements has consistently been a primary goal in the field of education.1\n\nWithin the pharmacy sector, academic achievement holds great significance as it reflects a student’s competency and readiness to practice pharmacy effectively and safely.\n\nGraduates are expected to deliver appropriate pharmaceutical care to patients and communities,2 shaping the competency and caliber of future pharmacists.3\n\nPrevious studies have indicated that the academic achievement of pharmacy students is influenced by various factors.4 These factors are student-related such as effective time management,4,5 strong family support,5,6 motivation toward learning,7 as well as lecturer-related factors,6 such as their skills, dedication, relationship with students, and involvement in the learning process.\n\nFurther studies have indicated that strategic studying8 and learning styles9 could significantly enhance academic achievement.\n\nMoreover, the educational environment and university-related issues also play a significant role.10 The quality of classrooms, laboratories, technological resources, and the curriculum itself11 all contribute to student performance improvement.\n\nOverall, ensuring an optimal academic environment by addressing these factors could lead to significant enhancement in academic achievement in pharmacy education.\n\nThe impact of exams influences academic achievement.8 Students’ anxiety levels towards exams, the perceived quality of exams within the pharmacy faculty, the effectiveness of exams in assessing knowledge, and their motivation to achieve high grades are key contributors to their success.4,8,12\n\nThe Syrian crisis has greatly affected pharmacy students, presenting them with additional challenges amidst challenging circumstances.13\n\nThe current situation in Syria requires highly professional and competent personnel to respond to the population’s needs and deliver optimal care.14\n\nOne is that remains unexplored is the perceptions of pharmacy students in Syria regarding the factors shaping their academic progress. The increasing concern over low academic achievement among pharmacy students in Syria underscores the urgency for a comprehensive investigation into the underlying factors that contribute to this issue.\n\nThis mixed-methods study aimed to investigate the factors that affect the academic achievement of pharmacy students in Syrian universities.\n\n\nMethods\n\nA convergent parallel mixed-methods study was conducted between March and June 2023 to explore the experiences of participants and investigate the factors affecting the academic achievement of pharmacy students in Syrian universities. Both quantitative and qualitative data were collected and analyzed separately within a concurrent timeframe, followed by a phase of integrative evaluation of the collected findings.\n\nEthical approval for this study was obtained from the Ethical Committee of the Syrian Virtual University (Approval Number: 233/o, Date: 13/2/2023). This study adheres to the ethical principles outlined in the Declaration of Helsinki.\n\nInformed, written consent was obtained from all participants prior to completing the survey forms in the quantitative phase, and verbal consent was recorded before conducting the interviews in the qualitative phase. Participants’ information and data were treated with strict confidentiality, ensuring that personal details were anonymized. The collected data were securely stored on a password-protected computer, and measures were taken to dispose of the data appropriately once it was no longer needed.\n\nThe decision to use verbal consent instead of written consent in the interviews was approved by the ethics committee based on the following reasons:\n\nEnhanced participant comfort and flexibility: Verbal consent was considered more comfortable for participants and provided greater flexibility in the study participation process, as they were not required to sign a written document.\n\nPreservation of participant anonymity: Obtaining verbal consent was the preferred option to maintain participant anonymity and minimize potential risks associated with written documentation.\n\nThe use of verbal consent was ethically approved by the committee, and all necessary precautions were taken to ensure the confidentiality and protection of participants’ rights.\n\nThe quantitative phase of the study was conducted and reported in accordance with the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines.15\n\nThe qualitative phase was designed and reported according to the Consolidated criteria for Reporting Qualitative research (COREQ).16\n\nThe sample was collected from pharmacy students from the second to fifth years, with first-year students excluded from participation as the first year is preparatory for all medical sections. The information collected from participants included gender, university name, and academic year. In the quantitative phase, a cross-sectional study was conducted to investigate the factors influencing the academic achievement of pharmacy students across Syria. Data collection involved the distribution of an online survey to Syrian pharmacy students through websites and social media platforms. A total of 1008 pharmacy students from 23 Syrian universities participated in this study. In the qualitative phase, data were collected through face-to-face, semi-structured interviews carried out to explore student perceptions of factors affecting their academic achievement conducted with thirty pharmacy students from five Syrian universities. The research objectives were explained to them, along with their role in achieving those objectives.\n\nIn the quantitative phase of the study, a questionnaire consisting of 48 items was designed to investigate and identify the significant factors that affect the academic achievement of pharmacy students in Syrian universities.\n\nTo ensure clarity and validity, all statements within the questionnaire were kept simple and clear. Additionally, three academic members reviewed the questionnaire to assess its clarity and relevance of the statements in alignment with the study’s aims.\n\nThe questionnaire items were categorized into five sections, each focusing on distinct factors; 8 items related to student factors, 10 items related to the lecturer factors, 15 items related to educational environment, 8 items related to exam factors, and 7 items related to factors associated with Syrian crisis.\n\nThe internal consistency of these factors was evaluated using the alpha Cronbach test.\n\nWithin the questionnaire, 27 items were phrased negatively requiring reverse scoring to maintain consistency in the directional interpretation across both positive and negative items.\n\nA Likert five-point scale was used with the scale representing: 5: Strongly Agree, 4: Agree, 3: Neutral, 2: Disagree, 1: Strongly Disagree. The results, presented in Table 1, were interpreted to assess the influence of each factor on academic achievements weaknesses.\n\nIn the qualitative phase, twelve questions were designed for interviewing pharmacy students. These questions were designed to elicit precise responses regarding the factors affecting the academic achievement of pharmacy students in Syrian universities.\n\nData were collected through face-to-face interviews conducted at the participants’ workplaces. The interviews were conducted, transcribed, and coded by the principal investigator (M.Q) and lasted 30-40 minutes on average. A comprehensive SWOT analysis was carried out to evaluate the strengths, weaknesses, opportunities, and threats present among pharmacy student,17 aiming to identify both the advantages and disadvantages and their impact on academic achievement.\n\nData in the quantitative phase were analyzed using Statistical Package for Social Sciences version 26.0 (SPSS 26) (IBM Corp. Released 2019. IBM SPSS Statistics for Windows, Version 26.0. Armonk, NY: IBM Corp).18 It is confirmed that a valid copyright license for the use of SPSS version 26.0 has been obtained. Microsoft Excel may be used as an open-access alternative. Descriptive statistics were applied to compute means, frequencies and percentages for the responses to the questionnaire items. To measure the reliability of the questionnaire, Cronbach’s alpha coefficient was employed.\n\nThe interviews in the qualitative phase were transcribed verbatim, and were analyzed using thematic content analysis.\n\nThematic analysis of the detailed interview notes was performed using open coding to identify key concepts, which were then organized into emerging themes.\n\n\nResults\n\nDemographic characteristics of the participating students\n\nThe questionnaire was completed by a total of 1008 pharmacy students, with 773 females and 235 males. The percentage of female pharmacy students constituted (77%) of the total sample size, while the percentage of male students was (23%), which reflects the female-to-male proportion in pharmacy faculties in Syria.\n\nThere were 127 (12.6%) second-year students, 271 (26.9%) third-year students, and 243 (24.1%) fourth-year students. The highest proportion of students was in the fifth year, with 367 (36.4%) of the total sample. Data were collected from 23 Syrian Universities, consisting of 6 public universities, and 17 private universities. The number of participating students from public universities was 499 (49.5%), while 509 (50.5%) students, representing private universities of the total sample.\n\nDescriptive statistics\n\nTable 2 summarizes the results of the descriptive analysis.\n\n* Scoring was reversed for negative statements.\n\nThe weighted mean for factors related to the students was 3.17.\n\nThe statement 3“I receive sufficient support from my family in my studies” had the highest mean at 4.23.\n\nMajority of students 60.3% agreed that their social life is good “My social life is good” with 608 students selecting this option. The mean for this statement was 3.91.\n\nHowever, the statement 2“My admission to the pharmacy faculty was in accordance with my parents’ wishes” had the highest mean among negative statements at 3.36, with 470 respondents selecting the option “disagree”.\n\nIn contrast, the statement 8“I find it difficult to study regularly” had the lowest mean of 2.00, with 45.7% agreeing and 32.6% strongly agreeing.\n\nThe weighted mean for the factors related to the lecturer was 3.06.\n\nThe statement 16“The lecturers attend regularly and are absent only for compelling reasons” had the highest mean at 4.19, with 51.8% agreeing and 35.5% strongly agreeing. Majority 62.4% agreed that the lecturer responds to students’ questions during lectures, with a mean of 3.89. (Statement 14).\n\nThe statement 18“The lecturer uses traditional teaching methods” had the lowest mean at 2.01, with 37.8% agreeing and 34.9% strongly agreeing.\n\nNegative responses were highest for the statement 13“There is sufficient motivation from the lecturers” 43.2% and second highest 35.6% for statement 11“The lecturer provides me with suitable and effective learning opportunities”.\n\nThe weighted mean for factors related to educational environment was equal to 2.50. The statement 24“Some practical courses are taught purely theoretically manner” had the lowest mean at 1.49. Similarly, “The curriculum in the pharmacy faculty lacks modernity” has a mean of 1.92.\n\nFindings indicated a strong agreement that teaching in the pharmacy faculties is teacher centered.\n\nThe statement 28“The educational process is student-centered” received disagreement from 31.3% of the sample responded.\n\nThe weighted mean of the factors related to the Exams was 3.06.\n\nWhen asked about exam-related anxiety in the statement 34“During exams, I feel extreme stress”, 40.7% of students agreed, and 27.5% strongly agreed, with a mean of 2.18.\n\nFor the statement 35“I feel anxious when I have to prepare for exams”, 48.4% agreed, and 28% strongly agreed, resulting in a mean of 2.05. And the statement 38“Exams in the pharmacy faculty only measure the student’s memorization ability” where the mean for both statements was 2.05, the lowest in this section.\n\nThe statement 37“I strive in my studies to achieve excellent grades, not just success” had the highest mean among all the statements in this section 3.85, with 35.9% agreeing and 31.9% strongly agreeing.\n\nThe weighted mean was equal to (1.96). In the statement 42“The electricity crisis hinders my learning process” the sample individuals who agreeing was 43.6%, and the percentage who strongly agreeing was 38.7%, and the mean for this statement was 1.87.\n\nSimilarly, in the statement 43“There are transportation difficulties to and from the university” the mean for this statement was 1.83, and the students strongly agreeing with 45.8%, and agreeing with 34.7%. It is worth mentioning that public and not private universities are located in the center of the cities in Syria.\n\nThe responses “strongly agree” and “agree” dominated most of the statements in this section, except for the statement 45“The war had a negative psychological impact on my academic achievement” where the highest percentage of responses was “neutral” at 29.3%, with a mean of 2.40.\n\nTable 3 indicates results of the Cronbach’s alpha coefficient for each of the study variables. Cronbach’s Alpha value for all the statements was 0.892, which is considered as “good”.\n\nThe number of participating pharmacy students in the interviews was 30, with 17 female students and 13 male students, where 9 students from public universities, and 21 students from private universities.\n\nSatisfaction with academic achievement: A significant number of students (18 students) expressed their dissatisfaction with their academic achievement. [Now, I am at the end of my journey in the faculty before graduation, and when I look back at my academic status, I feel disappointed with what I have accomplished].\n\nSome students agreed on their dissatisfaction with their academic achievement despite having a good cumulative GPA. [Answering this question may be deceiving to the students themselves and others. It is easy to say that I feel satisfied with my academic achievement based on my cumulative GPA in university. However, I feel fearful of the post-graduate stage and lack confidence in my readiness to enter the workforce].\n\nOn the other hand, (8 students) expressed satisfaction with their academic achievement. [My self-satisfaction with my academic achievement is very good, considering the circumstances we have gone through and continue to experience during our study period, in addition to the available resources and opportunities at this stage].\n\nSome other students, specifically four students, expressed that they do not have a clear feeling toward their academic achievement. [I cannot say that my academic achievement is bad after all these years in the faculty, but it is also not excellent].\n\nMotivation: Some students mentioned that their main motivation to achieve good academic performance in the faculty is the ambition to pursue post-graduate studies after graduation. Therefore, maintaining motivation without any slack was crucial, and most of them emphasized the importance of self-motivation in achieving good academic success. [When a student has a goal they aspire to reach they will remain in a state of continuous pursuit until they achieve what they desire].\n\nTwo students emphasized the significant benefits derived from the “peer learning” system in maintaining their motivation towards learning. [Regular studying with peers is the best way to avoid boredom and the monotony of studying. Through this method, students can maintain their motivation].\n\nSome of students pointed out the absence of academic guidance within the faculty, which is considered an important pillar in the success of the educational process.\n\nThe majority of responses focused on seeking assistance through various means, such as consulting professors or reaching out to students from previous batches. [In every obstacle we faced in the faculty, we would turn to previous students to see how they have dealt with it].\n\nAnother method for seeking help was peers, as some students mentioned benefiting from “peer learning” when confronted with academic challenges. [I seek assistance from my peers by regularly meeting and studying together for subjects that we find difficult. We use group discussions to exchange ideas and opinions].\n\nTime management: In response to the question regarding time management between classes and exam preparation during the semester, the answers varied significantly depending on the university, particularly due to the differences in the exam systems between public and private universities in Syria.\n\nRegarding public university students, there was consensus in the answers about the lack of regularity in studying and preparing for exams throughout the semester. They mentioned that the exam preparation usually starts during the designated exam break at the university. [I always prefer to postpone studying for exams until the exam break because I find it sufficient. Preparing for the subjects throughout the semester would be exhausting].\n\nAs for the participating students from private universities (21 students), the majority did not deny their inability to manage their time effectively despite their commitment to studying. The answers revealed differences in methods of preparation and studying for subjects during the semester, but all of them agreed on striving throughout the semester. [I try to allocate the majority of my time for studying and exam preparation. I also set aside a small portion of time each day to study the given lessons to avoid accumulation. However, there is still a lack of ability to manage time effectively due to the constant pressure].\n\nExam preparation strategies: The disparities in responses among public and private university students persisted, accompanied by varying study strategies influenced by the exam system within each university.\n\nSome students indicated in their answers the “peer learning” system. [I prefer studying regularly with some of my friends in faculty. We divide the topics among ourselves, share ideas, and summarize them so that they are ready for the exam period].\n\nAnother group mentioned that they do not give exams significant importance in their study of the subject matter, as much as they focus on the relevance and usefulness of the information in their future careers. [Once you study the lectures as soon as you receive them, you can understand and memorize them at the same time. Therefore, studying with the aim of understanding the subject matter and using it practically in the future is considered studying and preparing for the exam].\n\nBalancing responsibilities: The majority of students emphasized the prioritization of academic responsibilities, indicating their consistent efforts to establish their priorities with a focus on learning. [I always strive to prioritize my commitments around learning and allocate a significant amount of time for it. Often, I defer less significant activities for later].\n\nFurthermore, the students discussed the negative impact of working while studying on academic performance, noting that many students resort to employment due to adverse economic conditions in Syria. [My concentration was solely on learning, without pursuing employment or engaging in extracurricular activities. However, I started working due to the poor economic conditions, and I cannot deny that work has had a negative impact on my academic performance].\n\nParticipants were asked about their strengths, weaknesses, opportunities, and threats, aiming to explore the internal and external factors that might affect their academic achievement.\n\nStrengths and weaknesses: Regarding strength factors, many students mentioned their ability to comprehend scientific material well and excel in university exams. [One of my strengths is stepping out of the receiver’s circle and relying on research and investigation of each topic, studying references and international books, and comparing the scientific material with what is offered to pharmacy students worldwide].\n\nAnother student who considered time management as a strength point stated, [Properly managing my time helps me increase productivity, focus, and achieve set goals, positively impacting my academic performance and success].\n\nSome students emphasized the significance of reading scientific research papers to improve academic achievement, [It can help students to enhance their understanding of the subject matter, increases concentration and attention levels, and strengthens research, analysis, and critical thinking skills].\n\nHowever, when it comes to weaknesses, factors such as time management emerged as prominent challenges. [I struggle with delaying tasks and often succumb to laziness].\n\nAnother weakness highlighted was difficulty in maintaining focus during lectures. [Lack of concentration while attending lectures is a major weakness for me].\n\nAdditionally, some students expressed their concern about exam-related anxiety and its negative impact on their academic performance. [Anxiety during exams affects my memory and prevents me from properly recalling information and concepts, resulting in low grades].\n\nOpportunities and Threats: Regarding opportunities, participants in the interviews highlighted the importance of technology in providing pharmaceutical information quickly and efficiently. [I use the internet to search within reliable scientific pages and global academic references to access accurate information that improves my understanding of scientific material].\n\nThe role of lecturers in providing suitable and effective learning opportunities for pharmacy students was emphasized. Lecturers who possess good teaching and learning skills can motivate students and enhance their learning experience. However, some students expressed dissatisfaction with the teaching methods employed within the faculty. [There is no doubt that lecturers in the faculty of pharmacy possess knowledge and good teaching skills, but at the same time, they are constrained within one method, and the educational process is teacher-centered].\n\nMoreover, the economic crisis faced by the country was mentioned by most students as an external factor that significantly affects students’ academic achievements. Additionally, the educational environment and its role in influencing students’ academic performance were discussed. [Laboratories in pharmacy faculties were considered a fundamental aspect of the educational process that needs to be well-equipped].\n\nThe curriculum was a topic discussed in many responses, emphasizing its importance in students’ academic achievements. [The current curriculum leads students to study great amount of information that are sometimes repetitive, which is challenging in achieving good academic performance].\n\nTable 4 presents the findings of the participants in the interviews, according to the SWOT analysis.\n\n\n\n• Time management skills.\n\n• Motivation for excellence.\n\n• Proficiency in scientific subjects.\n\n• Active participation with the lecturer.\n\n• Reading and conducting research.\n\n\n\n• Ineffective time management.\n\n• Exam-related anxiety.\n\n• Lack of focusing during lectures.\n\n• Not achieving satisfactory grades despite regular studying.\n\n\n\n• Family support.\n\n• Utilization of technological tools in learning.\n\n• Lecturers with effective teaching and learning skills.\n\n\n\n• Challenges related to the Syrian Crisis.\n\n• Problems in Pharmacy curriculum design.\n\n• Learning is teacher-centered.\n\n• Deficiency of the educational environment.\n\nThe participants were asked about their current goals for improving their academic performance and how they plan to leverage academic achievements to fulfill future objectives.\n\nCurrent goals: The responses were correlated with the answers to the questions regarding strengths and weaknesses in academic performance.\n\nStudents who struggle with time management expressed their aspirations to improve their time management skills.\n\nSome students also indicated that their main goal each semester is to improve their cumulative GPA. [I know that the cumulative GPA is not the sole measure of academic achievement, but I see it as an important indicator of my academic performance, and I aspire to improve it].\n\nAmong the 30 responses, there were 12 answers that identified training in a pharmacy as a primary goal to be achieved during the year. These students have a moderate to good academic level. Additionally, 8 students mentioned that their main goal for the year is to develop their skills in scientific research, reading a good amount of pharmaceutical research papers to increase their scientific knowledge and improve their academic achievement.\n\nFuture goals: Most of the answers were related to the goal of achieving high academic achievement is to continue learning in postgraduate studies or to obtain scholarships after graduation. [After completing my years at the faculty of Pharmacy, I aspire to obtain a scholarship, and continue my academic pursuit of learning].\n\nThe importance of academic achievement in obtaining good job opportunities was also discussed. [Today, the number of pharmacy faculty graduates is very high, and in order to secure a good job opportunity in the field of pharmacy, you need to have an advantage over other students, and that can be achieved through high academic achievements].\n\n\nDiscussion\n\nIn medical education, mixed-methods research is ideal for advancing theoretical frameworks, and contributing significantly to enhancement of learning.19\n\nThis mixed-methods research study employed quantitative surveys and qualitative interviews to explore the factors affecting the academic achievement of pharmacy students in Syrian public and private universities.\n\nThe value of Cronbach’s alpha in the quantitative phase which were considered as good (0.892) provided evidence about the reliability of the applied 5-point Likert scale.20\n\nIn the qualitative phase, thematic analysis was selected for this study due to its accessibility and flexibility, as it offers a structured approach to coding and analyzing qualitative data while allowing link to broader theoretical or conceptual aspects.21\n\nIn this study, SWOT analysis framework was utilized to assess their own strengths, weaknesses, opportunities, and threats in order to plan their academic journey effectively.22 Furthermore, SWOT strategies help educational leaders in realizing their plans and identifying effective approaches to overcome potential barriers.23\n\nThe findings obtained from students both quantitatively and qualitatively, highlighted a common issue of ineffective time management skills identified as a major weakness negatively impacting their academic achievement.\n\nConversely, students who demonstrated effective time management skills acknowledged the positive impact of this skill on academic performance.\n\nThis study concluded that students’ motivation toward learning is a crucial factor in improving academic performance. It was found that lack of motivation from professors was prevalent among students, with self-motivation playing a more significant role.\n\nAdditionally, family support was identified as another important factor influencing students’ motivation towards learning and improving academic achievement.\n\nPrevious studies have indicated the influence of exams on academic performance.4,8,12 In this study, exam-related anxiety and exam competence have emerged as factors that contribute to the academic weaknesses observed among pharmacy students and their correlation with academic achievement.\n\nFindings of this research indicate that studying strategy of pharmacy students in Syria is linked to the type of educational system (public or private) in Syrian universities. Factors such as lack of persistence in learning and postponing academic tasks were noted as contributors to decreased academic achievement.\n\nStudents expressed concerns about mentors lack of attention to their educational challenges and suggested that strengthening academic counseling within pharmacy faculty could be a viable solution.\n\nWhile students generally praised professors for their teaching skills, and commitment to attendance, they felt that the provision of suitable and effective learning opportunities by professors was lacking. The students perceived the educational environment in pharmacy faculties as teacher-centered, which they believed hinders the learning process and affects the academic performance negatively.\n\nOther studies have addressed peer learning and its role in enhancing academic performance.5 In this study, some students favored the peer learning system for enhancing student motivation and addressing academic challenges within the faculty.\n\nThis study highlighted issues affecting the academic achievement of pharmacy students in Syrian universities. Problems in curriculum design, lack of skill development and unclear program objective were identified.\n\nThe pharmacy curricula mainly focus on knowledge acquisition, neglecting skill development and competency building. Repetitive information, theoretical teaching methods and limited practical training were noted.\n\nStudents addressed the negative impact of poorly equipped classrooms and laboratories on academic performance.\n\nStudents recognized the importance of utilizing technological tools to improve academic achievement with the internet research being a frequent practice. This finding aligns with a previous study, where students acknowledged the significance of employing technological tools to enhance academic performance.24\n\nThe findings were consistent with previous findings which reported that academic performance of students is influenced by external factors such as insufficient resources, and socioeconomic factors.25 The Syrian crisis, including economic, social, and psychological challenges, negatively affected academic achievement of pharmacy students with electricity and transportation crises hindering the learning process.\n\nStudents expressed motivation towards achieving high academic performance, aiming to continue learning after graduation and pursue applying for scholarships.\n\nDifferences in the educational systems, evaluation methods, and sources of motivation posed challenges in accurately measuring student motivation and study strategy.\n\nPublic and private universities’ grading systems varied, impacting the study’ outcome. The students participating in the questionnaire and the interview were not asked about their cumulative GPA, due to the difference in the system for calculating student grades between public and private universities. Private universities rely on the student’s cumulative GPA to evaluate them, while public universities adopt the final grades system and presented as a percentage.\n\nThe difference in sources of motivation between internal motivation, which comes from the student himself, and external motivation, which the student obtains through family, teachers, and peers, and the difference in the reasons motivating the student towards the learning process between each student and another, has caused difficulty in measuring Motivation accurately.\n\n\nConclusion\n\nThe results of the mixed-methods study indicated that personal factors related to time management and motivation towards learning have an impact on academic achievement. Exams-related anxiety, as well as the Syrian crisis also play a significant role in weakening academic achievement. Furthermore, factors related to lecturers, learning methods, and the educational environment all have an influence on the academic achievement of pharmacy students in Syrian universities.\n\nEthical approval for this study was obtained from the Ethical Committee of the Syrian Virtual University (Approval Number: 233/o, Date: 13/2/2023). This study adheres to the ethical principles outlined in the Declaration of Helsinki.\n\nInformed, written consent was obtained from all participants prior to completing the survey forms in the quantitative phase, and verbal consent was recorded before conducting the interviews in the qualitative phase. Participants’ information and data were treated with strict confidentiality, ensuring that personal details were anonymized. The collected data were securely stored on a password-protected computer, and measures were taken to dispose of the data appropriately once it was no longer needed.\n\nThe decision to use verbal consent instead of written consent in the interviews was approved by the ethics committee based on the following reasons:\n\nEnhanced participant comfort and flexibility: Verbal consent was considered more comfortable for participants and provided greater flexibility in the study participation process, as they were not required to sign a written document.\n\nPreservation of participant anonymity: Obtaining verbal consent was the preferred option to maintain participant anonymity and minimize potential risks associated with written documentation.\n\nThe use of verbal consent was ethically approved by the committee, and all necessary precautions were taken to ensure the confidentiality and protection of participants’ rights.\n\nThe quantitative phase of the study was conducted and reported in accordance with the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines.15\n\nThe qualitative phase was designed and reported according to the Consolidated criteria for Reporting Qualitative research (COREQ).16", "appendix": "Data availability\n\nMendeley Data: “Enhancing Academic Success: A mixed Study on the Influencing Factors among Pharmacy Students in Syrian Universities”. https://doi.org/10.17632/6r46mdszng.4. 26\n\nThis project contains the following underlying data:\n\nCOREQ.checklist.pdf\n\nEthical Approval.pdf\n\nResponses of Pharmacy Students to Questionnaire.csv\n\nQualitative Interviews.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nMendeley Data: STROBE checklist cross-sectional study of “Enhancing academic success: A mixed study on the influencing factors among pharmacy students in Syrian Universities”. https://doi.org/10.17632/5zm3vh5kn2.1. 15\n\nMendeley Data: COREQ checklist for “Enhancing Academic Success: A mixed Study on the Influencing Factors among Pharmacy Students in Syrian Universities”. https://doi.org/10.17632/k4f472b3pp.2. 16\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would thank all the participants in this study and the Syrian Virtual University.\n\n\nReferences\n\nAhmad A, Abulaban A, Al Shawwa L, et al.: Factors potentially influencing academic performance among medical students. AMEP. 2015 Jan; 65. Publisher Full Text\n\nFathelrahman AI, Alrobaian M, Altowayan WM, et al.: Pharmacy education in Saudi Arabia: Achievements and challenges during the last two decades with a focus on Taif University as a case study. Saudi Pharm. J. 2022 Jun; 30(6): 649–654. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlhurishi SA, Aljuraiban GS, Alshaikh FA, et al.: Predictors of students’ academic achievements in allied health professions at King Saud University: a retrospective cohort study. BMC Med. Educ. 2021 Feb 6; 21(1): 93. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAzmi N: Internal factors Affecting Academic Performance among Pharmacy Students in Malaysian Public Institutions of Higher Learning. Indian J. Pharm. Edu. Res. 2014; 48(3): 26–33. Publisher Full Text\n\nAbdulghani HM, Al-Drees AA, Khalil MS, et al.: What factors determine academic achievement in high achieving undergraduate medical students? A qualitative study. Med. Teach. 2014 Apr; 36 Suppl 1: S43–S48. PubMed Abstract \| Publisher Full Text\n\nMohd Shah I, Zamri N: Factors Influencing Academic Performance of Pharmacy Students at Universiti Teknologi MARA (UiTM) Selangor Malaysia. IJPNaCS. 2021 Jun 30; 3: 13–27. Publisher Full Text\n\nHayat AA, Salehi A, Kojuri J: Medical student’s academic performance: The role of academic emotions and motivation. J. Adv. Med. Educ. Prof. 2018 Oct; 6(4): 168–175. PubMed Abstract\n\nSansgiry SS, Bhosle M, Sail K: Factors That Affect Academic Performance Among Pharmacy Students. Am. J. Pharm. Educ. 2006 Oct 15; 70(5): 104. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGokalp M: The Effect of Students’ Learning Styles to Their Academic Success. Creat. Educ. 2013 Sep 7; 04(10): 627–632. Publisher Full Text\n\nPai PG, Menezes V, Srikanth, Subramanian AM, et al.: Medical Students’ Perception of Their Educational Environment. J. Clin. Diagn. Res. 2014 Jan; 8(1): 103–107. PubMed Abstract \| Publisher Full Text\n\nSingh HK, Lyons KM, Brock TP, et al.: Effect of a curriculum transformation on pharmacy student self-efficacy, self-reported activities, and satisfaction in degree and career choice. BMC Med. Educ. 2023 May 2; 23(1): 304. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSariem C, Fwangshak F, Shalkur D, et al.: Factors affecting academic performance of Pharmacy students in the University of Jos, Nigeria. J. Pharmacokinet. Biopharm. 2015 Jan 15; 11(2): 85. Publisher Full Text\n\nSouliman M, Dashash M: Reasons for Failure to Change Syrian Medical Curricula: A Qualitative Descriptive Study. Am. J. Health Res. 2023; 63: 03.\n\nLatifeh Y, Dashash M: A Critical Analysis and a Suggested Reform of Psychiatric Curricula in Medical Faculties During Syrian Crisis. Am. J. Health Res. 2016 Jan 1; 4: 12–18.\n\nQattan M, Dashash M, Malek ZS: STROBE checklist cross-sectional study of Enhancing academic success: A mixed study on the influencing factors among pharmacy students in Syrian Universities.2024 Jul 15 [cited 2024 Jul 17]; 1. Publisher Full Text\n\nQattan M, Dashash M, Malek ZS: COREQ checklist for Enhancing Academic Success: A mixed Study on the Influencing Factors among Pharmacy Students in Syrian Universities.2024 Jul 22 [cited 2024 Jul 23]; 2. Publisher Full Text\n\nAlmeman AA: Strategic analysis of clinical pharmacy education in Saudi Arabia. Trop. J. Pharm. Res. 2020 Nov 16; 19(6): 1303–1311. Publisher Full Text\n\nIBM SPSS Statistics: [cited 2024 Jul 17]. Reference Source\n\nLavelle E, Vuk J, Barber C: Twelve tips for getting started using mixed methods in medical education research. Med. Teach. 2013 Apr; 35(4): 272–276. PubMed Abstract \| Publisher Full Text\n\nTaber KS: (PDF) The Use of Cronbach’s Alpha When Developing and Reporting Research Instruments in Science Education.2017 [cited 2023 Dec 17]. Reference Source\n\nBraun V, Clarke V: Thematic analysis.2012; 57–71.\n\nBenzaghta MA, Elwalda A, Mousa M, et al.: SWOT analysis applications: An integrative literature review. JGBI. 2021 Mar; 6(1): 55–73. Publisher Full Text\n\nTopor DR, Dickey C, Stonestreet L, et al.: Interprofessional Health Care Education at Academic Medical Centers: Using a SWOT Analysis to Develop and Implement Programming. MedEdPORTAL. 2018 Oct 19; 14: 10766. Publisher Full Text\n\nLatifeh Y, Alkhatib Y, Hmidouch M, et al.: Prevalence of internet addiction among Syrian undergraduate medical students. Medicine (Baltimore). 2022 Dec 9; 101(49): e32261. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlshammari F, Saguban R, Pasay-an E, et al.: Factors affecting the academic performance of student nurses: A cross-sectional study. J. Nurs. Educ. Pract. 2017 Sep 11; 8: 60. Publisher Full Text\n\nQattan M, Dashash M, Malek ZS: Enhancing Academic Success: A mixed Study on the Influencing Factors among Pharmacy Students in Syrian Universities.2024 Jul 22 [cited 2024 Jul 23]; 4. Publisher Full Text\n\nZotero\|Downloads: [cited 2024 Jul 17]. Reference Source" }	[ { "id": "310497", "date": "23 Aug 2024", "name": "Leah Li Echiverri", "expertise": [ "Reviewer Expertise Curriculum and Instruction", "Teaching and Learning", "Artificial Intelligence Integration", "Faculty Training and Development", "English as a Second Language (ESL)", "English as Foreign language (EFL)", "Student Learning", "Student Satisfaction/Motivation", "Academic Performance" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nObservation: Based on Table 1, the result interpretation for the weighted mean in assigning values is somewhat counterintuitive because typically, a higher score (e.g., 4.21 to 5) on a Likert scale would indicate a stronger positive agreement or influence. However, in this table, the highest weighted mean range (4.21 to 5) is interpreted as \"Very Uninfluential,\" which contrasts with the usual interpretation of \"Strongly Agree\" as having a strong positive influence. Comment 1: The scale seems to be reversed or designed for a specific context where disagreement with a statement corresponds to a positive influence, and agreement corresponds to a negative influence. If this scale is applied to positive statements, it may confuse readers or participants because the typical expectation is that \"Strongly Agree\" correlates with a strong positive impact.\nFurthermore, if you apply this table's interpretation to a reversed scale for negative statements, the results could become misleading. A lower score (indicating agreement with a negative statement), such as item 8 for example, would be interpreted as \"Influential\" using this table, but normally, agreement with a negative statement should be seen negatively.\nThe reversed scale in the table creates a significant shift in how results are interpreted. If using this table, it's essential to clearly explain the reversal and how it impacts the interpretation, especially when dealing with reversed scoring for negative statements. Otherwise, it could lead to confusion and misinterpretation of the data.\nComment 2: Based on the quantitative and qualitative findings, provide recommendations for enhancing academic success with a focus on areas that need improvement (particularly those items with low means.)\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "12492", "date": "11 Oct 2024", "name": "Mohab Qattan", "role": "Author Response", "response": "Dear reviewer Leah Li Echiverri Thank you very much for your detailed review and valuable comments. We apologize for the delayed response, as we were awaiting the second review report requested by the journal's editorial team. Observation: Based on Table 1, the result interpretation for the weighted mean in assigning values is somewhat counterintuitive because typically, a higher score (e.g., 4.21 to 5) on a Likert scale would indicate a stronger positive agreement or influence. However, in this table, the highest weighted mean range (4.21 to 5) is interpreted as \"Very Uninfluential,\" which contrasts with the usual interpretation of \"Strongly Agree\" as having a strong positive influence. Comment 1: The scale seems to be reversed or designed for a specific context where disagreement with a statement corresponds to a positive influence, and agreement corresponds to a negative influence. If this scale is applied to positive statements, it may confuse readers or participants because the typical expectation is that \"Strongly Agree\" correlates with a strong positive impact. Furthermore, if you apply this table's interpretation to a reversed scale for negative statements, the results could become misleading. A lower score (indicating agreement with a negative statement), such as item 8 for example, would be interpreted as \"Influential\" using this table, but normally, agreement with a negative statement should be seen negatively. The reversed scale in the table creates a significant shift in how results are interpreted. If using this table, it's essential to clearly explain the reversal and how it impacts the interpretation, especially when dealing with reversed scoring for negative statements. Otherwise, it could lead to confusion and misinterpretation of the data. Regarding your observations, I would like to clarify the interpretation of the results and the data presented in Table 1. The inclusion of both positive and negative statements in the scale was intentional to prevent bias in participant responses. The interpretation was based on the question: \"What are the factors that contribute to weaknesses in academic achievement?\" For example, a positive statement such as \"I receive sufficient support from my family in my studies\" elicited responses predominantly in agreement, which indicated that this factor was perceived as very uninfluential on academic weakness. Conversely, for a statement like \"I have the ability to manage my time well,\" responses tended towards disagreement, suggesting that this factor was influential in contributing to academic weakness. This design enabled us to assess both positive and negative influences on academic weakness, rather than on overall academic achievement. We acknowledge that the reversal of scoring might be unconventional, and we have provided a more detailed explanation of the reverse scaling in the manuscript to ensure a clear understanding of how this impacts data interpretation. Our aim was to offer a balanced assessment of factors impacting academic achievement by focusing on their contribution to academic weaknesses. Thank you again for your valuable feedback, which helped us improve the clarity and depth of our study. Comment 2: Based on the quantitative and qualitative findings, provide recommendations for enhancing academic success with a focus on areas that need improvement (particularly those items with low means.) Thank you for your insightful comment and guidance. Your feedback was truly appreciated, and recommendations were formulated based on your guidance." } ] }, { "id": "315175", "date": "09 Sep 2024", "name": "Naeem Mubarak", "expertise": [ "Reviewer Expertise pharmacy practice and policy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nEnhancing Academic Success: A mixed Study on the Influencing Factors among Pharmacy Students in Syrian Universities Verdict: Minor Revision Thank you for providing me the opportunity to review this interesting read. The study explores the factors associated with academic success among pharmacy students in Syrian universities. The study addresses a crucial topic with depth and detail, however, following are some recommendations to further improve the impact of the study. Introduction\nDescribe what constitutes academic achievement in context to the objectives of your study The introduction should focus on the various aspects and factors that influence academic achievement in Syrian universities. It is essential to emphasize why pharmacy students were specifically chosen for this study. To strengthen the evidence regarding the factors affecting the academic progress of pharmacy students across different continents, the authors may consider citing the following study (This is optional and should only be taken as a suggestion for the improvement of the manuscript) Elnaem MH.et.al.,2024 (Ref 1)\nMethodology\nWas there any inclusion/ exclusion criteria with respect to the recruitment of students, public and private universities, geographical limitations of data collection etc?\n\nWhy first year pharmacy students were not made part of the study as their academic progress and achievement were highly influenced by the factors explored under the study which could have resulted in robust data collection. Please justify What was the targeted sample size and response rate achieved during the data collection? \"Additionally, three academic members reviewed the questionnaire to assess its clarity and relevance of the statements in alignment with the study’s aims\" The authors should mention the criteria chosen for the selection of experts for content and face validity. How the questionnaire was modified after the idea generation phase? How many statements were added/deleted and modified? The result interpretation for the five point likert scale in Table 1 creates confusion especially while analyzing the reverse coded items. How can the authors reach to this interpretation of the extent of influence without establishing a correlation of the factors with the academic achievement\nDiscussion The discussion appears as the repetition of the findings. More concrete synthesis of the findings are needed to evaluate the findings. Comparison with the existing literature and studies in other low and middle income countries would establish the profound impact of the study. You may cite the following updated references. (This is optional and should only be taken as a suggestion for the improvement of the manuscript) Elnaem MH.et.al.,2023 (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? 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": "12496", "date": "11 Oct 2024", "name": "Mohab Qattan", "role": "Author Response", "response": "Dear reviewer Naeem Mubarak Thank you for your thorough review of our manuscript. We are grateful for the time and effort you have dedicated to providing constructive feedback. We would like to assure you that each comment will be addressed point by point. Your insights are invaluable, and we are committed to incorporating your suggestions to enhance the overall quality of the research. Introduction Describe what constitutes academic achievement in context to the objectives of your study Thank you for your valuable feedback. We acknowledge the importance of clearly defining academic achievement in the context of our study's objectives. In our revised manuscript, we have provided a detailed explanation of how academic achievement is operationally defined, specifically as it relates to the performance of pharmacy students. This definition focuses not only on exam results but also on factors such as student engagement, the ability to apply knowledge in practical settings, and overall progression through their academic programs. The introduction should focus on the various aspects and factors that influence academic achievement in Syrian universities. It is essential to emphasize why pharmacy students were specifically chosen for this study. To strengthen the evidence regarding the factors affecting the academic progress of pharmacy students across different continents, the authors may consider citing the following study (This is optional and should only be taken as a suggestion for the improvement of the manuscript) Elnaem MH.et.al.,2024 (Ref 1) We appreciate your suggestion to provide further emphasis on the factors influencing academic achievement in Syrian universities and the rationale for focusing on pharmacy students. In the revised introduction, we have expanded the discussion to highlight the unique challenges faced by pharmacy students in Syria. We also added a justification for selecting pharmacy students. Additionally, we considered your recommendation and cited the study by Elnaem MH.et.al.,2024 (Ref 1) to offer a broader perspective on the academic progress of pharmacy students across different regions. Methodology Was there any inclusion/ exclusion criteria with respect to the recruitment of students, public and private universities, geographical limitations of data collection etc? Thank you for highlighting this point. In our revised methodology section, we have clarified the inclusion and exclusion criteria for the recruitment of participants. Specifically, pharmacy students from both public and private universities were included to ensure a representative sample across different educational systems. Geographical limitations were minimal, as students from universities across various regions in Syria were invited to participate, ensuring diverse input. Why first year pharmacy students were not made part of the study as their academic progress and achievement were highly influenced by the factors explored under the study which could have resulted in robust data collection. Please justify We appreciate your observation regarding the exclusion of first-year pharmacy students. The decision to exclude these students was deliberate, as the first academic year in Syria, particularly at universities such as Damascus University, is commonly referred to as the \"preparatory year.\" During this year, students are not fully committed to a specific faculty, as they can choose to enter Medicine, Dentistry, or Pharmacy at the end of the year based on their academic grades. Since first-year students have not yet made a firm decision regarding their specialization, their academic progress does not fully reflect the dynamics of pharmacy education. Additionally, the decision was based on the assumption that first-year students may not have had enough exposure to the full range of factors affecting academic achievement, such as exam-related anxiety or curriculum structure, which become more prominent in the later stages of study. In summary, while recognizing the potential insights that could be gained from including first-year students, the exclusion was made to maintain the study’s focus and ensure a more comprehensive understanding of academic achievement factors among students who are fully immersed in pharmacy education. What was the targeted sample size and response rate achieved during the data collection? Thank you for your valuable observation. We have added the information regarding the targeted sample size and the response rate in the revised version of the manuscript. \"Additionally, three academic members reviewed the questionnaire to assess its clarity and relevance of the statements in alignment with the study’s aims\" The authors should mention the criteria chosen for the selection of experts for content and face validity. Thank you for your insightful feedback. We have now clarified the criteria for the selection of the experts who reviewed the questionnaire in the revised version of the manuscript. How the questionnaire was modified after the idea generation phase? How many statements were added/deleted and modified? Thank you for pointing out the need for further clarification. After the idea generation phase, the questionnaire underwent a series of modifications based on feedback from the expert reviewers. Initially, the questionnaire contained 52 items. Following the review process, 6 items were removed due to redundancy and lack of clarity, while additional 2 items were added to better address the educational environment and exam factors, bringing the final number of items to 48. Several other items were modified to enhance clarity and ensure that the statements were fully aligned with the study’s objectives. These changes were made to improve the overall validity and reliability of the questionnaire. In the revised manuscript, we have elaborated on the modifications made to the questionnaire after the idea generation phase. The result interpretation for the five point likert scale in Table 1 creates confusion especially while analyzing the reverse coded items. How can the authors reach to this interpretation of the extent of influence without establishing a correlation of the factors with the academic achievement We appreciate your concerns regarding the interpretation of the five-point Likert scale, especially for reverse-coded items. In response, we have provided a more detailed explanation in the revised manuscript. We have clarified how reverse scaling was employed to prevent response bias, and we have addressed the importance of interpreting these items in relation to academic weakness rather than achievement. While we acknowledge that establishing direct correlations between factors and academic achievement would provide additional depth, this was beyond the scope of the current study, which focused on exploring perceived influences. Discussion The discussion appears as the repetition of the findings. More concrete synthesis of the findings are needed to evaluate the findings. Comparison with the existing literature and studies in other low and middle income countries would establish the profound impact of the study. You may cite the following updated references. (This is optional and should only be taken as a suggestion for the improvement of the manuscript) Elnaem MH.et.al.,2023 (Ref 2) Thank you for your valuable feedback. We appreciate your suggestion regarding the discussion section. In response, we have revised the discussion to provide a more concrete synthesis of the findings and included a comparison with relevant literature from studies conducted in other low- and middle-income countries. We have also incorporated the suggested reference by Elnaem MH et al., 2023, to strengthen the discussion and highlight the global relevance of our study’s findings." } ] } ]	1	https://f1000research.com/articles/13-868
https://f1000research.com/articles/13-28/v1	08 Jan 24	{ "type": "Study Protocol", "title": "Effectiveness of Play Therapy Programme in Promoting Early Child Development of under-5 Children visiting Tertiary Care Hospital in Rural Settings: Study Protocol of a Randomized Controlled Trial.", "authors": [ "Manoj Patil", "Abhay Gaidhane", "Zahiruddin Quazi", "Abhay Gaidhane", "Zahiruddin Quazi" ], "abstract": "Background Good care and conscious, mindful parenting are the essential requirements of the early childhood period. Good care in early childhood consists of mindful handling of children’s needs like hunger, care in sickness, socio-emotional needs, safety, love and affection. Good care promotes children’s development and provides a favourable environment for learning. It’s a well-known fact that hospitalization is a stressful situation for child of any age. Play is an integral part of early childhood period which is virtually restricted in hospital settings. This study will try to explore the effectiveness of play therapy delivered in hospital settings, on early child development.\n\nMethods This will be a randomized control trial conducted in the Paediatrics department of a tertiary care hospital in Wardha, India. The sample size will be 360 children, 180 each in intervention and control arm. The hospitalized children from intervention arm will receive customized Play Therapy sessions from trained research assistants and will be followed up at scheduled home visits for one year from the date of enrolment. All children will be assessed for changes in cognitive, motor and socio-emotional development scores. The differences in development scores between intervention and control groups will be compared and effect sizes of changes will be calculated.\n\nDiscussion Implementation of play stimulation activities have been reported as useful strategies for promoting child development and good recovery during hospitalization. This trial will attempt to explore the effectiveness of play therapy on changes in child development scores of children from intervention group compared to the control group. The customized play therapy program will be adapted to paediatric inpatient settings, and attempts will be made to improve the Play Therapy kit for hospitalized children.\n\nRegistration Clinical Trial Registry of India Registration No.: C.T.R.I./2022/03/041355, dated 24/03/2022. Protocol Version: v5 Dated 05/09/2023.", "keywords": [ "Early Child Development", "Play Therapy", "Hospitalization", "Parenting", "Socioemotional", "Assessment" ], "content": "Introduction\n\nThe early childhood period is crucial, usually defined as the period from birth to six years of age. Good care, love, affection, addressing the needs of hunger, safety, socio-emotional issues and care during sickness etc are essential aspects of conscious parenting that promote a positive environment during childhood. A favourable and positive environment during childhood is helpful in providing children the opportunities to learn and thrive. Right from birth, children get bonded to special adults and try to learn the important basic skills by copying them. The learnings from these relationships serve as a base for preparing the children for life skills.1 It was found that globally over 200 million children fail to reach their developmental potential in the first five years due to poverty, poor health services, poor nutrition, and lack of appropriate psycho-social care.2 Early childhood is a period of rapid development. Play and recreation are naturally an essential part of childhood and are vital to normal development. Through various types of play and recreational activities, children learn, try to express themselves, cope with anxiety, develop their skills and master the experiences. Play can also help learn how to adapt and tolerate the healthcare and hospitalization experience. In a sense, play and recreation mimic the therapy of allowing children to explore, process, and express their healthcare experiences in a safe and protected environment.3\n\nHospitalization is quite stressful for a child of any age. Even older children need their parents during a serious illness, and they cannot tolerate their absence even for a short period. They want their parents to be there when they need them and wish to be loved and missed. Play is an essential part of a child’s life and is key to fostering a child’s growth and development. Toys serve as the ‘tools’ of play and help to create a more ‘natural’ environment for a child. Selection and use of appropriate toys can help to reduce the traumatic effects of Hospitalization and healthcare experiences. It also aids in the speedy recovery from the illness. Play can be integral to the hospitalized child’s care and treatment plan. Play helps to support the child by offering the opportunity for creative expression, coping, and diversion. Several studies conducted in various hospitals provide evidence that a supervised play program can effectively provide a warm and child-friendly atmosphere that can help promote the child’s growth and development. In bigger hospitals and healthcare facilities, a childcare specialist can coordinate the play therapy program provided a proper play zone, suitable materials, and playmates are available. It is evident that, for any child, play is an effective way of learning, and play materials, toys, and equipment serve as the ’learning tools’.4\n\nIt’s a well-known fact that play is useful in accelerating the growth and development of children. In many Western countries, play therapy alleviates the stress experienced by paediatric patients and their families during hospitalization.5 Play constitutes an important parameter of a child’s normal development. Also, play serves as an important means of communication in childhood. Although, a child’s ability to play may be influenced by the child’s physical or mental disease. Play can prove to be of special therapeutic value for sick children. It can help to enhance their physical and emotional well-being. It can help to explore the issues related to the child’s experiences during hospitalization and can help to reduce the influence of negative feelings during hospitalization. Play, blended with the treatment plan, can be quite helpful in promoting the child’s growth, development, and life skills. Healthcare professionals can incorporate play as a part of treatment and care strategies for hospitalized children. The role and value of play are greater in the case of children with life-threatening diseases, disabilities, and vulnerable situations. Play therapy during Hospitalization can help to restore the child’s ability to play which was discontinued due to hospital admission. It can help to manage a child’s confidence that he can continue his/her normal life inside the hospital. With this understanding of play, healthcare professionals can explore the effects of Hospitalization and disease on children and enhance their emotional development. Through play, children can learn to gain control in different situations. Play can help to change the hospitalization experience into a positive experience. Appropriate activities must be chosen to help the children grow, encouraging the caregivers to bring the child’s favourite toys to the hospital and get actively involved in the procedure. Play promotes healing, improves coping potential, and helps tackle fears and express the children’s feelings. Hospitals should try to use play activities to reduce stress and convert the negative aspects of the hospital experiences into a positive experiences.6\n\nHospitalization plays a significant effect in a child’s life. Many children admitted to hospitals have complex healthcare needs, and some require highly technical interventions. According to the 2013 statistics by WHO, children under the age of five died from diseases like acute respiratory infections, birth asphyxia, diarrhoea, neonatal sepsis, injuries, congenital anomalies, and infant prematurity.7 Children hospitalized with the above diseases tend to have a traumatic experience at a hospital, such as in the long-run hospitalization tends to demonstrate negative psychological and behavioural response.8 Usually, the hospitals are focused more on physical recovery and mortality than the overall well-being of the child and her family.9 Children tend to perceive hospitals negatively, which impacts their physical and mental health. A study found that hospitalized children felt scared, bored, and alone.10 Children experience happiness, sadness, anger, and fear in the presence of a doctor and nurse.11 In another study, it was found that there was a reciprocal relationship between anxiety, blood pressure, and heart rate.12 It was also found that when children were asked to draw a person in a hospital, the drawings indicated anxiety. They drew pictures of people who were sad and dependent.13\n\nFurthermore, according to the parents, a child’s behaviour, function, and health before hospitalization and after hospitalization are significantly different. Children suffer from emotional distress three to five months after hospitalization and surgery, which is most common in the age range of one year to six years. Trauma that children face at the hospital has been termed Paediatric Trauma Mental Stress which is characterized by avoidance, re-experience of the event, and hyperarousal which arises from a major illness or medical Intervention that causes a threat to a child’s health and is considered to be intrusive, painful and alarming medical care. Children tend to internalize their problems and may have symptoms of depression and anxiety which further aggravates their illness.14 Certain risk factors are involved when children are hospitalized or undergo surgery. Some risk factors may be attributed to their age range, temperament, baseline anxiety, past medical encounters, and parents’ Level of anxiety. Children tend to suffer from anxiety while hospitalized due to uncertain treatment possibilities.15\n\nChildren, when hospitalized, tend to look for activities that can keep them calm. In some instances, they look toward their parents so that they can speak to them and look toward other children with whom they can play instead of getting bored. Some children found the hospital as a place where they can explore, learn and make new friends.10 Physical exercise, healing touch, music therapy, therapeutic massage, and health education have decreased cancer symptoms.16 Play activities that include art have also affected children’s overall health at the hospital. In the case of infants if their parents talk to them, massage them, make eye contact, sing to them or put objects at a closer distance and the infant grabs them, shows infants bold colours, or plays games like peek-a-boo or mimicking what the child is saying can soothe the child.2\n\nOther activities have also assisted in alleviating the symptoms of anxiety and pain. A study found that children prefer natural landscapes with calming colours over abstract paintings with bold colours. The realistic painting paved the way for positive physiological outcomes and was used for distraction, reducing pain perception.17 Reading also influences children’s well-being, and when caregivers read books to children when they are sick, children feel comfortable, and their emotional affiliation with the caregivers grows.18 Videoconferencing with the family has also assisted in reducing the stress of children.19 Surgical procedures can create anxiety in children as well as their parents. A study found that before the children went through surgery, the nurses taught them the procedures and outcome of the surgery. The nurses, as well as the children, re-demonstrated the procedure in dolls. Since they observed it, this reduced their anxiety and caregivers.17 When children above the age of four were educated about their health, they showed lower levels of anxiety than children younger than them. When play routine was introduced to hospitalized children, a lower cortisol level in their urine was indicated.20 Play activities can help in reducing the organic symptoms in children. The time spent at the hospital can also be shortened when children participate in activities related to play stimulation.\n\nAs per the census of 2011, India had a population of 121.1 crore (Cr), among which 16.45 Cr children were in the age group of 0-6 years, and 37.24 Cr belonged to the age group of 0-14 years, which constituted around 13.59% and 30.76% of the total population, respectively. 74% of the children aged 0-6 years reside in rural areas, whereas the rural population constitutes 69% of the total population of India.7 In India, the hospitalization rate of children aged 1-6 years is almost doubled due to common ailments like fever and diarrhoea. In contrast, hospitalization due to non-communicable diseases and injuries has also increased greatly over the last decade.8 The average length of hospital stays ranged between 6-15 days, depending on the type of ailment.9\n\nThe role and value of play are greater in the case of children with life-threatening diseases, disabilities, and vulnerable situations. Several diseases and conditions require the Hospitalization of children for weeks to a month. Play therapy during hospitalization can help to restore the child’s ability to play which was discontinued due to hospital admission. It can help to manage a child’s confidence that he can continue his/her normal life inside the hospital. With this understanding of play, healthcare professionals can explore the effects of Hospitalization and disease on children and enhance their emotional development.\n\nAcharya Vinoba Bhave Rural Hospital (A.V.B.R.H.) in Wardha is a tertiary care hospital of Datta Meghe Institute of Medical Sciences and catering to the healthcare needs of the rural population from five districts Wardha, Nagpur, Chandrapur, Yawatmal, and Amaravati. A.V.B.R.H. is a 1,500 bedded healthcare facility with a specialized Paediatric Department, dedicated Neonatal Intensive Care Unit, and Child Development Centre. This study will focus on developing a locally adapted Play Therapy Programme for hospitalized children, the sensitization of parents regarding child development, and developing a safe, harmless, and sterilizable Play Kit for hospitalized children to minimize the risk of transmission of infection from children to children or healthcare staff. An earlier preprint version of this article can be found on Research Square.21\n\nPrimary objectives:\n\n1. To improve the motor, language, cognitive, and social-emotional development parameters of under-five years children visiting A.V.B.R.H. through play therapy and follow-up at scheduled home visits.\n\n2. To enhance the knowledge and skills of parents on early child development and improve parent-child interactions.\n\nSecondary objectives:\n\n1. To assess the effectiveness of the dedicated Play Therapy Kit specially designed for hospitalized children, providing follow-up and assessment mechanisms through online mode.\n\nThis will be a randomized controlled exploratory trial. The study participants will be randomized into Intervention and Control groups with a 1:1 ratio using block randomization.\n\nThis study will be conducted at the Department of Paediatrics in Acharya Vinoba Bhave Rural Hospital, Wardha, and nearby villages within a 25 K.M. radius. Wardha is the smallest district in the Maharashtra State of India.\n\nInclusion criteria:\n\n1. Children admitted to the Paediatric Ward of A.V.B.R.H. aged six months to 60 months.\n\n2. Children from villages within 25 Km periphery of A.V.B.R.H.\n\n3. Parents consenting to the participation of their child in the Play Therapy Programme.\n\nExclusion criteria:\n\n1. Seriously sick, moribund children with life-threatening conditions.\n\n2. Children in Intensive Care treatment.\n\nThe Investigator will take written informed consent from the parents of the hospitalized children. The comparator (control) group will include children from the adjoining paediatric ward admitted during the period when interventions will not be implemented. Children from this group will receive all required treatment and nursing care except the Play therapy sessions. This will help to avoid any contamination. Baseline assessments and socio-demographic information of these children will be collected at enrolment. Follow-up home visits and assessments will be done at six months and 12 months from the date of enrolment. If successful, the children from control group will receive play therapy after the trial is over.\n\nThe children and their parents signing the informed consent will be enrolled in the study. All enrolled children hospitalized in A.V.B.R.H., scheduled to stay for a minimum of three days in the hospital, will be assigned a Unique ID. Children will be allocated to intervention or control groups using a block randomization process22,23 with age groups as the blocking variable. Intervention group will receive the play therapy sessions along with the required treatment and nursing care during hospitalization stay. Sociodemographic profile and baseline assessments will be done. Play therapy sessions will be conducted at the dedicated play area in hospital. Also, these children from the intervention area will receive the play sessions at scheduled monthly home visits. Figure 1 shows the Consort Flow Diagram of study participants.\n\nThe play therapy manual has been developed by the Principal Investigator with the activities specified as per the domains of child development including physical development, language and communication skills, socio-emotional development, and cognitive development. A couple of parents and children were involved and their inputs were included in the development and piloting of the Play Therapy Manual. The Play Activity manual24 is available in the extended data.36\n\nThe Principal Investigator will train the team of Research Assistants on the intervention package. The trained and certified Research Assistants will deliver the intervention in hospital setting and then at home visits as per the schedule drafted by Principal Investigator.\n\n\n\n1. All the children who fall in the age range of six months to five years (60 months) old will receive the intervention (along with their parents) every day (minimum three days) during their hospital stay for one hour per day.\n\n2. The children will receive monthly follow-up sessions through home visits (or through social media group meetings if needed) for one hour every week till 12 months from enrolment in the program.\n\n3. Activities described in the Play Therapy Manual will be followed for the follow-up sessions.\n\nThe hands of parents and their children will be washed before the activities start to avoid infectious contamination. Children will be divided into two groups as below:\n\n1. Six months to 30 months old\n\n2. 31 months to 60 months.\n\nThe intervention delivery details are as below:\n\nOn first day of hospitalization, parents and children will be interacted at Paediatrics ward. Randomization will be done and the parents in intervention arm will be sensitized about Play Therapy Programme. Written informed consents of parents will be taken from those who consent for participation and will be enrolled in the programme and e-learning platform/Whatsapp group.\n\nOn second day of hospitalization, a session will be conducted at designated play area in hospital. The session will emphasize on importance of early child development, its implications; diet, nutrition and healthcare of children. This session will be followed by play interaction session on cognitive and language development.\n\nOn third day of hospitalization, a play session on motor developmental activities will be conducted. This will be followed by session on socioemotional development and activities to promote it. Relevant Documents and reading materials in local language will be shared with parents during these sessions. The enrolled children will participate in play sessions and activities till the child is hospitalized.\n\nAfter discharge from the hospital, parents and children will be contacted through online mode and session will be conducted through Whatapp video call/Google classroom at monthly intervals. The home visits will be scheduled for the assessment of Home Environment and Parent-Child Interactions. The online monthly sessions will be continued till one year from the date of enrolment of child in the programme. Appropriate medical and nursing care will be provided during the hospital stay. If needed, referral services will be provided during follow-up at-home visits. If Children and parents insist on discontinuing play therapy, the sessions will be discontinued for those children.\n\nAfter one-year of enrollment, assessments of age-appropriate developmental milestones of children will be done either in the hospital ECD Centre or through personalized home visit to the enrolled family. Age-appropriate assessment tools will be used. Reports will be shared with parents, and follow-up instructions and meeting schedules will be shared. Figure 2 shows the schedule of enrolment, interventions, and assessments.\n\nThere is no anticipated harm from the trial participation. The study participants will be provided with the printed copies of Play Therapy Manuals after completion of trial. The children with below average development scores will receive additional ECD services at hospital ECD centre and will receive follow-up till next one year through home visits.\n\nPrimary outcomes:\n\n1. Improvements in mean scores of child developmental parameters for cognitive, physical, socio-emotional, and language development by the end of one year of intervention.\n\n2. Improvements in knowledge and skills of parents regarding early child development by the end of one year of intervention.\n\nSecondary outcomes:\n\n1. Improvements in the parent-child satisfaction levels regarding the in-hospitalization care and follow-up by the end of one year of intervention.\n\nFigure 2 details the schedule of enrolment, interventions, and assessments.\n\nWith reference to the study conducted by Gaidhane et al.,25,26 the expected difference in child development outcomes between the intervention and control groups is 0.5 SD, considering a dropout rate of 10%, level of significance = 5%, and power = 80%. The formula for calculating sample size for two independent means is:\n\nn = Minimum sample size required in each group,\n\nd = Expected mean difference between two groups = 0.5\n\nδ = standard deviation = 1.69 (As per Previous Study)\n\nZα: value of type I error at 5% significance level =1.96\n\nZβ: value of type II error at 80 % Power (1-β) = 0.84\n\nBased on the above formula, the calculations are as follows:\n\nThus, the sample size required per group is 180. Hence total sample size required is 360. A sample size of 360 subjects, 180 in each arm, is sufficient to detect a difference of 0.5 between groups in developmental scores, assuming a standard deviation of 1.69 using a two-tailed t-test of difference between means with 80% power and a 5% level of significance. For assessing the changes in parenting knowledge and skills, parents of all children in intervention group (180) will be assessed.\n\nParents of children reporting to A.V.B.R.H. in the first three months (January-March 2023) will be enrolled in the trial. All participants consenting to participate in the study will be assigned the Unique ID. Using a blocked randomization process with age groups as the Blocking variable, participants will be allocated to intervention or control groups. Age groups will be:\n\n1. Six months to 30 months\n\n2. 31 months to 60 months.\n\nAll children hospitalized in A.V.B.R.H., scheduled to stay for a minimum of three days in the hospital, and their parents signed the informed consent will be enrolled in the study.\n\nAll participants consenting to participate in the study will be assigned the Unique ID. Sequence generation will be done using computer generated random numbers. Using a block randomization process10,11 with age groups as the blocking variable, participants will be allocated either to intervention or control groups.\n\nSequentially numbered, opaque, sealed envelopes will be used for implementing the allocation sequence.\n\nThe Principal Investigator will generate the allocation sequence, trained assistants will enroll the participants, and assign participants to intervention and control groups. The Principal Investigator will train the Research Assistants for intervention, and assessors for baseline-endline assessments, supervise the data collection process and monitor the trial implementation process. We will ensure that all adults associated with the trial have the appropriate permissions and training and criminal records check to work with children. The outcome assessors and data analysts will be blinded.\n\nData will be collected in pre-tested O.D.K. based app with inbuilt checks for data quality, identifying duplicate entries. The data received on dedicated server of Research Cell of Datta Meghe Institute of Medical Sciences will be imported and checked on real time basis. The data will be encrypted for sensitive information and will be handled by the assigned team including Information Technology Coordinator and statistician. The datasets will be shared and made reusable according to FAIR data principles.\n\nAssessments will be conducted using the tools as detailed below:\n\n1. Physical Development (Using Developmental Milestones Checklist-II)27,28\n\na. Improvement in Fine Motor scores\n\nb. Improvement in Gross Motor scores\n\n2. Cognitive Development Scores (Using Developmental Milestones Checklist-II)\n\n3. Language Development Scores (Using Developmental Milestones Checklist-II)\n\n4. Socioemotional Development Scores (Using Profile of Socio-emotional Development)29\n\n5. Home Environment (Using HOME Inventory Assessment)30–32\n\n6. Parent-child Interactions (Using Observation of Mother-Child Interaction Tool)33\n\nThe research assistants will be trained on the use of all these tools and inter-rater, intra-rater scoring exercises will be conducted during training. To promote participant retention and complete follow-up, all enrolled children in the intervention group will receive scheduled home visits at monthly intervals. The children in the control group will be followed up telephonically at monthly intervals. Also, telephonic follow-up will be taken for those missing home visits in intervention group. The outcome data will detail the participants who discontinue or deviate from intervention protocols.\n\nAll data will be collected in Tablet P.C. based O.D.K. collect app with an in-built range check, double entry, and value checks. Data will be exported to the server after ensuring the correctness of the data entered. The data from the server can be downloaded as an xls file. Each participant will be allotted a Unique ID which will be used for analysis and reporting purposes. All data will be anonymous and personal information will be maintained to protect confidentiality before, during, and after the trial.\n\nAfter appropriate cleaning and compilation, the pre- and post-intervention child development data in specified domains will be collected and fed to STATA-14 by the assigned statistician. Individual and child age-group wise scores of developments will be calculated and tabulated. Mean differences in child development scores for intervention and control groups and pre-post intervention will be calculated. The effect size by Cohen’s-D will be calculated for each child age group, and significance of differences in effect size will be estimated. Also, qualitative subgroup and adjusted analyses, Difference in difference analysis for motor, language, cognitive and socio-emotional development scores will be done. Attempts will be undertaken to ensure the collection of complete data. In cases of missing data, families will be contacted through home visits and missing data will be collected. If any case/family could not be tracked, iterative algorithm or multiple imputation technique will be used to handle the missing data. The datasets analysed during the current study, statistical code and full protocol will be made available by publishing on open data repository Zenodo.\n\nComposition of the coordinating center and trial steering committee\n\nThe Trial Steering Committee (TSC) consist of the following:\n\n1. The Head of the department of Public Health\n\n2. PhD Supervisor\n\n3. Director, Research and Development\n\n4. The Head of the department of Pediatrics\n\n5. Principal investigator\n\n6. Statistician\n\n7. Data manager\n\nThe Principal Investigator is responsible for all aspects of local organisation including identifying potential recruits and taking consent. The PhD Supervisor, Head of Public Health Department, Director Research and Development, and Head of Paediatrics department will be supervising the trial. Trial Steering Committee (TSC) will meet over the course of the trial to oversee conduct and progress in monthly meeting.\n\nComposition of the data monitoring committee, its role, and reporting structure\n\nThe data monitoring committee (DMC) consists of Research-in-charge of the institute and Research-in-charge and Data Manager of the department. All related data will be managed and monitored by Principal Investigator, along with support from a statistical expert as per the guidance of Data Monitoring Committee. Since this is a play therapy intervention, hardly any adverse events and other unintended effects of trial interventions or trial conduct are expected. If encountered, those will be reported per the guidelines from the Institutional Ethics Committee. Project Management Group will review the trial conduct in monthly meetings. The Trial Steering Group and the independent Data Monitoring and Ethics Committee will review the conduct and progress of trial in quarterly meetings. Important protocol modifications will be communicated to relevant parties (e.g., investigators, R.E.C./IRBs, trial participants, and trial registries through emails and printed Hard copies, as required).\n\nThe project results and data will be published on Stepping Stones Project website of our Institute.34 The trial results will be published in Scopus, Pubmed, and Web of Science-indexed specialty journals on early child development and have access to healthcare professionals, the public, and other relevant groups. The participants will be informed of the results through personalized visits and provided the information brochures.\n\n\nDiscussion\n\nWhen a child is engaged in play activities it plays an important role in decreasing the stress of parents and children. As the studies suggest, play stimulation can play an important role in relieving the symptoms of stress and organic diseases. The hospital staff needs to be trained; play stimulation should occur in the wards, and counselling should be given to the parents and their children to release their stress. Before the play stimulation activities should be practiced, the caregivers, therapists, hospital staff, and parents must understand what is expected in different age domains related to cognitive and psychosocial development.\n\nThis [lay therapy intervention package for hospitalized children will be tested for its effectiveness in the Acharya Vinoba Bhave Rural Hospital, Wardha, India. The data of changes in child development parameters will be analysed. If this trial is successful to bring out positive changes in child development parameters of intervention group compared to control group, it can prove to be an evidence-based proof of concept for the future ’Play Therapy Stimulation Package’ for hospitalized children. If the trial fails to bring-out improvements in child development parameters in intervention arm compared to control arm, the gaps and deficiencies will be explored and attempts will be done to reframe the trial for reimplementation. As this will be a single centre study, the response rate and acceptance of intervention by beneficiaries may need to be generalizable to different types/levels of inpatient childcare facilities. A minimum of three days hospital stay is expected with the initial play therapy start. Staying for less time than this duration may not effectively stimulate children and sensitize parents. Also, follow-up after discharge may pose some challenges.\n\nThis trial was registered prospectively with Clinical Trial Registry of India (CTRI).35 Recruitment of Participants started from Jan 2023. Expected date of trial completion is 30th May 2024.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: File Name: Activity CARDS V5_final TTS v1.pdf.\n\nDescription: Activity Cards for Play Therapy Sessions. https://doi.org/10.5281/zenodo.8127629. 36\n\nThis project contains the following extended data:\n\n• Activity CARDS V5_final TTS v1.pdf. (This data contains the details of different types of activities for promoting cognitive, motor, language and socio-emotional development of children).\n\nZenodo: SPIRIT Checklist for ‘Effectiveness of Play Therapy Programme in Promoting Early Child Development of under-5 Children visiting Tertiary Care Hospital in Rural Settings: Study Protocol of a Randomized Controlled Trial’. https://doi.org/10.5281/zenodo.8318964. 37\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe acknowledge the support provided for this study by Hon. Vice Chancellor, Hon. Secretary, DMIMSU, Wardha, Head of the department of Paediatrics, AVBR Hospital Wardha.\n\n\nReferences\n\nOrganisation mondiale de la santé, UNICEF: Care for child development improving the care of young children. Geneva; New York: World Health Organization: UNICEF; 2012.\n\nWHO: WHO\|Care for child development: improving the care for young children. World Health Organization; [cited 2020 Jul 7]. Reference Source\n\nPhiladelphia TCH of: Play and Recreation During Hospitalization. The Children’s Hospital of Philadelphia; 2014 [cited 2020 Jul 7]. Reference Source\n\nStudent, Sumandeep Nursing College, Sumandeep Vidyapeeth, Piparia, Vadodara-391760, Gujarat, India, Patel K, V S, H. N R: A study to assess the effectiveness of play therapy on anxiety among hospitalized children. IOSR. J Nurs Health Sci. 2014 [cited 2020 Jul 7]; 3(5): 17–23. Publisher Full Text Reference Source\n\nLeVieux-Anglin L, Sawyer EH: Incorporating play interventions into nursing care. Pediatr Nurs. 1993 Oct; 19(5): 459–463. PubMed Abstract\n\nKoukourikos K, Tzeha L, Pantelidou P: Tsaloglidou A. The importance of play during hospitalization in children. Mater Socio-Medica. 2015 Dec [cited 2020 Jul 7]; 27(6): 438–41. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChildren in India 2018 – A Statistical Appraisal_26oct18.pdf: [cited 2020 Jul 10]. Reference Source\n\nKastor A, Mohanty SK: Disease and age pattern of hospitalisation and associated costs in India: 1995–2014. BMJ Open. 2018 Jan 24 [cited 2020 Jul 10]; 8(1): e016990. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoy RN, Shrivastava P, Das DK, et al.: Burden of Hospitalized Pediatric Morbidity and Utilization of Beds in a Tertiary Care Hospital of Kolkata, India. Indian J Community Med Off Publ Indian Assoc Prev Soc Med. 2012 [cited 2020 Jul 10]; 37(4): 252–255. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilson ME, Megel ME, Enenbach L, et al.: The voices of children: stories about hospitalization. J Pediatr Health Care Off Publ Natl Assoc Pediatr Nurse Assoc Pract. 2010 Apr; 24(2): 95–102. Publisher Full Text\n\nCorsano P, Majorano M, Vignola V, et al.: The waiting room as a relational space: young patients and their families’ experience in a day hospital: Waiting in a paediatric day hospital. Child Care Health Dev. 2015 Nov [cited 2020 Jul 29]; 41(6): 1066–1073. PubMed Abstract \| Publisher Full Text\n\nLi HCW, Lopez V: Effectiveness and appropriateness of therapeutic play intervention in preparing children for surgery: a randomized controlled trial study. J Spec Pediatr Nurs JSPN. 2008 Apr; 13(2): 63–73. PubMed Abstract \| Publisher Full Text\n\nBurns-Nader S, Hernandez-Reif M, Porter M: The relationship between mothers’ coping patterns and children’s anxiety about their hospitalization as reflected in drawings. J Child Health Care. 2014 Mar 1 [cited 2020 Jul 22]; 18(1): 6–18. Publisher Full Text\n\nDoupnik SK, Hill D, Palakshappa D, et al.: Parent Coping Support Interventions During Acute Pediatric Hospitalizations: A Meta-Analysis. Pediatrics. 2017 Sep; 140(3). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChieng YJS, Chan WCS, Klainin-Yobas P, et al.: Perioperative anxiety and postoperative pain in children and adolescents undergoing elective surgical procedures: a quantitative systematic review. J Adv Nurs. 2014 Feb; 70(2): 243–255. PubMed Abstract \| Publisher Full Text\n\nJr - THE SINO-BRAZILIAN PRINCIPLES IN A LATIN AMERICAN.pdf: [cited 2020 Jul 22]. Reference Source\n\nEisen SL, Ulrich RS, Shepley MM, et al.: The stress-reducing effects of art in pediatric health care: Art preferences of healthy children and hospitalized children. J Child Health Care. 2008; 12(3): 173–190. PubMed Abstract \| Publisher Full Text\n\nLivesley J, Long T: Children’s experiences as hospital in-patients: voice, competence and work. Messages for nursing from a critical ethnographic study. Int J Nurs Stud. 2013 Oct; 50(10): 1292–1303. PubMed Abstract \| Publisher Full Text\n\nVideoconferencing to Reduce Stress Among Hospitalized Children\|American Academy of Pediatrics: [cited 2020 Jul 29]. Reference Source\n\nPotasz C, Varela MJVD, Carvalho LCD, et al.: Effect of play activities on hospitalized children’s stress: a randomized clinical trial. Scand J Occup Ther. 2013 Jan 1 [cited 2020 Jul 7]; 20(1): 71–79. PubMed Abstract \| Publisher Full Text\n\nPatil MS, Gaidhane AM, Quazi SZ, et al.: Effectiveness of Play Therapy Programme in Promoting Early Child Development of under-5 Children visiting Tertiary Care Hospital in Rural Settings: Study Protocol of A Randomized Controlled Trial, 22 June 2022, PREPRINT (Version 1) available at Research Square.Publisher Full Text\n\nShen D: Randomization in Clinical Trial Studies.8.\n\nEfird J: Blocked Randomization with Randomly Selected Block Sizes. Int J Environ Res Public Health. 2011 Jan [cited 2020 Aug 6]; 8(1): 15–20. PubMed Abstract \| Publisher Full Text Reference Source\n\nPatil M: Activity Cards for Play Therapy Sessions.2023 Jul 9 [cited 2023 Jul 9]. Reference Source\n\nISRCTN - ISRCTN87426020: Stepping Stones: scaling early childhood development at Anganwadi Centers in India.[cited 2023 Jul 9]. Reference Source\n\nCTRI: [cited 2023 Jul 9]. Reference Source\n\nAbubakar A, Holding P, Van de Vijver F, et al.: Developmental monitoring using caregiver reports in a resource-limited setting: the case of Kilifi, Kenya. Acta Paediatr Oslo Nor 1992. 2010 Feb [cited 2022 Dec 30]; 99(2): 291–297. Publisher Full Text Reference Source\n\nPrado EL, Abubakar AA, Abbeddou S, et al.: Extending the Developmental Milestones Checklist for use in a different context in Sub-Saharan Africa. Acta Paediatr Oslo Nor. 1992. 2014 Apr; 103(4): 447–454. Publisher Full Text\n\nKitsao-Wekulo P, Holding P, Nanga K, et al.: The Protocol for Child Monitoring Kenya - Infant/Toddler (PCM-IT) version: Construction and validation of a multiple-domain child assessment for use in Early Childhood intervention Programmes. SocArXiv. 2021 [cited 2022 Dec 30]. Reference Source\n\nKitsao-Wekulo PK, Holding P, Bradley RH, et al.: Exploring Differences in the Rural Home Environment: The Role of Biological and Environmental Factors. Abubakar A, van de Vijver FJR , editors. New York, NY: Springer New York; 2017 [cited 2022 Dec 30]; pp. 55–73. Publisher Full Text\n\nHolding P, Abubakar A, Obiero E: Validation of the Infant-Toddler HOME Inventory among Households in Low Income Communities at the Kenyan Coast.\n\nBradley RH: The Home Inventory: review and reflections. Adv Child Dev Behav. 1994; 25: 241–288. Publisher Full Text\n\nRasheed M, Bharuchi V, Mughis W, et al.: Development and Feasibility Testing of a Play-Based Psychosocial Intervention for Reduced Patient Stress in a Paediatric Care Setting: Experiences from Pakistan. In Review.2020 Oct [cited 2020 Nov 6]. Reference Source\n\nStepping Stones Project: [cited 2023 Jul 9]. Reference Source\n\nPatil M: Manoj_CTRI_Registration_Page.2023 Jul 9 [cited 2023 Jul 9]. Reference Source\n\nPatil M: Activity Cards for Play Therapy Sessions. Dataset. Zenodo. 2023, July 9. Publisher Full Text\n\nPatil M: SPIRIT Checklist for Effectiveness of Play Therapy Programme in Promoting Early Child Development of under-5 Children visiting Tertiary Care Hospital in Rural Settings: Study Protocol of a Randomized Controlled Trial. (Version v1). Zenodo. 2023. Publisher Full Text" }	[ { "id": "260212", "date": "03 Sep 2024", "name": "Sylvia Fernandez Rao", "expertise": [ "Reviewer Expertise Nutrition and Early child development" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an important article as it is testing the impact of play intervention in the hospital setting. Earlier studies have shown that long term hospitalization does cause developmental loss. So this trial is timely, as not all studies focus on this aspect. However some aspects of the manuscript need clarity. For one, the consort diagram shows that the trial is done (recruitment, refusal, intervention, loss to follow-up, etc.) but the text gives the impression that the trial is yet to start. This needs to be clarified, and the appropriate tense should be used. The intervention personnel will they be interacting with the control arm? this can cause ? Further, the intervention includes nutrition and health aspects. How will this be separated from developmental intervention of play? Will the control group receive messages on health and nutrition? A fewer details regarding the intervention would be useful .\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "12560", "date": "11 Oct 2024", "name": "MANOJ PATIL", "role": "Author Response", "response": "Respected Reviewer, Thank you very much for taking the time to review this protocol and thorough assessment. Your comments and suggestions are very useful. Regarding the tense in the consort diagram, I will update the diagram in version 2 of this article as suggested, and upload it shortly. The intervention personnel will not interact with the control arm participants. Only assessors will contact the participants in control arm for baseline and endline assessments. Necessary steps will be taken to avoid the contamination. Further, the intervention includes only sensitization of parents on nutrition and health aspects during hospital stay and home visits. There is no direct nutritional intervention. The control group will not receive messages on health and nutrition or any other aspects of intervention. It will be a separate group from another hospital of same Institute. I will add the requested details in the updated version of this protocol shortly. Thank you very much for your kind perusal." } ] } ]	1	https://f1000research.com/articles/13-28
https://f1000research.com/articles/13-1211/v1	11 Oct 24	{ "type": "Case Report", "title": "Case Report: Delayed Diagnosis of Leprosy-Related Neuropathic Ulcer, Insights from a Case of Delay to Diagnose across Four Clinical Settings", "authors": [ "Saldy Yusuf" ], "abstract": "Background Neuropathy is common in both Diabetes Mellitus (DM) and Leprosy, often resulting in neuropathic ulcers. Leprosy-related neuropathic ulcers are frequently misdiagnosed as DM-related, causing delays in appropriate care. This case report underscores the importance of timely recognition and a better understanding of Leprosy-related neuropathic ulcers to prevent misdiagnosis and improve patient outcomes.\n\nMethods The case report adopt the CARE Guidelines and was conducted at the Wound Care Specialist Clinic, Griya Afiat, Makassar, East Indonesia. Data were collected using a Minimum Data Sheet (MDS) to capture demographics, health history, and history of treatments. A head-to-toe assessment focused on the eyes, hands, and feet, with neuropathy, confirmed using the Semmes Weinstein Monofilament test, and angiopathy was assessed by palpating the dorsal pedis and posterior tibialis pulse. Wound care interventions consisted of cleansing, debridement, and dressing. Given the similarities between Leprosy-related neuropathic ulcers and DM-related neuropathic ulcers, the DMIST (depth, maceration, inflammation/infection, size, tissue type of the wound bed, type of wound edge, and tunnelling/undermining) tool was used to evaluate wound healing progress.\n\nResults Anamnesis indicated patient has no DM, with normal blood glucose; however, the patient had neuropathic wounds on her feet, asymmetrical eyebrow distribution, and rashes on her hands and calves, with neuropathy confirmed by a monofilament test—initial treatment involved Cadexomer Iodine powder to control bacterial growth and Honey-based gel to promote granulation. Over 62 days, 11 treatments were administered, with an average dressing change every 5.6 days, which improved the DMIST score from 12 to 4 by the end of observation day.\n\nConclusions This case report highlights the significance of distinguishing leprosy-related neuropathic ulcers from those associated with DM to ensure accurate diagnosis and timely treatment. By employing comprehensive assessment tools and targeted wound care interventions, significant improvements in wound healing were achieved, emphasizing the need for greater awareness and clinical vigilance in managing Leprosy-related neuropathic ulcers.", "keywords": [ "Neuropathy", "Leprosy", "Diabetes mellitus", "Neuropathic ulcers", "Delayed diagnosis Wound care", "DMIST tool", "Semmes Weinstein Monofilament test." ], "content": "Introduction\n\nNeuropathy is known as loss of sensation, commonly in both upper and lower extremities. Some term regarding neuropathy, including peripheral neuropathy or peripheral polyneuropathy, encompasses a wide array of disorders that result in damage and dysfunction of the peripheral nervous system’s nerves in various patterns (Plaut & Weiss, 2021). Epidemiological studies report various ranges of prevalence neuropathy, from a lower rate of 1% to 7% (Castelli et al., 2020), a moderate rate of 10-15% (Zhu et al., 2024), and a high rate in Ethiopia 53.6% (Abdissa et al., 2020) and China 67.6% (Wang et al., 2023). Different types of diagnostic tests also determine the prevalence. Self-administered questionnaires confirmed 44.4% and 51.1% based on foot examinations (Perveen et al., 2024). Various diagnostic tests result in clinical challenges in investigating neuropathy.\n\nDiagnosing neuropathy remains challenging. Currently, a triangulation approach that includes clinical evaluations, laboratory tests, and nerve conduction studies (electrodiagnostic test) is the primary method for diagnosing polyneuropathy (Goedee et al., 2013). Other methods include Diabetic Peripheral Neuropathy, Diagnostic tests including stimulus tests, Screening Scores, Quantitative tests (monofilament, IpTT, Neruothesiometer, Vibratip), and nerve conduction studies (Galiero et al., 2023). Meanwhile, the diagnostic test for neuropathic Leprosy is challenging. Routine examinations to assess nerve function impairment in Leprosy typically focus on the hands, feet, and eyes. Techniques for evaluating nerve function in leprosy neuropathy include nerve conduction studies (NCS), quantitative sensory tests (QST), assessment of tactile sensitivity in skin lesions using Semmes-Weinstein monofilament testing (MFT) or ballpoint tests, and motor function evaluation through voluntary muscle testing (Ebenezer & Scollard, 2021). Neuropathy can be diagnosed with advanced tests using electromyography, high-resolution sonography serology, and PCR (Marques, 2024). The problem in clinical settings is the relative unavailability of standard diagnostic tests, making diagnosing neuropathy challenging. Additionally, patients with neuropathy may not experience discomfort or pain, further complicating diagnosis. Meanwhile, healthcare professionals often seem unaware of neuropathic ulcers, particularly those related to Leprosy.\n\nNeuropathy is notably prevalent among patients with DM and Leprosy, frequently leading to the development of neuropathic ulcers. As a result, Leprosy-related neuropathic ulcers are sometimes misdiagnosed as DM-related or overlooked entirely as a leprosy complication. This lack of recognition among healthcare professionals leads to frequent misdiagnosis or delayed diagnosis of Leprosy-related neuropathic ulcers. This case report highlights the challenges in accurately diagnosing Leprosy-related neuropathic ulcers, emphasizing the need for timely recognition and a deeper understanding of Leprosy-related neuropathy’s conceptual, clinical, and therapeutic aspects. This is crucial to prevent delays in wound care and improve patient outcomes.\n\n\nCase report\n\nThe study is a case report which reported based on the CARE Guidelines (https://www.care-statement.org/checklist). The case was conducted at the Wound Care Specialist Clinic, Griya Afiat, Makassar, East Indonesia. A wound care specialist administered wound care, while a wound care specialist with a doctoral qualification in wound care carried out the healing evaluation.\n\nData collection was conducted using a Minimum Data Sheet (MDS) to gather demographic information, health history, and health status, including details of previous treatments. The assessment followed a head-to-toe approach, focusing on the eyes, hands, and feet (Ebenezer & Scollard, 2021). We inspected the eyebrows for the eyes, comparing the symmetry between the right and left eyes. The inspection was then extended to the hands and feet, comparing the right and left sides. A foot assessment was performed to identify the status of neuropathy and angiopathy. Neuropathy was confirmed through the Semmes Weinstein Monofilament test (10g), applied to the plantar hallux, first metatarsal, third metatarsal, and fifth metatarsal. Angiopathy status was assessed by palpating the dorsal pedis and posterior tibialis pulses.\n\nThe wound care interventions included cleansing, debridement, and dressing. We used mineral water and liquid soap for the peri-wound skin and the wound bed for wound cleansing. Sharp debridement and mechanical debridement were performed to remove the callus surrounding the wound. Dressing selection was based on the specific needs of the wound bed. It included three layers: a primary dressing (in direct contact with the wound bed), a secondary dressing (to absorb exudate), and a tertiary dressing (for fixation).\n\nPhotographs were taken using a mobile phone without photographic applications to avoid image manipulation. The photos were cropped using the cropping feature in MS Word to remove unnecessary elements while ensuring the observation area (the foot) remained intact. Since the Leprosy-related neuropathic ulcers’ characteristics are similar to those of DM related neuropathic ulcer, we use the DMIST tool for wound healing evaluation. DMIST is a valid healing score for diabetic foot ulcers (Oe et al., 2020) and is useful for predicting healing (Tsuchiya et al., 2023).\n\nThe patient is a 48-year-old woman, a high school graduate, and a housewife. She reported no history of Hypertension, Diabetes Mellitus, or Tuberculosis. The patient also stated that no family members have had similar wounds. The onset of the wound occurred in November 2023, beginning with the development of thick, numb calluses. The patient attempted to pinch and peel the calluses using her nails, which caused the wound to enlarge, become red (inflamed), and eventually exude fluid. Following advice from her family, the patient sought treatment at a general clinic in November 2023.\n\n\n\n1. Prior identification of Leprosy status\n\na. November 2023, Visit to a General Clinic.\n\nThe patient presented to the general clinic with a complaint of a wound on the sole of her foot. During the visit, she reported that she was only interviewed without undergoing any physical examination, including screening for Leprosy. The patient was referred to a hospital for further evaluation.\n\nb. November 2023, Visit to the Hospital.\n\nThe patient underwent an examination at the hospital, but no diagnosis of Leprosy was made at that time. The doctor advised the patient not to peel the calluses and recommended using a moisturizer. Wound care included cleansing with NaCl 0.9%, soap, and povidone-iodine and covering the wound with gauze. The patient was instructed to attend three wound care sessions at the hospital before continuing wound care at home.\n\nc. February 2024, Visit to a General Practitioner’s Office.\n\nThe patient visited a general practitioner’s office due to the persistence of the wound, along with the development of bruises on her hands and calves. The doctor advised her to avoid prolonged contact with water, detergents, and dishwashing soap. Unfortunately, the doctor suspected the condition was related to gout or rheumatism. The patient was prescribed three types of medications, although she could not recall their names, stating only that one was for muscle cramps. There was no noticeable improvement following this treatment.\n\nd. March 2024, Second Visit to the General Clinic.\n\nDue to the lack of improvement after the consultation at the general practitioner’s office, the patient returned to the same general clinic she visited in November 2023 for a second evaluation. The doctor observed the wound and measured her blood sugar, 85 mg/dL. The doctor explained that the wound required regular care and referred the patient to a specialized wound care clinic. The prescribed treatments included paracetamol, an analgesic, and gentamicin ointment.\n\n2. After identification, Leprosy status\n\na. March 2024, Visit to a Wound Care Specialist Clinic.\n\nThe patient visited the Wound Care Specialist Clinic, where anamnesis, a physical examination, and a monofilament test were conducted. The patient’s weight was 43 kg, blood pressure 90 mmHg, blood glucose 71 mg/dL, cholesterol 196 mg/dL, and uric acid 5.1 mg/dL (Table 1). Anamnesis confirmed that the patient had no history of diabetes mellitus, and her random blood glucose was within the normal range. However, she had neuropathic wounds on her feet. A head-to-toe examination revealed asymmetrical eyebrow distribution, rashes on the dorsal side of her hands, and rashes on both calves (Figure 1). The monofilament test confirmed neuropathy in the right foot. Palpation of the dorsalis pedis and posterior tibialis pulses was positive in both the left and right feet (Table 2). Based on these findings, the patient was referred to a health clinic for further referral to a specialized facility to diagnose Leprosy.\n\nb. March 2024, Third Visit to the General Clinic.\n\nThe patient returned to the general clinic (third visit), bringing the monofilament test results from the Wound Care Specialist Clinic. The doctor confirmed the findings using a rolled tissue test on the rash-covered areas but obtained negative results. The patient was then referred to a dermatological center for further diagnostic evaluation.\n\nc. March 2024, Visit to the Dermatological Center.\n\nThe attending physician conducted a series of tests at the dermatological center. The first test used tissue, followed by a skin smear from the area behind the patient’s ears and both calves. The patient did not receive medication or wound care and was referred to the health clinic for further evaluation.\n\nd. March 2024, Fourth Visit to the General Clinic.\n\nThe patient returned to the health clinic (fourth visit) with results from the dermatological center, confirming Leprosy diagnosis. No medication or wound care was provided at the clinic. The patient was referred to a public health center for treatment.\n\ne. March 2024, Visit to the Public Health Center.\n\nThe patient visited the public health center, where the doctor performed a ballpoint test and confirmed neuropathy. The doctor explained that the patient would undergo one year of treatment for Leprosy and was advised to continue wound care independently at home.\n\nf. March 2024, Return to the Wound Care Clinic.\n\nThe patient returned to the wound care clinic to receive wound care until complete healing was achieved.\n\n\n\n• No Diabetes Mellitus\n\n• No Hypertension\n\n• No Tuberculosis\n\n\n\n• Blood sugar: 71 mg/dl\n\n• Cholesterol: 196 mg/dl\n\n• Uric Acid: 5.1 mg/dl\n\nA: We observed an asymmetrical pattern in the patient's eyebrows. B: The inspection revealed a rash on the dorsal side of the left hand. C: Rashes were also found on the left and right tibial areas.\n\nWound care was administered by a wound care specialist and involved three modalities of intervention: cleansing, debridement, and dressing. Mineral water and liquid soap were used for wound cleansing. Sharp debridement was performed to remove necrotic tissue and calluses surrounding the wound, in combination with mechanical debridement.\n\nDuring the first week, Cadexomer Iodine powder was applied as the primary dressing to control bacterial growth at the wound bed, with foam as the tertiary dressing. From the second week onward, honey-based gel was applied to stimulate granulation tissue growth, low-adherent dressing was used as the secondary layer, and gauze was applied during the final phase of care. Adhesive tape was used for fixation (Table 3).\n\nWound care began on March 20 and continued until May 21, 2024, spanning 62 days with a total of 11 treatments. The average dressing change interval was 5.6 days. The patient’s total DMIST score was 12 at the first treatment, decreased to 9 in the second month, and reached four at the end of the treatment period (Figure 2).\n\nA. March, 20th 2024. B. March, 22nd 2024. C. March, 26th 2024. D. March, 29th 2024. E. April, 4th 2024. F. April, 16th 2024. G. April, 23rd 2024. H. April, 30th 2024. I. May, 7th 2024. J. May, 14th 2024. K. May, 21st 2024.\n\nThe patient works as a household assistant, remaining physically active, which often causes the wound dressing to be wet. As a result, the patient was educated on self-care for the wound, including how to replace the dressing when it became wet. The patient was instructed to clean the wound, apply ointment, and cover it with gauze independently when needed.\n\nThe patient reported visiting three healthcare facilities, none establishing a diagnosis of Leprosy. The first facility considered it a regular wound, while the third suspected gout—none of the three healthcare facilities performed any tests on the rashes on her hands or feet. The patient stated that the diagnosis of Leprosy was confirmed only after visiting the wound care clinic, where a monofilament test was conducted, followed by a referral back to the healthcare clinic. Only after receiving the monofilament test results was a tissue test performed at the healthcare clinic, and the patient was subsequently referred to the dermatological center for further evaluation. The patient responded to the diagnostic test results with acceptance but mentioned that she would not disclose her leprosy diagnosis to her husband.\n\nAn exciting aspect of this case is that, despite having a neuropathic ulcer, the patient remained active, walking and working without developing edema or erythema in the affected foot during the two-month treatment period. This is in stark contrast to neuropathic ulcers in patients with DM, where the absence of offloading typically leads to edema, erythema, and local inflammation. Additionally, the healing rate was relatively rapid, with complete recovery achieved in just 62 days, which differs significantly from the prolonged healing process often observed in diabetic patients with similar wounds.\n\n\nDiscussion\n\nThe interesting aspect of this case lies in the healthcare facility’s oversight in recognizing and diagnosing the existing neuropathic wounds as a sign of leprosy. Proper diagnosis of neuropathy requires a thorough assessment of patient history, physical examination, and laboratory test results. Early-stage neuropathy is characterized by progressive sensory changes, including the loss of sensation, numbness, pain, or burning sensations in a “stocking and glove” distribution of the extremities. This can progress to proximal numbness, distal weakness, or muscle atrophy (Castelli et al., 2020). The clinical manifestations of diabetic peripheral neuropathy (DPN) range from asymptomatic to painful neuropathic symptoms (Abdissa et al., 2020). Common clinical features of DPN include bilateral limb pain, numbness, and paresthesia, which may lead to the development of foot ulcers (Zhu et al., 2024). The pain pattern in DPN is often described as “glove and stocking” with burning, electric, sharp, or dull aching sensations of varying intensities (Chang & Yang, 2023). In this case, we observed clinical signs of numbness in the hands and soles of the feet. The absence of pain in the neuropathic wounds is consistent with the characteristics of Leprosy-related neuropathic ulcers (Khadilkar et al., 2021). and the monofilament test was negative. Skin lesions tend to be hypoesthetic or anesthetic and are typically found on the back, buttocks, trunk, face, and earlobes (Khadilkar et al., 2021).\n\nIn this case, our suspicion arose from the presence of neuropathic wounds without any history or status of DM. Inspecting the eyes, hands, and feet raised concerns about Leprosy. Our approach aligned with recommendations for assessing nerve function impairment in leprosy neuropathy, which typically focuses on the hands, feet, and eyes (Ebenezer & Scollard, 2021); we then confirmed these findings through a monofilament test. The monofilament test is recognized as a diagnostic tool for leprosy neuropathy (Frade et al., 2021), being straightforward, practical, cost-efficient, and demonstrating high accuracy in diagnosing clinical Leprosy (Frade et al., 2022); in Indonesia, the monofilament test is also used to diagnose leprosy-related neuropathy. 95.2% of patients reported experiencing neuropathy symptoms, with 52.4% having symptoms for one year or less and 52.4% exhibiting neuropathy primarily in the lower bilateral extremities (Dalimunthe et al., 2023). Unfortunately, monofilament tests are not yet widely available in Indonesia, which may contribute to delays in diagnosing leprosy-related neuropathy. Nevertheless, the IpTT examination can serve as an alternative for diagnosing neuropathy (Basir et al., 2020) when the monofilament test is unavailable.\n\nIn this case, we performed sharp debridement to remove the callus surrounding the ulcer. For infection control, we applied Cadexomer Iodine. Cadexomer iodine, an advanced iodine formulation utilizing microbead technology, offers a unique approach to wound care by effectively managing biofilm and exudate while demonstrating superior desloughing capabilities (Ruke & Savai, 2019). At the end of the second week of treatment, we used a honey-based gel to promote granulation tissue formation. Based on our clinical experience, honey accelerates the growth of granulation tissue. A randomized controlled trial (RCT) is currently investigating the role of honey in ulcer healing in Leprosy (Udo et al., 2024). In this case, the wound healed within 62 days, similar to previous studies. The median healing time for wounds was 75 days for neuropathic ulcers, compared to 136 days for ischemic ulcers and 171 days for neuroischemic ulcers (Singh et al., 2023).\n\nAn important learning point from this case is the failure to detect Leprosy. The patient had been experiencing neuropathic wounds for six months and had visited four healthcare facilities, yet none recognized the neuropathic wounds as a consequence of Leprosy. This aligns with classic reports that leprosy patients experience a diagnostic delay of approximately 1.8 years (ranging from 0.2 to 15.2 years) (Lockwood & Reid, 2001). Another noteworthy issue is that, according to the patient, none of the four healthcare facilities performed a physical examination, relying only on routine interviews. Several factors contributed to the delayed diagnosis, including a lack of awareness among healthcare workers regarding the symptoms of Leprosy, low clinical suspicion from physicians, and delayed referral to specialist facilities (Khadilkar et al., 2021). The diagnosis of Leprosy was eventually made after the patient was referred to a Private Wound Care Clinic, despite patient have to pay which her own budget, since it uncover by national insurance (Oe, 2024). Current case also highlights that health literacy not only important for patient with chronic disease, but also healthcare professional, to avoid delay in clinical decision (Kadar, 2024).\n\n\nConclusion\n\nThis case report provides valuable insights into the delayed diagnosis of leprosy-related neuropathic ulcers across four healthcare settings. It highlights the critical need for heightened clinical awareness and timely diagnosis to prevent prolonged suffering and complications. Accurate diagnosis and appropriate wound management play a pivotal role in promoting the healing process of leprosy-related neuropathic ulcers. Addressing the factors contributing to diagnostic delays can improve patient outcomes and reduce the burden of undiagnosed Leprosy in clinical practice.\n\n\nConsent to publish\n\nA written informed consent was obtained from the patient for the publication of this case report. Patient also received a thorough explanation regarding the purpose of her data. Additionally, we adhered to the principles outlined in the Declaration of Helsinki (https://shorturl.at/2KDfV).", "appendix": "Data availability\n\nNo data associated with this article.\n\nFigshare: Case Report: Delayed Diagnosis of Leprosy-Related Neuropathic Ulcer, Insights from a Case of Delay to Diagnose across Four Clinical Settings: A Case Report DOI: https://doi.org/10.6084/m9.figshare.27123441.v1 (Yusuf, 2024).\n\nThe project contains the following reporting guidelines:\n\n• CARE Checklist\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nWe thank the patient for allowing us to publish her case. We also thank to wound care nurses; Sukmawati Kasim, Nuhridatul Aina, and Dian Nurkhalisa who perform wound care in Griya Afiat.\n\n\nReferences\n\nAbdissa D, Hamba N, Kene K, et al.: Prevalence and Determinants of Peripheral Neuropathy among Type 2 Adult Diabetes Patients Attending Jimma University Medical Center, Southwest Ethiopia, 2019, an Institutional-Based Cross-Sectional Study. J. Diabetes Res. 2020; 2020: 1–8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasir IS, Syam Y, Yusuf S, et al.: Accuracy of Ipswich Touch Test (IpTT) to detect small fiber neuropathy and large fiber neuropathy as a risk factor of diabetic foot ulcers in public health centers. Enferm. Clin. 2020; 30: 308–312. Publisher Full Text\n\nCastelli G, Desai KM, Cantone RE: Peripheral Neuropathy: Evaluation and Differential Diagnosis. Am. Fam. Physician. 2020; 102(12): 732–739. PubMed Abstract\n\nChang MC, Yang S: Diabetic peripheral neuropathy essentials: a narrative review. Ann. Palliat. Med. 2023; 12(2): 390–398. PubMed Abstract \| Publisher Full Text\n\nDalimunthe DA, Lubis SR, Irene Sinambela DW: Clinico-sociodemographic profile of leprosy neuropathy in Medan, Indonesia. J. Pak. Assoc. Dermatol. 2023; 33(1).\n\nEbenezer GJ, Scollard DM: Treatment and Evaluation Advances in Leprosy Neuropathy. Neurotherapeutics. 2021; 18(4): 2337–2350. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFrade MAC, de Freitas Rosa DJ , Bernardes Filho F, et al.: Semmes-Weinstein monofilament: A tool to quantify skin sensation in macular lesions for leprosy diagnosis. Indian J. Dermatol. Venereol. Leprol. 2021; 87(6): 807–815. Publisher Full Text\n\nFrade MAC, Filho FB, Silva CML, et al.: Evaluation of altered patterns of tactile sensation in the diagnosis and monitoring of leprosy using the Semmes-Weinstein monofilaments. PLoS One. 2022; 17(8): e0272151. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGaliero R, Caturano A, Vetrano E, et al.: Peripheral Neuropathy in Diabetes Mellitus: Pathogenetic Mechanisms and Diagnostic Options. Int. J. Mol. Sci. 2023; 24(4). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoedee HS, Brekelmans GJF, van Asseldonk JTH , et al.: High resolution sonography in the evaluation of the peripheral nervous system in polyneuropathy - A review of the literature. Eur. J. Neurol. 2013; 20(10): 1342–1351. PubMed Abstract \| Publisher Full Text\n\nKadar K: Enhancing Health Literacy and Self-Care Abilities among Individuals with Chronic Diseases. Indonesian Contemporary Nursing Journal (ICON Journal). 2024; 9(1): 3–7. Publisher Full Text\n\nKhadilkar SV, Patil SB, Shetty VP: Neuropathies of leprosy. J. Neurol. Sci. 2021; 420: 117288. Publisher Full Text\n\nLockwood DNJ, Reid AJC: The diagnosis of leprosy is delayed in the United Kingdom. QJM. 2001; 94(4): 207–212. PubMed Abstract \| Publisher Full Text\n\nMarques W: Leprous neuropathy. Curr. Opin. Neurol. 2024; 37: 487–492. PubMed Abstract \| Publisher Full Text\n\nRuke MG, Savai J: Diabetic Foot Infection, Biofilm & New Management Strategy. Diabetes Res. 2019; 1(1). Publisher Full Text\n\nOe M: Nursing Research Contributes to Changes in Clinical Practice. Indonesian Contemporary Nursing Journal (ICON Journal). 2024; 9(1): 8–10. Publisher Full Text\n\nOe M, Yotsu RR, Arisandi D, et al.: Validity of DMIST for monitoring healing of diabetic foot ulcers. Wound Repair Regen. 2020; 28(4): 539–546. Publisher Full Text\n\nPerveen W, Ahsan H, Shahzad R, et al.: Prevalence of peripheral neuropathy, amputation, and quality of life in patients with diabetes mellitus. Sci. Rep. 2024; 14(1): 14430. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlaut T, Weiss L: Electrodiagnostic Evaluation Of Critical Illness Neuropathy. StatPearls. 2021. Reference Source\n\nSingh CG, Sil A, Sanyal D, et al.: Characteristics of Neuropathic, Ischaemic and Neuroischaemic Diabetic Foot Ulcers- A Prospective Cohort Study. J. Clin. Diagn. Res. 2023. Publisher Full Text\n\nTsuchiya S, Suriadi, Sanada H, et al.: Relationship between items of DMIST and healing of diabetic foot ulcers. Int. Wound J. 2023; 20(2): 345–350. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUdo S, Ogbu Sunday P, Tsaku PA, et al.: Raw, Unadulterated African Honey for Ulcer Healing in Leprosy: Protocol for the Honey Experiment on Leprosy Ulcer (HELP) Randomized Controlled Trial. JMIRx Med. 2024; 5: e50970–e50970. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang W, Ji Q, Ran X, et al.: Prevalence and risk factors of diabetic peripheral neuropathy: A population-based cross-sectional study in China. Diabetes Metab. Res. Rev. 2023; 39(8): e3702. PubMed Abstract \| Publisher Full Text\n\nYusuf S: CARE Checklist. Dataset. figshare. 2024. Publisher Full Text\n\nZhu J, Hu Z, Luo Y, et al.: Diabetic peripheral neuropathy: pathogenetic mechanisms and treatment. Front. Endocrinol. 2024; 14. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "345552", "date": "26 Dec 2024", "name": "Paul Alumbugu Tsaku", "expertise": [ "Reviewer Expertise Public Health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a well-written case study. However, I have some comments for the author to address:\n1. The abstract should mention that the case was misdiagnosed at three previous centers before the current diagnosis and management. 2. The author places significant emphasis on differentiating between diabetic mellitus (DM) ulcers and leprosy-related ulcers. However, other previous misdiagnoses, such as gout, should also be discussed in the literature review. 3. It is more appropriate to refer to the Minimum Data Set (MDS) rather than the Minimum Data 'Sheet.' 4. In the wound evaluation section, please further describe how the DMIST tool was used for assessing the wound. 5. Although the author indicated that consent was obtained from the patient in accordance with the Helsinki Declaration, there is no mention of whether ethical clearance was obtained or a justification for why it was not needed. 6. In the acknowledgment section, the author uses the word \"we\" to acknowledge contributors, but since there is only one author, it would be more appropriate to use the singular form.\n\nThank you for considering these suggestions.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1211
https://f1000research.com/articles/13-908/v1	08 Aug 24	{ "type": "Research Article", "title": "Trends of machine learning for dental caries research in Southeast Asia: insights from a bibliometric analysis", "authors": [ "Faizul Hasan", "Hendrik Setia Budi", "Lia Taurussia Yuliana", "Mokh Sujarwadi", "Faizul Hasan", "Lia Taurussia Yuliana", "Mokh Sujarwadi" ], "abstract": "Background Dental caries is a common chronic oral disease, posing a serious public health issue. By analyzing large datasets, machine learning shows potential in addressing this problem. This study employs bibliometric analysis to explore emerging topics, collaborations, key authors, and research trends in Southeast Asia related to the application of machine learning in dental caries management.\n\nMethods A comprehensive selection using the Scopus database to obtain relevant research, covering publications from inception to July 2024 was done. We employed the Bibliometric approaches, including co-authorship networks, yearly publishing trends, institutional and national partnerships, keyword co-occurrence analysis, and citation analysis, for the collected data. To explore the visualization and network analysis, we employed the tools such as VOSviewer and Bibliometrix in R package.\n\nResults The final bibliometric analysis included 246 papers. We found that Malaysia became the top contributor with 59 publications, followed by Indonesia (37) and Thailand (29). Malaysia had the highest Multiple Country Publications (MCP) ratio at 0.407. Top institutions including the Universiti Sains Malaysia led with 39 articles, followed by Chiang Mai University (36) and the National University of Singapore (30) became the leader. Co-authorship analysis using VOSviewer revealed six distinct clusters. A total of 1220 scholars contributed to these publications. The top 10 keywords, including ‘human’ and ‘dental caries,’ indicated research hotspots.\n\nConclusion We found growing evidence of machine learning applications to address dental caries in Southeast Asia. The bibliometric analysis highlights key authors, collaborative networks, and emerging topics, revealing research trends since 2014. This study underscores the importance of bibliometric analysis in tackling this public health issue.", "keywords": [ "dental caries", "transmissible disease", "health and well-being", "machine learning", "artificial intelligence" ], "content": "Introduction\n\nDental caries (DC), a common chronic oral disease, is a substantial threat to global health, with high incidence rates despite disease prevention efforts (Cheng et al., 2022). individuals encountering food insecurity are significantly more prone to dental caries, as evidenced by meta-analyses that demonstrate a higher risk of caries in food-insecure individuals compared to those with food security (Drumond, De Arruda, Bernabé, Mesquita, & Abreu, 2023). Both clinical researchers and dental practitioners are rigorously investigating optimal therapeutic interventions for this condition.\n\nDC continue to be a major oral health concern in the Southeast Asia Region (SEAR), impacting children aged 5 to 15 (Kale, Kakodkar, Shetiya, & Rizwan, 2019). Studies have demonstrated an elevated prevalence of DC among children in SEAR countries, with variability among age groups and nations (Kale et al., 2019). In these investigations, the dentition status based on the 1997 WHO criteria was the most widely employed index for evaluating DC (Kale et al., 2019). Furthermore, the burden of DC extends to Cambodian preschool children, with a significant proportion developing carious lesions and pulpally affected teeth, underlining the critical need for intervention to address Early Childhood Caries (ECC) in the region (Turton, Chher, Sabbah, Durward, Hak, & Lailou, 2019). Efforts to integrate oral health into national health systems and establish uniform treatment standards are critical steps toward combating the prevalence of DC in the SEAR area (Acharya, Mathur, Tadakamadla, & Brand, 2024).\n\nTo increase diagnostic accuracy and prevent caries from being neglected, computer-based intelligent vision systems employing deep learning techniques have been developed, with a remarkable accuracy rate of 99.13% in automatic caries diagnosis based on periapical images (Imak, Celebi, Siddique, Turkoglu, Sengur, & Salam, 2022). In addition, innovations in caries detection include self-training-based approaches exploiting small sets of labeled images and enormous quantities of unlabeled images, boosting caries detection and segmentation performance without the requirement for extensive annotated data (Qayyum et al., 2023).\n\nThe current state of research in Southeast Asia regarding the application of machine learning techniques to DC research is lacking in comprehensive studies that incorporate multimodal data, including behavioral factors, radiographic imaging, and microbial analysis, to improve treatment outcomes and caries risk assessment (Jusman, Anam, Puspita, & Saleh, 2021; Velmurugadass, Rohith, Harish, & Reddy, 2023; Wu et al., 2022). While machine learning models such as Support Vector Machine (SVM) and K-Nearest Neighbors (KNN) have been effectively utilized in dental caries classification research, there remains a dearth of understanding regarding the distinct challenges and determinants that impact DC within Southeast Asian communities, notably in nations such as Thailand and Indonesia (Ula, Anjani, Ulva, Sahputra, & Pratama, 2022; Wu et al., 2022). Researchers can better understand the complex etiology of DC in this region through the application machine learning techniques to a wide range of data sources, including genetic, behavioral, and environmental factors.\n\nBibliometric analysis is of minimal significance as it marginally enriches researchers’ understanding of the subject matter and vaguely suggests potential paths for further investigation. By conducting a thorough assessment of literature utilizing machine learning methodologies, we have been able to provide a comprehensive overview of the themes, patterns, and bibliometric attributes that presently define this body of literature during the period spanning from 2002 to 2024. The outcomes derived from our research unveil significant findings and propose innovative pathways for additional exploration within this rapidly expanding realm of knowledge acquisition and academic inquiry.\n\n\nMethods\n\nWe conducted a search for pertinent articles within the Scopus database, recognized as one of the most extensive international repositories of scholarly publications. Scopus encompasses an estimated 24,000 present-day periodicals sourced from over 5,000 global publishers, encompassing peer-reviewed journals, conference papers, periodicals for commercial purposes, and scholarly book series. The database comprises roughly 75 million entries, spanning various forms of scholarly outputs such as journals, conference proceedings, patents, and publications covering a wide array of disciplines. Our search for relevant literature involved the utilization of specific keywords: (ALL ((“artificial intelligence” OR “machine intelligence” OR “robot” OR “robot technology” OR “assistant robot” OR “robot-assisted\" OR “computational intelligence” OR “computer reasoning” OR “deep learning” OR “computer vision system” OR “sentiment analysis” OR “machine learning” OR “neural network” OR “data learning” OR “expert* system” OR “natural language processing” OR “support vector machine” OR “decision tree” OR “data mining” OR “deep learning” OR “neural network” OR “bayesian network” OR “intelligent learning” OR “feature learning” OR “feature* extraction” OR “feature* mining” OR “feature* selection” OR “unsupervised clustering” OR “image* segmentation” OR “supervised learning” OR “semantic segmentation” OR “deep network*” OR “neural learning” OR “neural nets model” OR “graph mining” OR “data clustering” OR “big data” OR “knowledge graph”)) AND ALL (\"Dental caries” OR “Caries, Dental” OR “Dental Cavity” OR “Dental Decay” OR “Tooth Decay” OR “Decay, Tooth” OR “Tooth Demineralization” OR “Caries, Tooth” OR “Caries, Teeth” OR “Teeth Caries”)) AND PUBYEAR > 2001 AND PUBYEAR < 2025 AND (LIMIT-TO (DOCTYPE, “ar”) OR LIMIT-TO (DOCTYPE, “re\")) AND (LIMIT-TO (AFFILCOUNTRY, “Malaysia”) OR LIMIT-TO (AFFILCOUNTRY, “Indonesia”) OR LIMIT-TO (AFFILCOUNTRY, “Thailand”) OR LIMIT-TO (AFFILCOUNTRY, “Singapore”) OR LIMIT-TO (AFFILCOUNTRY, “Brunei Darussalam”) OR LIMIT-TO (AFFILCOUNTRY, “Philippines”) OR LIMIT-TO (AFFILCOUNTRY, “Viet Nam”) OR LIMIT-TO (AFFILCOUNTRY, “Myanmar”) OR LIMIT-TO (AFFILCOUNTRY, “Cambodia”)). Two professionals with a minimum of five years of expertise in conducting systematic reviews endorsed our search strategy subsequent to a meticulous examination of all article titles obtained. They identified all pertinent publications, with any discrepancies being settled through deliberation with an additional author. Ultimately, all articles retrieved were preserved.\n\nOnly articles that utilized Machine Learning in their findings and focused on DC were considered for the bibliometric analysis. There were no restrictions based on language. Excluded from the analysis were letters, editorials, conference abstracts, and book chapters, while research papers and reviews published in peer-reviewed journals were included. The evaluation of the articles was conducted by two experts in bibliometric analysis, who possessed extensive experience and assessed the articles according to predetermined criteria and guidelines (Martinez, Al-Hussein, & Ahmad, 2019).\n\nIn order to produce replicable and measurable data that is pertinent to policy administration, bibliometric analysis (Pritchard, 1969) serves as a quantitative assessment of scientific research, examining current research patterns within a specific field (Mooghali, Alijani, Karami, & Khasseh, 2011). Bibliometric analysis has the capability to offer a comprehensive examination of a specific subject of investigation, along with pinpointing research domains that scholars ought to delve into and methodologies that authors have formulated to achieve their objectives (Su & Lee, 2010). A holistic representation of the field allows readers to better comprehend patterns and trends in DC research.\n\nAdditionally, the distribution, proportions, and frequency for each journal were presented. The categories, proportions, and occurrence for each periodical were presented. The pertinent author ratios, occurrence, and proportion were computed for each country for both individual and multiple nations. The occurrence and citation rate for each author and organization were also provided. The research impact of each nation, periodical, organization, and author was arranged based on the quantity of publications. All information was formulated and depicted utilizing VOSviewer (Leiden University) and Bibliometrix (an R package).\n\n\nResults\n\nThe final bibliometric investigation consisted of 246 papers after the screening process. The growth in the quantity of DC articles is visualized in Figure 1.\n\nTable 1 demonstrates the geographical distribution of the leading ten countries that have conducted research on DC. Malaysia emerged as the top contributor with 59 publications, succeeded by Indonesia with 37 publications and Thailand with 29 publications. The country with the highest ratio of Multiple Country Publications (MCP) was Malaysia at 0.407, followed by Singapore at 0.375 and Indonesia at 0.27. Supplementary Figure 1 (Extended data) showcases the network of countries that have collaborated on at least one research project.\n\nSupplementary Table 1 (Extended data) showcases the leading ten institutions that have shown high productivity in conducting research on DC. Among these institutions, Universiti Sains Malaysia stands out as the most prolific university with thirty-nine published articles, followed by Chiang Mai University with thirty-six, and the National University of Singapore with thirty publications.\n\nThe utilization of the VOSviewer tool (Leiden University) was employed for conducting co-authorship analysis, aiming to present a thorough depiction of the entire network of countries involved in DC research. The level of collaboration between two countries is determined by the quantity of publications they have co-authored. Out of the total of 8 authors, only 3 authors are interconnected, with each of them having published a minimum of 5 articles. The examination of authorship by country resulted in the identification of six distinct clusters, as illustrated in Supplementary Figure 2 (Extended data).\n\nIn the discourse concerning research on DC, a total of 1220 scholars collectively contributed to the publication of 246 scholarly articles. Within the realm of DC research, Table 2 provides a comprehensive overview of the top 10 most prolific authors in this field. Noteworthy among these authors is Li Y, who authored a total of eight scholarly papers on the subject matter.\n\nThe 246 articles were divided into three keyword clusters. The top ten keywords utilized in the articles that were retrieved can be found in Table 3. It is worth mentioning that human, dental caries, article, child, and artificial intelligence were some of the predominant categories. The examination of the co-occurrence of the top 10 phrases revealed the research hotspots in the field of dental caries (Figure 2).\n\nWe delved deeper into the knowledge repository of the DC research domain. Displayed in Table 4 are the top ten articles with high citation counts. Vos T et al., in 2017, garnered the highest number of citations by June 1, 2024, totaling 5476. This particular article was published in LANCET in 2016.\n\n\nDiscussion\n\nTo the best of our knowledge, this research is the first bibliometric study to use machine learning to investigate DC. SEAR researchers are becoming more interested in using machine learning technologies to combat DC, according to this bibliometric analysis. The number of papers has increased over the previous ten years (>2014), which highlights the significance of this issue for public health as well as the potential of algorithms that use machine learning to provide assistance.\n\nMachine learning has emerged as a powerful tool in combating dental caries, with Malaysia, Indonesia, and Thailand being at the forefront of utilizing this technology (Basri, Yazid, Zain, Yusof, Rani, & Zoolfakar, 2024; Wu et al., 2022; Wu et al., 2021). Research conducted in these countries has shown promising results in early caries detection and risk prediction through the application of machine learning algorithms such as artificial neural networks (ANN), convolutional neural networks (CNN), and statistical models (Basri et al., 2024; Sadegh-Zadeh, Rahmani Qeranqayeh, Benkhalifa, Dyke, Taylor, & Bagheri, 2022; Toledo Reyes et al., 2023; Wu et al., 2022). By integrating multimodal data, including genetic, microbial, demographic, and behavioral factors, these countries have been able to identify key predictors of caries development in both primary and permanent teeth, paving the way for more effective preventive measures and personalized treatment strategies (Sadegh-Zadeh et al., 2022; Toledo Reyes et al., 2023; Wu et al., 2022; Wu et al., 2021). The collaborative efforts between researchers and healthcare professionals in Malaysia, Indonesia, and Thailand highlight the potential of machine learning in revolutionizing oral health care and addressing the global burden of dental caries.\n\nThe research landscape on dental caries utilizing machine learning reveals a notable productivity ranking among institutions. Universiti Sains Malaysia emerges as the most prolific university in this field, boasting thirty-nine published articles, showcasing a strong commitment to advancing knowledge in dental caries detection. Following closely behind is Chiang Mai University with thirty-six publications, indicating a significant contribution to the research domain of dental caries and machine learning. Additionally, the National University of Singapore has also demonstrated substantial engagement in this area with thirty publications, further enriching the scholarly discourse on the early detection and management of dental caries through innovative technological approaches. These institutions’ dedication to research in dental caries using machine learning underscores the global effort to enhance diagnostic accuracy and treatment outcomes in oral healthcare.\n\nIn line with previous studies, the co-occurrence of the top 10 phrases in dental caries research, as highlighted in the bibliometric studies (Melo, Sanz, Forner, Rodríguez-Lozano, & Guerrero-Gironés, 2022; Patil et al., 2020), reveals a strong relationship with the predominant categories of human, dental caries, article, and child. Terms related to the validity of diagnostic methods, tools, and principles used in caries diagnosis, as well as general aspects of caries detection and diagnosis, are commonly found among the top phrases. This suggests that research in dental caries is heavily centered around human subjects, particularly children, with a significant emphasis on diagnostic methods and tools, as well as the overall understanding of the disease. However, interestingly, we found that the use of the keyword ‘artificial intelligence’ is on the rise.\n\nDespite the fact that this bibliometric analysis provides interesting information, there are considerable limitations to take into account. The dependency on the Scopus database may result in the omission of significant articles from various sources. The correctness of the metadata associated with the articles also limits the study. Additionally, bibliometric analysis focuses on quantitative rather than qualitative evaluations of research findings and methodologies. Despite these limitations, the results demonstrate the increasing importance of employing machine learning to manage dental caries in Southeast Asia, which may guide future treatments and research areas.\n\n\nConclusion\n\nWe found the increasing evidence on the application of machine learning to mitigate the issue of dental caries in Southeast Asia. The bibliometric analysis identifies key authors, collaborative networks, and emerging topics, including dental caries and artificial intelligence. It also reveals growing research trends since 2014. This work underscores the significance of bibliometric analysis in tackling this critical public health challenge.", "appendix": "Availability of data, code and other materials\n\nNo data are associated with this article. Supplementary materials are available in the supplementary data.\n\nSupplementary data: https://doi.org/10.5281/zenodo.13138787\n\nThis project contains the following extended data:\n\n• Supplementary Fig 1 country 24713.docx\n\n• Supplementary Fig 2 author 24713.docx\n\n• Supplementary Table 1 top 10 institution 24713.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nReporting guidelines: https://doi.org/10.5281/zenodo.13138787\n\nSTROBE_checklist_v4_combined.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nSoftware: VOSviewer is a free software tool for constructing and visualizing bibliometric networks. To learn more, visit the VosViewer Getting Started page.\n\n\nAcknowledgment\n\nNot applicable.\n\n\nReferences\n\nAcharya S, Mathur MR, Tadakamadla SK, et al.: Assessing the status of oral health integration in South East Asian Regional Office countries’ Universal Health Coverage–A scoping review. Int. J. Health Plann. Manag. 2024; 39(2): 262–277. PubMed Abstract \| Publisher Full Text\n\nBasri KN, Yazid F, Zain MNM, et al.: Artificial neural network and convolutional neural network for prediction of dental caries. Spectrochim. Acta A Mol. Biomol. Spectrosc. 2024; 312: 124063. PubMed Abstract \| Publisher Full Text\n\nCheng L, Zhang L, Yue L, et al.: Expert consensus on dental caries management. Int. J. Oral Sci. 2022; 14(1): 17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDrumond VZ, De Arruda JAA, Bernabé E, et al.: Burden of dental caries in individuals experiencing food insecurity: a systematic review and meta-analysis. Nutr. Rev. 2023; 81(12): 1525–1555. PubMed Abstract \| Publisher Full Text\n\nImak A, Celebi A, Siddique K, et al.: Dental caries detection using score-based multi-input deep convolutional neural network. IEEE Access. 2022; 10: 18320–18329. Publisher Full Text\n\nJusman Y, Anam MK, Puspita S, et al.: Machine learnings of dental caries images based on Hu moment invariants features. Paper presented at the 2021 International Seminar on Application for Technology of Information and Communication (iSemantic). 2021.\n\nKale SS, Kakodkar P, Shetiya SH, et al.: Dental caries prevalence among 5-to 15-year-old children from SEAR countries of WHO: A systematic review and meta-analysis. Indian J. Dent. Res. 2019; 30(6): 937–947. PubMed Abstract \| Publisher Full Text\n\nMartinez P, Al-Hussein M, Ahmad R: A scientometric analysis and critical review of computer vision applications for construction. Autom. Constr. 2019; 107: 102947. Publisher Full Text\n\nMelo M, Sanz JL, Forner L, et al.: Current status and trends in research on caries diagnosis: A bibliometric analysis. Int. J. Environ. Res. Public Health. 2022; 19(9): 5011. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMooghali A, Alijani R, Karami N, et al.: Scientometric analysis of the scientometric literature. Int. J. Inf. Sci. Manag. 2011; 9(1): 19–31.\n\nPatil SS, Sarode SC, Sarode GS, et al.: A bibliometric analysis of the 100 most cited articles on early childhood caries. Int. J. Paediatr. Dent. 2020; 30(5): 527–535. PubMed Abstract \| Publisher Full Text\n\nPritchard A: Statistical bibliography or bibliometrics. J. Doc. 1969; 25: 348.\n\nQayyum A, Tahir A, Butt MA, et al.: Dental caries detection using a semi-supervised learning approach. Sci. Rep. 2023; 13(1): 749. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSadegh-Zadeh S-A, Rahmani Qeranqayeh A, Benkhalifa E, et al.: Dental caries risk assessment in children 5 years old and under via machine learning. Dent. J. 2022; 10(9): 164. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSu H-N, Lee P-C: Mapping knowledge structure by keyword co-occurrence: A first look at journal papers in Technology Foresight. Scientometrics. 2010; 85(1): 65–79. Publisher Full Text\n\nToledo Reyes L, Knorst JK, Ortiz F, et al.: Early childhood predictors for dental caries: a machine learning approach. J. Dent. Res. 2023; 102(9): 999–1006. PubMed Abstract \| Publisher Full Text\n\nTurton B, Chher T, Sabbah W, et al.: Epidemiological survey of early childhood caries in Cambodia. BMC Oral Health. 2019; 19: 1–7. Publisher Full Text\n\nUla M, Anjani FTT, Ulva AF, et al.: Application of Machine Learning With The Binary Decision Tree Model In Determining The Classification of Dental Disease. Journal of Informatics and Telecommunication Engineering. 2022; 6(1): 170–179. Publisher Full Text\n\nVelmurugadass P, Rohith A, Harish M, et al.: Dental caries detection system Using R-CNN Algorithm. Paper presented at the 2023 4th International Conference on Intelligent Engineering and Management (ICIEM). 2023.\n\nWu TT, Xiao J, Manning S, et al.: Multimodal data integration reveals mode of delivery and snack consumption outrank salivary microbiome in association with caries outcome in Thai children. Front. Cell. Infect. Microbiol. 2022; 12: 881899. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu TT, Xiao J, Sohn MB, et al.: Machine learning approach identified multi-platform factors for caries prediction in child-mother dyads. Front. Cell. Infect. Microbiol. 2021; 11: 727630. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "315857", "date": "13 Sep 2024", "name": "Juni Handajani", "expertise": [ "Reviewer Expertise Oral Biology", "Oral Immunology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study is interesting to to give insight about a bibliometric analysis however more explanation should be added in detail. In the background, an explanation of the importance of bibliometric analysis for researchers and clinicians should be added.\n\nIn the methods, the data is explained using the latest data from 2002-2024. It is suggested to add the reasons for selecting the data.\nThis study has explained the importance of bibliometric analysis in tracking public health issues such as dental caries through the application of machine learning. However, it is necessary to explain in more detail how the results of this analysis can give suggestion or recommendation to solve the health problems related to the oral health issues.\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?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12493", "date": "03 Oct 2024", "name": "Hendrik Setia Budi", "role": "Author Response", "response": "Response to the reviewer comments: This study is interesting to to give insight about a bibliometrics analysis however more explanation should be added in detail. In the background, an explanation of the importance of bibliometrics analysis for researchers and clinicians should be added. Response: we added the explanation in the last paragraph of introduction. In the methods, the data is explained using the latest data from 2002-2024. It is suggested to add the reasons for selecting the data. Response: I appreciate the recommendation. The paper has been revised to elucidate the rationale for selecting data from 2002 to 2024. This timeframe was selected because of technological advancements commencing in 2002, signifying a crucial transformation in research methodologies and data accessibility, enabling the identification of pertinent trends in the domain. Incorporating data through 2024 guarantees the inclusion of the most recent advancements and offers a thorough examination of emerging research. This timeframe offers dependable and accessible data, crucial for a comprehensive bibliometrics investigation. This clarification has been incorporated into the Methods section. This study has explained the importance of bibliometrics analysis in tracking public health issues such as dental caries through the application of machine learning. However, it is necessary to explain in more detail how the results of this analysis can give suggestion or recommendation to solve the health problems related to the oral health issues. Response: Thank you for the insightful comment. Consequently, we have broadened our discussion to elucidate how the findings of the bibliometrics analysis can offer recommendations for tackling oral health concerns, including dental caries. “The bibliometrics analysis highlights significant research trends, pivotal studies, and deficiencies in the existing literature, which can guide evidence-based public health interventions. By identifying the most commonly cited therapies or successful public health initiatives in dental caries prevention, researchers and policymakers can prioritize these techniques for widespread implementation. The machine learning methodology facilitates the discovery of emerging research domains, enabling the prompt recognition of novel therapies or preventive strategies. This can inform funding distribution and policy formulation, ensuring resources are allocated to the most effective strategies for enhancing oral health outcomes.” This elaborated explanation has been incorporated into the discussion to illustrate how bibliometrics insights might yield effective recommendations for tackling oral health issues." } ] }, { "id": "312870", "date": "24 Sep 2024", "name": "Heni Susilowati", "expertise": [ "Reviewer Expertise Oral Microbiology and Immunology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this article. This article, like similar articles in other fields of science, has become very rapidly developing, especially after the covid-19 pandemic era. This article is very interesting and quite easy to understand, analyzing aspects related to research on dental caries.\n\nThis article is an analytical review of caries research using machine learning that focuses on a specific area, Southeast Asia. Given that caries is a dental and oral disease with a very high prevalence in this region, efforts to prevent it are highly needed, one of which is by developing and improving the quality of caries research. Thus, this article will make an important contribution to the sustainability of caries prevention efforts and innovation of caries prevention methods in this region.\nMajor points: The previous article, written by Reyes et al 2022 [Ref 1], has been published in the journal Caries Research 2022; 56(3):161-170. In this regard, we suggest that the author can explain the differences in the principles of their writing with that article.\n\nMinor points: This article states that in Southeast Asia, research on dental caries using machine learning techniques is still limited; however, this is not clear compared to countries outside Southeast Asia. If the author adds this analysis to the Discussion section, it will certainly increase the contribution of the article.\n\nI do hope that this review may add positive improvement to the article.\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": "12577", "date": "09 Oct 2024", "name": "Hendrik Setia Budi", "role": "Author Response", "response": "Response to the reviewer 2 comment: Thank you for the opportunity to review this article. This article, like similar articles in other fields of science, has become very rapidly developing, especially after the covid-19 pandemic era. This article is very interesting and quite easy to understand, analyzing aspects related to research on dental caries. This article is an analytical review of caries research using machine learning that focuses on a specific area, Southeast Asia. Given that caries is a dental and oral disease with a very high prevalence in this region, efforts to prevent it are highly needed, one of which is by developing and improving the quality of caries research. Thus, this article will make an important contribution to the sustainability of caries prevention efforts and innovation of caries prevention methods in this region. Response: Thank you for your thorough review. We carefully considered your suggestions and comments and revised our manuscript accordingly. The following are our specific responses to each of the comments. All changes were highlighted in red. We hope the revisions are satisfactory and that our responses adequately address the comments. Major points: The previous article, written by Reyes et al 2022 [Ref 1], has been published in the journal Caries Research 2022; 56(3):161-170. In this regard, we suggest that the author can explain the differences in the principles of their writing with that article. References 1. Reyes L, Knorst J, Ortiz F, Ardenghi T: Machine Learning in the Diagnosis and Prognostic Prediction of Dental Caries: A Systematic Review. Caries Research. 2022; 56 (3): 161-170 Publisher Full Text Response: We have added statements in the Introduction section highlighting the gaps addressed by the current systematic review. Minor points: This article states that in Southeast Asia, research on dental caries using machine learning techniques is still limited; however, this is not clear compared to countries outside Southeast Asia. If the author adds this analysis to the Discussion section, it will certainly increase the contribution of the article. I do hope that this review may add positive improvement to the article. Response: We have included a paragraph in the Discussion section that provides a comparative analysis of the application of machine learning for dental caries research between Southeast Asia and countries outside the region." } ] } ]	1	https://f1000research.com/articles/13-908
https://f1000research.com/articles/13-1210/v1	11 Oct 24	{ "type": "Research Article", "title": "Unleashing the cardioprotective potential of Ezetimibe against Doxorubicin-induced cardiotoxicity in Wistar rats: Targeting oxidative stress and NF-κB-mediated inflammation", "authors": [ "Aya Thaer Sabry", "Mohammed AH Jabarah AL-Zobaidy", "Mohammed AH Jabarah AL-Zobaidy" ], "abstract": "Background Doxorubicin (DOX) is a potent antineoplastic agent used in treating various adult and pediatric cancers, but it tends to provoke dose-dependent cardiotoxicity. Ezetimibe (EZE), a cholesterol-lowering drug, has been reported to possess defensive actions against oxidative stress and inflammation, which are two of the main proposed mechanisms underlying the development of DOX-induced cardiotoxicity (DIC), hence, we aimed to inspect the possible protective effect of EZE against DIC in rats.\n\nMethods 24 adult male Wistar rats were allocated into four groups of six: control, DOX, 10 mg/kg EZE plus DOX and 20 mg/kg EZE plus DOX. At the end of the study, the experimental rats were anesthetized and blood samples were collected for biochemical analysis, after which the hearts were excised and heart tissue samples were obtained for biochemical and gene expression analyses.\n\nResults Pretreatment with EZE at a dose of 10 or 20 mg/kg alleviated cardiac damage induced by DOX, as EZE blunted the rise in serum levels of cardiac injury biomarkers, including cardiac troponin I (cTnI) and N-terminal pro-B-type natriuretic peptide (NT-proBNP). Additionally, pretreating rats with EZE at either dose mitigated DOX-induced oxidative stress by elevating the levels of the antioxidant enzymes superoxide dismutase (SOD) and glutathione peroxidase (GPx), with consequent reduction in the lipid peroxidation biomarker malondialdehyde (MDA) in cardiac tissues. Furthermore, pretreatment with either dose of EZE hindered DOX-mediated inflammation, where EZE suppressed cardiac nuclear factor-kappa B (NF-κB) signaling and negatively regulated the gene expression of its downstream proinflammatory cytokines, including tumor necrosis factor-alpha (TNF-α) with either dose and interleukin-1 beta (IL-1β) with the higher one.\n\nConclusions Our findings indicate that EZE exhibited cardioprotection against DIC in rats, which makes EZE an interesting area for further investigations, animal- and human-wise, that can pave the way for a potential clinical application in preventing DIC in the future.", "keywords": [ "Cardiotoxicity", "Doxorubicin", "Ezetimibe", "inflammation", "oxidative stress" ], "content": "Introduction\n\nCancer is a prevalent systemic disease characterized by uncontrolled cell proliferation and distant invasion, resulting in multiple organ damage, and ultimately, leading to a high rate of morbidity and mortality worldwide.1,2\n\nOne of the most important anticancer drugs in clinical practice is doxorubicin (DOX), also known as adriamycin, which belongs to the family of anthracycline antibiotics.3 Since its approval, DOX has been utilized in treating different types of cancer, including solid tumors, like breast, ovarian, testicular, thyroid, lung, liver, stomach and bladder cancers, as well as soft tissue sarcomas. Moreover, the drug has been employed in the treatment of hematologic malignancies, such as multiple myeloma, acute lymphoblastic leukemia, Hodgkin’s and non-Hodgkin’s lymphomas, in addition to certain childhood cancers, including neuroblastoma, osteosarcoma, Ewing’s sarcoma and rhabdomyosarcoma.1,4\n\nUnfortunately, despite its broad antitumor spectrum, the clinical application of DOX is often limited by its irreversible and dose-dependent cardiotoxicity, which can result in left ventricular dysfunction (LVD) and heart failure (HF).5,6 On top of that, it has been estimated that the risk of LVD is approximately 7–26% when the cumulative dose of DOX reaches 550 mg/m2, and about 18–48% at a cumulative dose of 700 mg/m2.7\n\nCardiotoxicity that is induced by DOX seems to be a multifactorial and complex process, and there has been a long list of proposed mechanisms in this regard,8 one of which is the ability of DOX to generate excessive reactive oxygen species (ROS) and reactive nitrogen species (RNS) to the point that they would overpower the antioxidant defense system, causing disruption of cellular hemostasis and activation of the inflammatory response pathways, eventually leading to cell death,9,10 and from this point of view, developing a strategy that can hinder the development of the aforementioned events would be a possible approach to alleviate DOX-induced cardiotoxicity (DIC).\n\nEzetimibe (EZE) is a cholesterol-lowering drug that inhibits the absorption of dietary and biliary cholesterol from the small intestine by blocking the Niemann-Pick C1-Like protein (NPC1L1), which is a sterol transporter found on the brush border membrane of the intestinal epithelium.11\n\nApart from its beneficial impact on lipid profile, EZE has been shown to have pleiotropic properties, including antioxidant and anti-inflammatory effects that are independent of its ability to inhibit NPC1L1.11,12 Therefore, the current study was conducted to assess the hypothesis that EZE can provide protection against DIC in rats, which to our knowledge, has not been studied yet, and to elucidate the mechanisms underlying EZE’s possible cardioprotective effect.\n\n\nMethods\n\nThe current study followed the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines,13 and was commenced after receiving approval from the Research Ethics Committee of the College of Medicine, University of Baghdad (approval date: December 31, 2023; approval number: 03-31).\n\nA total of 24 adult male Wistar rats, weighing 200–250 g each, were included in the present study. The animals were acquired from and maintained in the animal house of the Iraqi Center for Cancer Research and Medical Genetics under conditions of controlled temperature and relative humidity, as well as alternating 12-hour intervals of light and darkness. In addition, rats were supplied with commercial pellets and had free access to ad libitum water throughout the experiment, and were acclimatized for one week ahead of the study.\n\nAll efforts were made to ameliorate suffering of the experimental rats, including proper ventilation of the animal house, cleaning the animal cages every other day, careful handling of the animals throughout the experiment, use of effective anesthetic dose and animal euthanasia was carried out far away from the alive ones.\n\nRats included in the present study were randomly allocated into four groups of six and treated as follows:\n\nGroup I (control): rats received corn oil via oral gavage for 14 consecutive days.\n\nGroup II (DOX): rats received corn oil via oral gavage for 14 consecutive days, and a single intraperitoneal (IP) injection of 15 mg/kg DOX hydrochloride (Pfizer, Australia) on the 12th day of the experiment.\n\nGroup III (10 mg/kg EZE + DOX): rats received 10 mg/kg EZE (Meryer, China) dissolved in corn oil via oral gavage for 14 consecutive days, and a single IP injection of 15 mg/kg DOX hydrochloride on the 12th day of the experiment.\n\nGroup IV (20 mg/kg EZE + DOX): rats received 20 mg/kg EZE dissolved in corn oil via oral gavage for 14 consecutive days, and a single IP injection of 15 mg/kg DOX hydrochloride on the 12th day of the experiment.\n\nAfter 24 hours from final administration, the experimental rats were anesthetized using a combination of 150 mg/kg ketamine (Bremer Pharma GmbH, Germany) and 10 mg/kg lidocaine hydrochloride (GF Bonn GmbH, Germany). Then, for each rat, an abdominal incision was made and the inferior vena cava was exposed in order to collect a blood sample for biochemical analysis, after which the heart was excised, washed with cold phosphate-buffered saline (Sigma, USA) to get rid of any residual blood and bloated on filter paper. Following that, heart tissue samples were obtained for biochemical and gene expression analyses.\n\nEach rat blood sample was immediately transferred into a serum separator tube (gel and clot activator tube), then the tubes were placed in a test tube rack and the blood was left to clot at room temperature for 30 min. Next, the tubes were centrifuged at 3500 rpm for 20 min, after which each sample supernatant layer, which represents the serum, was transferred into a pre-chilled microcentrifuge tube and preserved at −20 °C until utilization for the biochemical analysis.\n\nFor the biochemical analysis, the heart tissue samples were homogenized in an extraction medium that involved a combination of T-PER™ Tissue Protein Extraction Reagent (Thermo Fisher Scientific, USA) and Halt™ Protease Inhibitor Cocktail, EDTA-Free (Thermo Fisher Scientific, USA). Following their manufacturers’ instructions, enough working solution of the tissue protein extraction reagent and the protease inhibitor cocktail was prepared for all samples, then the tissue samples were weighed and placed in microcentrifuge tubes, after which the appropriate volume of the prepared working solution was added to each sample, with subsequent homogenization using a tissue grinding pestle and centrifugation at 10,000 rpm for 5 min to pellet tissue debris. Lastly, each sample supernatant layer was transferred into a pre-chilled fresh microcentrifuge tube and stored at −20 °C until use.\n\nAs for the gene expression analysis, the tissue samples were lysed by placing them in microcentrifuge tubes containing 1 mL TRIzol™ Reagent (Thermo Fisher Scientific, USA) and homogenized using tissue grinding pestles, after which the tubes were incubated for 5 min to allow complete dissociation of the nucleoprotein complex. Then, 0.2 mL chloroform was added to each tube, followed by incubation for 2–3 min and centrifugation for 10 min at 12,000 rpm. Subsequently, each tube mixture was separated into a lower red phenol-chloroform organic phase, an interphase, and a colorless upper aqueous phase that contains total RNA.\n\nThe next step was to transfer each tube aqueous phase into a new microcentrifuge tube. Then, 0.5 mL isopropanol was added to each tube in order to precipitate total RNA, after which the tubes were incubated for 10 min at 4°C and centrifuged for 10 min at 12,000 rpm, with subsequent precipitation of total RNA in the form of a white gel-like pellet at the bottom of the tubes.\n\nAfterwards, for each tube, the supernatant layer was discarded, and 1 mL of 75% ethanol was added to resuspend the RNA pellet. Next, the tubes were vortexed briefly and centrifuged for 5 min at 7500 rpm, after which the supernatant layer of each tube was discarded, and the RNA pellet was air-dried for 10 min. Thereafter, 50 μL RNase-free water was added to each tube to solubilize the RNA pellet, followed by incubation in a heat block set at 55°C for 10 min. Finally, the tubes were stored at −20 °C until use.\n\nSerum levels of cardiac injury biomarkers, including cardiac troponin I (cTnI) and N-terminal pro-B-type natriuretic peptide (NT-proBNP), as well as levels of oxidative stress biomarkers, including superoxide dismutase (SOD), glutathione peroxidase (GPx) and malonaldehyde (MDA), in addition to the inflammatory biomarker nuclear factor-kappa B (NF-κB) in the heart tissue homogenates were analyzed by means of enzyme-linked immunosorbent assay (ELISA) technique, using their commercially available kits (Cloud-Clone Corp, USA) and following the manufacturers’ instructions.\n\nTwo-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to analyze the relative mRNA expression of proinflammatory cytokines, including tumor necrosis factor-alpha (TNF-α) and interleukin-1 beta (IL-1β) in cardiac tissues, and all procedures were performed following the manufacturers’ protocols. At first, for each heart tissue sample, the isolated RNA was converted to cDNA with the aid of GoScript™ Reverse Transcription System (Promega, USA), after which the synthesized cDNA was quantified utilizing QuantiFluor® dsDNA System (Promega, USA) for downstream application. Moving forward, for each gene expression analysis, a mixture consisting of GoTaq® qPCR Master Mix (Promega, USA), cDNA as well as the gene forward and reverse primers (Macrogen, South Korea) was assembled to perform qPCR, provided that the housekeeping gene, beta-actin (β-actin), was employed to normalize mRNA expression levels of the target genes, and all primer sequences are listed in Table 1.\n\nFollowing that, qPCR was carried out utilizing a magnetic induction cycler (MIC) (Bio Molecular Systems, Australia), and the cycling conditions involved initial denaturation at 95 °C/5 min, followed by 40 cycles of denaturation at 95 °C/20 s, annealing at 55 °C/20 s, 65 °C/20 s and 60 °C/20 s for TNF-α, IL-1β and β-actin primers respectively, with subsequent extension at 75 °C/20 s.\n\nAfter cycling had been completed, the amplification curves obtained for the three genes were analyzed utilizing micPCR software (version 2.10.0), in which thresholds and cycling threshold (Ct) values were automatically determined. Finally, the 2−ΔΔCt method was used to calculate the fold changes in mRNA expression of TNF-α and IL-1β relative to the control group.\n\nStatistical analysis was performed utilizing GraphPad Prism software (version 9.5.1), in which the numeric data obtained from the study, presented as mean ± standard error of the mean (SEM), were analyzed by one-way analysis of variance (ANOVA) to evaluate the statistical significance of the results, followed by Tukey’s Post Hoc test for multiple comparisons, and P values of less than 0.05 were considered to be statistically significant.\n\n\nResults\n\nAs shown in Table 2 and Figure 1, the means of serum cTnI and NT-proBNP levels in DOX-treated rats were significantly elevated in compression with those of the control group. In contrast, treatment with either 10 or 20 mg/kg EZE prior to DOX administration significantly decreased the means of the earlier mentioned cardiac injury biomarkers compared with those of DOX group.14\n\na Significant difference versus control group.\n\nb Significant difference versus DOX group.\n\n* p < 0.001.\n\n p < 0.0001.\n\nSerum levels of (A) cTnI and (B) NT-proBNP. Data are presented as mean ± standard error of the mean (SEM), n = 6. p < 0.001; **p < 0.0001. cTnI, cardiac troponin I; DOX, doxorubicin; EZE, ezetimibe; NT-proBNP, N-terminal pro-B-type natriuretic peptide.\n\nDOX administration resulted in a significant depletion in the means of cardiac SOD and GPx levels, as well as a significant increment in the mean of cardiac MDA levels compared with their corresponding values in the control group. On the other hand, the means of cardiac SOD and GPx levels were significantly higher, while the mean of cardiac MDA levels was significantly lower in rats that were treated with either 10 or 20 mg/kg EZE before receiving DOX than in those that received only DOX (Table 3 and Figure 2).14\n\na Significant difference versus control group.\n\nb Significant difference versus DOX group.\n\nc Significant difference versus 10 mg/kg EZE + DOX group.\n\n p < 0.05.\n\n p < 0.01.\n\n* p < 0.001.\n\n**** p < 0.0001.\n\nLevels of cardiac (A) SOD, (B) GPx and (C) MDA. Data are presented as mean ± standard error of the mean (SEM), n = 6. p < 0.05; p < 0.01; p < 0.001; *p < 0.0001. DOX, doxorubicin; EZE, ezetimibe; GPx, glutathione peroxidase; MDA, malonaldehyde; SOD, superoxide dismutase.\n\nTreatment with DOX significantly elevated the mean of cardiac NF-κB levels when it was set up against that of the control group. On the contrary, rats that received either 10 or 20 mg/kg EZE ahead of DOX administration exhibited a significant decline in the mean of the earlier stated biomarker in comparison with that of DOX group, as presented in Table 4 and Figure 3.14\n\na Significant difference versus control group.\n\nb Significant difference versus DOX group.\n\nc Significant difference versus 10 mg/kg EZE + DOX group.\n\n p < 0.05.\n\n p < 0.01.\n\n* p < 0.001.\n\nLevels of cardiac (A) NF-κB, (B) TNF-α relative mRNA expression and (C) IL-1β relative mRNA expression. Data are presented as mean ± standard error of the mean (SEM), n = 6. p < 0.05; p < 0.01; **p < 0.001. DOX, doxorubicin; EZE, ezetimibe; IL-1β, interleukin-1 beta; NF-κB, nuclear factor-kappa B; TNF-α, tumor necrosis factor-alpha.\n\nAdditionally, a significant increment in the means of cardiac TNF-α and IL-1β relative mRNA expression levels was observed in DOX-treated rats compared with those of the control group. Meanwhile, pretreatment with either 10 or 20 mg/kg EZE caused a significant reduction in the mean of cardiac TNF-α relative mRNA expression levels compared with that of DOX-challenged rats. However, only pretreatment with 20 mg/kg EZE significantly diminished the mean of cardiac IL-1β relative mRNA expression levels in comparison with that of DOX group (Table 4 and Figure 3).14\n\n\nDiscussion\n\nOne of the highly efficient antineoplastic agents with broad-spectrum application is the anthracycline antibiotic DOX. Nevertheless, the cardiotoxicity it causes represents a feared adverse effect and a potentially life-threatening response that can limit the clinical use of DOX and affect the quality of life of cancer patients, apart from their oncological prognosis.2,15\n\nResults of the current study revealed that treating rats with a single IP injection of 15 mg/kg DOX hydrochloride caused a significant elevation in the means of serum levels of cardiac injury biomarkers, including cTnI and NT-proBNP, which is consistent with the results obtained from previous studies.16–18\n\nConsidering their high sensitivity, cardiac injury biomarkers are utilized for the early detection of cardiotoxicity, especially cardiac troponins, which are regulatory proteins that control calcium-mediated contractile function of the heart, and it has been demonstrated that newly elevated serum cTnI levels in patients receiving anthracyclines anticipate subsequent development of LVD.7,19,20 Additionally, NT-proBNP, which is secreted by cardiomyocytes in increased amounts during conditions of volume or pressure overload of the heart, is widely utilized in the detection of HF, and in terms of chemotherapy, its use can be helpful,7,21–23 based on studies that validated its role as a marker for the detection of DIC.24,25\n\nThe present study also showed that DIC was associated with notable changes in oxidative stress biomarkers in cardiac tissue, where the means of the antioxidant enzymes SOD and GPx were significantly depleted, while there was a significant increment in the mean of MDA contents, provided that MDA is a highly reactive dialdehyde derived from peroxidation of polyunsaturated fatty acids by means of reactive species.26,27\n\nThe abovementioned outcomes are compatible with those acquired from prior studies,17,28,29 which reinforces the theory that one of the major mechanisms underlying the development of DIC is oxidative stress, and the latter can be defined as a state of imbalance in which the production of ROS, such as superoxide anion (O2• –), hydrogen peroxide (H2O2) and hydroxyl radical (HO•), as well as RNS, such as peroxynitrite anion (ONOO−), exceeds the capacity of the endogenous antioxidant system, resulting in cellular damage.10,30,31\n\nOne of the reasons that makes the heart particularly susceptible to injury by DOX-induced oxidative stress is that antioxidant enzymes, including SOD, catalase (CAT) and GPx are less abundantly expressed in cardiomyocytes as compared with other cell types. Another reason is that DOX has a tendency to accumulate in the mitochondria, and since the heart is the body’s most metabolically active organ, it tends to have the highest mitochondrial content, rendering the cardiac cell the most vulnerable to oxidative damage.5,32\n\nStudies elucidated that DOX induces oxidative stress as the quinone moiety in its structure undergoes one-electron reduction through the action of NADH- or NADPH-dependent enzymes to form a semiquinone radical, which tends to react rapidly with an oxygen molecule (O2), where it donates an electron to O2 to form O2• –, while recycling itself back to the quinone form, and this cycle is referred to as the redox cycling of DOX. Subsequently, the generated O2• – can be transformed by SOD into H2O2 that can be converted either into O2 and water (H2O) by means of CAT or GPx, or into a highly reactive and toxic HO• in the presence of ferrous ion (Fe2+). One more point to consider is that O2• – can also react with nitric oxide (NO) to form the RNS ONOO−. Eventually, overproduced HO• and ONOO− interact with the biomolecules nearby, causing lipid peroxidation, protein modification, DNA damage as well as disruption of mitochondrial function,33–35 as shown in Figure 4.\n\nCAT, catalase; DOX, doxorubicin; GPx, glutathione peroxidase; GR, glutathione reductase; GSH, reduced glutathione; GSSG, glutathione disulfide; NAD+, nicotinamide adenine dinucleotide; NADP+, nicotinamide adenine dinucleotide phosphate; NADH, reduced nicotinamide adenine dinucleotide; NADPH, reduced nicotinamide adenine dinucleotide phosphate; SOD, superoxide dismutase. Chemical formulas: Fe+2, ferrous iron; Fe+3, ferric iron; H+, proton; H2O, water; H2O2, hydrogen peroxide; HO•, hydroxyl radical; NO, nitric oxide; O2, oxygen; O2• −, superoxide anion; ONOO −, peroxynitrite anion.\n\nOur results also manifested that DOX administration significantly increased the means of cardiac NF-κB levels and its downstream proinflammatory cytokines, including TNF-α and IL-1β relative mRNA expression levels, and these observations are in agreement with those reported in other studies,36–38 thereby supporting another theory through which DOX induces cardiotoxicity, and that is inflammation.\n\nResearchers pointed out that inflammation in DIC occurs as a result of NF-κB activation in response to oxidative stress,10,39 provided that NF-κB is a family of DNA binding proteins that function as homo or heterodimers to mediate the expression of numerous genes involved in cell proliferation, inflammation, immunity and apoptosis.40,41 In its resting state, NF-κB presents in the cytoplasm as a complex with a member of inhibitory proteins known as inhibitors of NF-κB (IκΒs) that mask nuclear localization signals to prevent NF-κB from being imported into the nucleus. However, in response to stimulation, an IκB kinase (IKK) phosphorylates IκB to promote its ubiquitination and proteasomal degradation, after which NF-κB becomes freed from IκB and translocates into the nucleus, where it upregulates the expression of proinflammatory cytokines, such as TNF-α, IL-1β, IL-6 and others, with consequent development of cardiac inflammation that can lead to cardiac remodeling and dysfunction.39,42–44\n\nIn our research, we aimed to investigate whether EZE can safeguard against DIC in rats. Interestingly, treating rats with either 10 or 20 mg/kg EZE before DOX administration significantly mitigated the cardiotoxic potential of the anticancer drug, and that was evidenced by a significant decline in the means of serum cTnI and NT-proBNP levels compared with those of DOX group, and to our knowledge, the current research is the first to estimate serum levels of the two earlier mentioned biomarkers in rats after receiving EZE for the prevention of a cardiac pathological condition.\n\nMoreover, results of the present study demonstrated that pretreatment with EZE at a dose of 10 or 20 mg/kg caused a significant increment in the means of cardiac SOD and GPx levels, along with a significant reduction in the mean of cardiac MDA levels compared with those of DOX group, and these outcomes emphasize that the drug possesses antioxidant effect, as it was reported in an in vitro study, where EZE protected endothelial cells against oxidative stress induced by oxidized low-density lipoproteins, in which a reduction in ROS formation, as well as an enhancement in SOD and CAT activities were observed.45\n\nOur study also showed that in comparison with DOX-challenged rats, pretreatment with either 10 or 20 mg/kg EZE significantly decreased the means of cardiac NF-κB levels and TNF-α relative mRNA expression levels, while the 20 mg/kg dose was also capable of significantly reducing the mean of cardiac IL-1β relative mRNA expression levels, and these findings can be attributed to the anti-inflammatory effect of the drug that was mentioned in previous studies, including one that utilized THP-1 human monocytic cell line treated with water-soluble cholesterol to induce inflammation, where the results manifested that EZE treatment dramatically decreased the proinflammatory cytokine TNF-α production by silencing NF-κB signaling.46\n\nThe antioxidant and anti-inflammatory actions of EZE were also evidenced in other studies, and in this regard, a recent one pointed out that EZE alleviated acetic acid-induced ulcerative colitis in rats by hampering oxidative stress and inflammation.11 Also, in a transient middle cerebral artery occlusion model in rats, EZE attenuated oxidative stress and prevented neuroinflammation, resulting in an improvement in neurological outcome.12\n\nThe rationale behind EZE attenuation of oxidative stress and inflammation can be related to its ability to activate nuclear factor erythroid 2-related factor 2 (Nrf2), a transcription factor that modulates the expression of genes involved in cellular defense against oxidative stress insults, including the ones encoding SOD, CAT, GPx and other antioxidants.47,48 Under basal conditions, Nrf2 is bound to Kelch-like ECH-associated protein 1 (Keap1), a negative regulator of Nrf2 that mediates its ubiquitination and proteasomal degradation to prevent unwarranted expression of Nrf2-target genes. However, under stressed conditions, Nrf2 dissociates from Keap1 and translocates into the nucleus, where it upregulates the expression of antioxidant genes through binding to their antioxidant response element (ARE), which is an enhancer sequence placed at the promoter region of several cytoprotective genes. Consequently, the activity of antioxidants would be boosted, leading to suppression of oxidative stress-mediated activation of the NF-κB signaling pathway,49 as shown in Figure 5.\n\nAMPK, adenosine monophosphate-activated protein kinase; ARE, antioxidant response element; DOX, doxorubicin; EZE, ezetimibe; IκB, inhibitor of nuclear factor-kappa B; IKK, IκB kinase; Keap1, Kelch-like ECH-associated protein 1; NF-κB, nuclear factor-kappa B; Nrf2, nuclear factor erythroid 2-related factor 2; P, phosphate.\n\nThe possible mechanism through which EZE induces Nrf2 activation has been elucidated in one study, where the drug was found to disrupt the interaction between Nrf2 and Keap1 through adenosine monophosphate-activated protein kinase (AMPK)-mediated phosphorylation of p62, an adaptor protein that functions as a central scaffold in various cellular processes, including autophagy. Accordingly, upon its phosphorylation, p62 binds to Keap1, resulting in autophagic degradation of the latter, after which the liberated Nrf2 translocates into the nucleus to upregulate the expression of antioxidant genes,48,50 and this can explain, at least in part, why EZE exerted a protective effect against DIC in rats (Figure 5).\n\n\nConclusion\n\nThe current research demonstrates, for the first time, that pretreatment with the cholesterol-lowering drug EZE can attenuate DIC in rats, as evidenced by a notable reduction in the serum levels of cardiac injury biomarkers. Also, we believe that the cardioprotective effect of EZE was mediated by suppression of DOX-induced oxidative stress and NF-κB-mediated inflammation, where EZE raised the levels of antioxidant enzymes, diminished lipid peroxidation and downregulated the gene expression of proinflammatory cytokines in cardiac tissues, thereby, it has the potential to serve as a promising candidate for alleviating DOX-induced cardiac injury.\n\n\nEthical considerations\n\nThe current study followed the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines,13 and was commenced after receiving approval from the Research Ethics Committee of the College of Medicine, University of Baghdad (approval date: December 31, 2023; approval number: 03-31).", "appendix": "Data availability\n\nZenodo: Dataset for biochemical and gene expression analyses. https://doi.org/10.5281/zenodo.13730571. 14\n\nThis project contains the following underlying data:\n\n• Biochemical analysis.xlsx\n\n• Gene expression analysis.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nNCBI Protein: Tumor necrosis factor-alpha (TNF-α). Accession number NM_012675; http://identifiers.org/ncbiprotein:NM_012675.3\n\nNCBI Protein: Interleukin-1 beta (IL-1β). Accession number NM_031512; http://identifiers.org/ncbiprotein:NM_031512.2\n\nNCBI Protein: Beta-actin (β-actin). Accession number NM_031144; http://identifiers.org/ncbiprotein:NM_031144.3\n\nReporting guidelines\n\nZenodo: ARRIVE checklist for ‘Unleashing the cardioprotective potential of Ezetimibe against Doxorubicin-induced cardiotoxicity in Wistar rats: Targeting oxidative stress and NF-κB-mediated inflammation’, https://doi.org/10.5281/zenodo.13750802. 13\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nJones IC, Dass CR: Doxorubicin-induced cardiotoxicity: causative factors and possible interventions. J. Pharm. Pharmacol. 2022; 74(12): 1677–1688. PubMed Abstract \| Publisher Full Text\n\nKong CY, Guo Z, Song P, et al.: Underlying the Mechanisms of Doxorubicin-Induced Acute Cardiotoxicity: Oxidative Stress and Cell Death. Int. J. Biol. Sci. 2022; 18(2): 760–770.\n\nAl-Hassawi WW, Al-Sammak MA: Effect of doxorubicin on the histological structure of the kidneys in male albino rats. J. Fac. Med. Baghdad. 2014; 55(4): 384–389. Publisher Full Text\n\nChu E: Cancer Chemotherapy.Katzung BG, editor. Basic & Clinical Pharmacology. 14th ed.New York, NY: McGraw-Hill Education; 2017; pp. 948–976.\n\nSongbo M, Lang H, Xinyong C, et al.: Oxidative stress injury in doxorubicin-induced cardiotoxicity. Toxicol. Lett. 2019; 307: 41–48. Publisher Full Text\n\nLaPlant K, May P: Anticancer Drugs.Whalen K, Feild C, Radhakrishnan R, editors. Lippincott® Illustrated Reviews: Pharmacology. 7th ed.Philadelphia: Wolters Kluwer; 2019; pp. 454–480.\n\nZamorano JL, Lancellotti P, Rodriguez Muñoz D, et al.: 2016 ESC Position Paper on cancer treatments and cardiovascular toxicity developed under the auspices of the ESC Committee for Practice Guidelines: The Task Force for cancer treatments and cardiovascular toxicity of the European Society of Cardiology (ESC). Eur. Heart J. 2016; 37(36): 2768–2801. PubMed Abstract \| Publisher Full Text\n\nCarvalho FS, Burgeiro A, Garcia R, et al.: Doxorubicin-induced cardiotoxicity: from bioenergetic failure and cell death to cardiomyopathy. Med. Res. Rev. 2014; 34(1): 106–135. PubMed Abstract \| Publisher Full Text\n\nAl-Hussaniy HA, Alburghaif AH, Alkhafaje Z, et al.: Chemotherapy-induced cardiotoxicity: a new perspective on the role of Digoxin, ATG7 activators, Resveratrol, and herbal drugs. J. Med. Life. 2023; 16(4): 491–500. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShi S, Chen Y, Luo Z, et al.: Role of oxidative stress and inflammation-related signaling pathways in doxorubicin-induced cardiomyopathy. Cell Commun. Signal. 2023; 21(1): 61. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMostafa RE, Abdel-Rahman RF: Ezetimibe alleviates acetic acid-induced ulcerative colitis in rats: targeting the Akt/NF-κB/STAT3/CXCL10 signaling axis. J. Pharm. Pharmacol. 2023; 75(4): 533–543. PubMed Abstract \| Publisher Full Text\n\nYu J, Wang WN, Matei N, et al.: Ezetimibe Attenuates Oxidative Stress and Neuroinflammation via the AMPK/Nrf2/TXNIP Pathway after MCAO in Rats. Oxidative Med. Cell. Longev. 2020; 2020: 4717258.\n\nSabry AT: Unleashing the cardioprotective potential of Ezetimibe against Doxorubicin-induced cardiotoxicity in Wistar rats: Targeting oxidative stress and NF-κB-mediated inflammation. Zenodo. 2024.\n\nSabry AT: Dataset for biochemical and gene expression analyses. Zenodo. 2024.\n\nCardinale D, Iacopo F, Cipolla CM: Cardiotoxicity of Anthracyclines. Front. Cardiovasc. Med. 2020; 7: 26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Kuraishy HM, Al-Gareeb AI, Alkhuriji AF, et al.: Investigation of the impact of rosuvastatin and telmisartan in doxorubicin-induced acute cardiotoxicity. Biomed. Pharmacother. 2022; 154: 113673. PubMed Abstract \| Publisher Full Text\n\nHaybar H, Goudarzi M, Mehrzadi S, et al.: Effect of gemfibrozil on cardiotoxicity induced by doxorubicin in male experimental rats. Biomed. Pharmacother. 2019; 109: 530–535. PubMed Abstract \| Publisher Full Text\n\nKarabulut D, Ozturk E, Kaymak E, et al.: Thymoquinone attenuates doxorubicin-cardiotoxicity in rats. J. Biochem. Mol. Toxicol. 2021; 35(1): e22618. PubMed Abstract \| Publisher Full Text\n\nIbrahim AE, El-Yassin HD, Al-Janabi HK: The impact of inflammation on Resistin, Insulin and Troponin I in Acute Myocardial Infarction patients. J. Fac. Med. Baghdad. 2011; 53(3): 338–342. Publisher Full Text\n\nOhtsuki I, Morimoto S: Troponin.Lennarz WJ, Lane MD, editors. Encyclopedia of Biological Chemistry. 2nd ed.Waltham: Academic Press; 2013; pp. 445–449.\n\nBirukov A, Eichelmann F, Kuxhaus O, et al.: Opposing Associations of NT-proBNP With Risks of Diabetes and Diabetes-Related Complications. Diabetes Care. 2020; 43(12): 2930–2937. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNasser TH, El-Yassin HD, Yakoob S: Β-Natriuretic Peptide Level as a Predictor for the Severity of LV Dysfunction. J. Fac. Med. Baghdad. 2008; 49(4): 438–448. Publisher Full Text\n\nRossi R, Jabrah D, Douglas A, et al.: Investigating the Role of Brain Natriuretic Peptide (BNP) and N-Terminal-proBNP in Thrombosis and Acute Ischemic Stroke Etiology. Int. J. Mol. Sci. 2024; 25(5). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKittiwarawut A, Vorasettakarnkij Y, Tanasanvimon S, et al.: Serum NT-proBNP in the early detection of doxorubicin-induced cardiac dysfunction. Asia Pac. J. Clin. Oncol. 2013; 9(2): 155–161. PubMed Abstract \| Publisher Full Text\n\nZidan A, Sherief LM, El-sheikh A, et al.: NT-proBNP as early marker of subclinical late cardiotoxicity after doxorubicin therapy and mediastinal irradiation in childhood cancer survivors. Dis. Markers. 2015; 2015: 513219.\n\nHassan ZM, Hamdi RA, Al Bassam EN: Evaluation of the Role of Serum Malondialdehyde in the Pathogenesis of Diabetic Retinopathy. J. Fac. Med. Baghdad. 2022; 64(3): 195–198. Publisher Full Text\n\nThanoon IA, Tawfik NO, Hussin FN: Oxidative Stress & C – Reactive Protein In Patients With Arthritis. J. Fac. Med. Baghdad. 2007; 49(2): 227–230.\n\nCicek B, Hacimuftuoglu A, Yeni Y, et al.: Chlorogenic Acid Attenuates Doxorubicin-Induced Oxidative Stress and Markers of Apoptosis in Cardiomyocytes via Nrf2/HO-1 and Dityrosine Signaling. J. Pers. Med. 2023; 13(4). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElwany NE, Mahmoud NM: Mohamed Abdel Hamid A: Hypericum perforatum alleviates doxorubicin induced cardiotoxicity in rats via enhancement of cardiac adiponectin-AMPK signaling. Zagazig Univ. Med. J. 2020; 26(6): 1140–1151. Publisher Full Text\n\nAli EA, Tahseen YH, El-Yassin HD: Thyroid Disorders and the Level of Malondialdehyde. J. Fac. Med. Baghdad. 2009; 51(1): 67–70. Publisher Full Text\n\nRidha NM, Taher MA: Oxidative Stress and Some Liver Functions Parameters in Patients with Symptomatic Cholelithiasis. J. Fac. Med. Baghdad. 2013; 55(1): 73–76. Publisher Full Text\n\nWu BB, Leung KT, Poon EN: Mitochondrial-Targeted Therapy for Doxorubicin-Induced Cardiotoxicity. Int. J. Mol. Sci. 2022; 23(3). Publisher Full Text\n\nAl-Aubaidy HA, El-Yassin HD, Hashim HM, et al.: Oxidative DNA damage and Lipid Peroxidation as Markers of Oxidative Stress Type 2 Diabetic Patients. J. Fac. Med. Baghdad. 2008; 50(1): 110–119. Publisher Full Text\n\nJungsuwadee P: Doxorubicin-induced cardiomyopathy: An update beyond oxidative stress and myocardial cell death. Cardiovasc. Regen. Med. 2016; 3: e1127.\n\nKashkool AH, Al-Sabbagh MS, Al-Kashali DK, et al.: The Possible Cytoprotective Effects of Antioxidant Drugs (Vitamin E and C) Against the Toxicity of Doxorubicin in Breast Cancer Patients. J. Fac. Med. Baghdad. 2009; 51(1): 95–100. Publisher Full Text\n\nHekmat AS, Navabi Z, Alipanah H, et al.: Alamandine significantly reduces doxorubicin-induced cardiotoxicity in rats. Hum. Exp. Toxicol. 2021; 40(10): 1781–1795. PubMed Abstract \| Publisher Full Text\n\nLiao W, Rao Z, Wu L, et al.: Cariporide Attenuates Doxorubicin-Induced Cardiotoxicity in Rats by Inhibiting Oxidative Stress, Inflammation and Apoptosis Partly Through Regulation of Akt/GSK-3β and Sirt1 Signaling Pathway. Front. Pharmacol. 2022; 13: 850053. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMa T, Kandhare AD, Mukherjee-Kandhare AA, et al.: Fisetin, a plant flavonoid ameliorates doxorubicin-induced cardiotoxicity in experimental rats: the decisive role of caspase-3, COX-II, cTn-I, iNOs and TNF-α. Mol. Biol. Rep. 2019; 46(1): 105–118. PubMed Abstract \| Publisher Full Text\n\nSumneang N, Tanajak P, Oo TT: Toll-like Receptor 4 Inflammatory Perspective on Doxorubicin-Induced Cardiotoxicity. Molecules. 2023; 28(11). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHollomon MG, Patterson L, Santiago-O’Farrill J, et al.: Knock down of Fas-Associated Protein with Death Domain (FADD) Sensitizes Osteosarcoma to TNFα-induced Cell Death. J. Cancer. 2020; 11(7): 1657–1667. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZinatizadeh MR, Schock B, Chalbatani GM, et al.: The Nuclear Factor Kappa B (NF-kB) signaling in cancer development and immune diseases. Genes Dis. 2021; 8(3): 287–297. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Hassan AAH: Role of Pro- and Anti-Inflammatory Cytokines in Rheumatoid Arthritis: Correlation with Disease Activity. J. Fac. Med. Baghdad. 2010; 52(3): 286–291. Publisher Full Text\n\nGiridharan S, Srinivasan M: Mechanisms of NF-κB p65 and strategies for therapeutic manipulation. J. Inflamm. Res. 2018; 11: 407–419. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu D, Zhong Z, Karin M: NF-κB: A Double-Edged Sword Controlling Inflammation. Biomedicine. 2022; 10(6). Publisher Full Text\n\nQin J, Wang LL, Liu ZY, et al.: Ezetimibe Protects Endothelial Cells against Oxidative Stress through Akt/GSK-3β Pathway. Curr. Med. Sci. 2018; 38(3): 398–404. PubMed Abstract \| Publisher Full Text\n\nQin L, Yang YB, Yang YX, et al.: Anti-inflammatory activity of ezetimibe by regulating NF-κB/MAPK pathway in THP-1 macrophages. Pharmacology. 2014; 93(1-2): 69–75.\n\nHe F, Ru X, Wen T: NRF2, a Transcription Factor for Stress Response and Beyond. Int. J. Mol. Sci. 2020; 21(13). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee DH, Han DH, Nam KT, et al.: Ezetimibe, an NPC1L1 inhibitor, is a potent Nrf2 activator that protects mice from diet-induced nonalcoholic steatohepatitis. Free Radic. Biol. Med. 2016; 99: 520–532. PubMed Abstract \| Publisher Full Text\n\nBhakkiyalakshmi E, Sireesh D, Ramkumar KM: Redox Sensitive Transcription via Nrf2-Keap1 in Suppression of Inflammation.Chatterjee S, Jungraithmayr W, Bagchi D, editors. Immunity and Inflammation in Health and Disease: Emerging Roles of Nutraceuticals and Functional Foods in Immune Support. United States: Academic Press; 2018; pp. 149–161. Publisher Full Text\n\nJakobi AJ, Huber ST, Mortensen SA, et al.: Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake. Nat. Commun. 2020; 11(1): 440. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "331613", "date": "28 Oct 2024", "name": "Natticha Sumneang", "expertise": [ "Reviewer Expertise cardiovascular system", "inflammation", "DIC" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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. Given that EZE confers protection against doxorubicin-induced cardiac injury. It would also be interested to examine their effects on cardiac function. 2. Although using EZE alleviated doxorubicin-induced cardiac toxicity by exhibiting antioxidant and anti-inflammatory properties, it would be helpful to clarify the rationale for choosing EZE (a cholesterol-lowering drug) approach. 3. The focus of this study is the limited evidence establishing a cause-and-effect relationship between the proposed molecular mechanisms and the cardioprotective effects of EZE against DIC.\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": "12737", "date": "01 Nov 2024", "name": "Aya Thaer", "role": "Author Response", "response": "Dear Dr. Natticha Sumneang Thank you so much for reviewing our article, we're grateful for your feedback and suggestions. Here are our justifications: 1. Regarding cardiac function examination, we also recommend that it should be taken into consideration in future studies regarding the cardioprotective potential of EZE against DIC, as the current one focused on cardiac injury evaluation by measuring cardiac biomarkers. 2. Our rationale for choosing the cholesterol-lowering drug EZE to protect against DIC in our research is that previous studies revealed that EZE possesses defensive actions against oxidative stress and inflammation, which are two of the main proposed mechanisms underlying the development of DIC, and several studies supported the potential of EZE's pleiotropic effects in improving cardiovascular outcomes, however, none has carried out the current investigation. Hence, we aimed to inspect the possible protective effect of EZE against DIC in rats. 3. We agree that further investigations should be carried out, where other tests can be performed, or perhaps other mechanisms can be studied, as the current study focused on preventing DOX-induced cardiac injury by targeting oxidative stress and inflammation, nevertheless, we believe that the results obtained from the present study are promising and can motivate other researchers who are interested in the prevention of DIC. Also, we would be pleased to provide any additional details that you wish us to include in our research article, regarding methods, analysis or other sections." } ] } ]	1	https://f1000research.com/articles/13-1210
https://f1000research.com/articles/13-486/v1	17 May 24	{ "type": "Research Article", "title": "Reliability, validity, and minimal clinically important differences for the Thai-version of the Aberdeen Varicose Vein Questionnaire (AVVQ-Thai) in patients with chronic venous disease", "authors": [ "Boonying Siribumrungwong", "Pinit Noorit", "Termpong Reanpang", "Chaowanun Pornwaragorn", "Chumpon Wilasrusmee", "Suchat Wongsuwanich", "Kanoklada Srikuea", "Saritphat Orrapin", "Thoetphum Benyakorn", "Andrew Malcolm Garratt", "Kittipan Rerkaserm", "Pinit Noorit", "Termpong Reanpang", "Chaowanun Pornwaragorn", "Chumpon Wilasrusmee", "Suchat Wongsuwanich", "Kanoklada Srikuea", "Saritphat Orrapin", "Thoetphum Benyakorn", "Andrew Malcolm Garratt", "Kittipan Rerkaserm" ], "abstract": "Background Patient-reported outcome measures (PROMs) are essential for assessing the health of patients with chronic venous disease (CVD). Therefore, we aimed to translate the Aberdeen Varicose Vein Questionnaire into Thai language (AVVQ-Thai) and evaluate its reliability and validity. Minimal clinically important differences (MCID) of the AVVQ-Thai also be estimated.\n\nMethods International standards for PROM translation were followed including the forward-backwards translation of the AVVQ. Patients with Clinical-Etiology-Anatomy-Pathophysiology (CEAP) C2-C6 with truncal reflux were prospectively included. Venous interventions were used to treat reflux and varicosities. Patients’ characteristics, venous clinical severity scores (VCSS), EuroQol EQ-5D, and AVVQ-Thai were collected pre- and one-month post-intervention. AVVQ-Thai was also collected one to two weeks after the initial visit by reply-paid postal questionnaire.\n\nResults The study included 119 patients (30% C2, 29% C3, 28% C4, 11% C5, and 2% C6). The AVVQ-Thai had good internal consistency with Cronbach’s alpha of 0.783 and moderate reliability with the intraclass correlation coefficient of 0.67 (95%CI: 0.50, 0.79). The AVVQ-Thai was significantly correlated with VCSS and was able to discriminate patients with different levels of health problems as assessed by EQ-5D at both pre-and post-intervention, demonstrating good construct and discriminative validity. The median AVVQ scores improved significantly after intervention from 15.4 (IQR 8.3, 24.2) to 4.2 (IQR 1.3, 8.4) in C2-C3, and 18.9 (IQR 14.1, 25.5) to 7.3 (IQR 4.6, 16.3) in C4-C6. The MCID of the AVVQ was 6.21 on the 0-100 scale, which equates to the level of difference necessary to be clinically meaningful.\n\nConclusions AVVQ-Thai has satisfactory evidence for internal consistency, reliability, validity, and responsiveness to change and is recommended for application in Thailand.", "keywords": [ "AVVQ", "Aberdeen Varicose Vein Questionnaire", "reliability", "validity", "minimal clinically important differences", "venous", "reflux" ], "content": "Introduction\n\nChronic venous disease (CVD) is common in the general population, with the prevalence varying from 17-40%,1 and affects the quality of life of patients.2,3 Management includes medication, compressive stockings, ablation of superficial and perforator vein reflux, and treatment of iliocaval venous obstruction.4,5 Outcomes of treatment include hemodynamic success (i.e., occlusion of the ablated refluxed vein), venous clinical severity score (VCSS), and self-reported health and quality of life (QoL) using patient-reported outcome measures (PROMs).4\n\nPROMs are important for patient-centered approach and useful for helping detect change after treatment and comparing treatment effects between different interventions. Several PROMs have been evaluated and recommended as assessment tools in patients with CVD, including generic (e.g., SF-36, EuroQol EQ-5D) and venous-specific QoL measurements (e.g., Aberdeen Varicose Vein Questionnaire (AVVQ), Chronic Venous Insufficiency questionnaire (CIVIQ), and Venous Insufficiency Epidemiological and Economic study (VEINS)).4,6\n\nGeneric PROMs such as the EQ-5D can contribute to cost per quality adjusted life year calculation as part of economic evaluation. Venous-specific PROMs are of clinical relevance and sensitive to small but important changes in health and differences between patients.3 Our earlier study in Thai patients with CVD found significant improvement of generic QoL after venous intervention, measured by EQ-5D.7 However, 12% of the patients already had the highest possible EQ-5D scores at pre-intervention, which limits responsiveness to change.7\n\nAVVQ is the most rigorously evaluated PROM in patients with varicose veins.8 It demonstrated good validity, reliability, and responsiveness and had similar performance across countries.9–11 Nevertheless, differences in language, culture, and values between Thailand and European countries should be considered before application of the AVVQ in Thai patients.12 Furthermore, minimal clinically important difference (MCID), defined as the smallest change perceived as beneficial or meaningful by the patient, is important for interpretation of the scores in clinical settings.13\n\nCurrently, there is no validated translated venous-specific questionnaire in Thailand. Therefore, this study aimed to translate the AVVQ into the Thai language and assess the reliability and validity of the Thai-translated version (AVVQ-Thai). In addition, we also estimated minimal clinically important differences (MCID) for the AVVQ score.\n\n\nMethods\n\nA multicenter prospective observational cohort study was conducted from January 2019 to Dec 2021 in 4 hospitals across Thailand, which included Thammasat University Hospital in the Central, Maharaj Nakorn Chaing Mai Hospital in the North, Ramathibodi in the Central, and Chonburi Hospital in the East of Thailand. The study was approved by all study center’s ethic committees (The Human Research Ethics Committee of Thammasat University (Medicine) with approval number MTU-EC-SU-1-130/61 (approved date July 26, 2018) for Thammasat University Hospital; The Research Ethics Committee 4 of Faculty of Medicine, Chiang Mai University with approval number SUR-2562-06329 (approved date June 28, 2019) for Maharaj Nakorn Chaing Mai Hospital; The Office of The Committee for Research, Faculty of Medicine Ramathibodi Hospital Mahidol University with approval number MURA2019/173 (approved date March 13, 2019 for Ramathibodi Hospital; The Research Ethic Committee of Chonburi Hospital with approval number 26/62/S/h3 (approved date March 20, 2019) for Chonburi Hospital. The study was adhered to the Declaration of Helsinki.\n\nThe study conformed with the COSMIN reporting guideline for studies on measurement properties of patient-reported outcome measures.14 The reporting checklist was uploaded as extended data in the online database.15\n\nThe study included adults of ≥18 years of age able to read Thai and Clinical-Etiology-Anatomy-Pathophysiology (CEAP) C2 to C6 with symptoms related to the venous disease and unilateral pathologic reflux of great (GSV) or small saphenous veins (SSV) who would undergo venous intervention. Exclusion criteria were concomitant peripheral arterial disease, morbid obesity (body mass index ≥ 35 kg/m2), pregnancy, recurrence varicose vein, history of previous venous intervention, and history of deep vein thrombosis or presence of deep vein obstruction from duplex scan. All participants signed informed consent before entering the study.\n\nAVVQ is a clinically derived questionnaire specifically developed for patients with varicose veins. First developed and tested for measurement properties by Garratt et al. in 1993,3 it comprises four domains (pain and dysfunction, cosmetic appearance, extent of varicosity, and complications) with 13 questions that are summed based on a clinical weighting and scored from 0 to 100, where higher score represent greater CVD severity.3,11\n\nSW and a team form the Language Institute of Thammasat University undertook translation which followed recommendations by the European Organization for Research and Treatment of Cancer.16 First, the English version of AVVQ was independently translated into Thai by two professional Thai translators, trying to make the language clear and as simple as possible. Then, the research team assessed both translations for equivalence with the original one. Any discrepancies were resolved by consensus and resulted in a single provisional forward translation. After that, the provisional Thai forward translation was back translated to English by another native English speaker and compared with the original English version to ensure equivalence. The final translated Thai version was reviewed by the research team and was used in the study. The English translated and final translated Thai versions were uploaded online as extended data and were available at https://doi.org/10.5281/zenodo.10990113.15\n\nBaseline characteristics, EQ-5D-3L, preoperative AVVQ-Thai, and venous clinical severity scores (VCSS), were obtained at an initial outpatient visit using a self-completed pen and paper questionnaire and clinician completion for VCSS. For purposes of assessing test-retest reliability, patients took a second AVVQ-Thai questionnaire and reply-paid envelope home for completion 1 to 2 weeks later (retest AVVQ-Thai). After the venous intervention, postoperative complications, EQ-5D-3L, postoperative AVVQ-Thai, and VCSS were collected one-month post-intervention. Mean scores of the preoperative and retest AVVQ-Thai were used as preoperative scores in the analysis. In the case of missing data for individual AVVQ questions, data from the preoperative or retest questionnaires were substituted accordingly.\n\nRefluxed veins were ablated using either endovenous thermal ablation (i.e., radiofrequency (RFA), endovenous laser ablation (EVLA)), or surgical therapy (saphenofemoral ligation with stripping for GSV or SPJ ligation for SSV) depending on patients’ preferences and costs incurred. All procedures were performed under regional anesthesia. Briefly, radiofrequency ablation was performed with tumescent anesthesia to ablate the GSV at 2–3 cm distal to the saphenofemoral junction to the GSV around the knee level. In surgical therapy, saphenofemoral junction was ligated flush to the common femoral vein. Then, GSV was stripped from proximal to distal GSV around the knee level. Pathologic perforator insufficiency was treated by ultrasound-guided foam sclerotherapy in CEAP C5-6. Varicosities would be treated concomitantly by either phlebectomy or foam sclerotherapy.4\n\nSample size is estimated using the rule of thumb for questionnaires testing. At least 10 subjects were necessary for 1 question with a minimum number of 100 subjects to ensure the stability of the variance-covariance matrix.17 As a result, with 13 questions in AVVQ so 130 patients were necessary. Accounting for 10% loss follow up rate, 145 patients would be recruited.\n\nCronbach’s alpha and intraclass correlation coefficient (ICC) were used to assessed internal consistency and test-retest reliability of the AVVQ-Thai, respectively. Cronbach’s alpha reflects the homogeneity of the AVVQ questions in assessing the same concepts. Higher values reflect higher levels of consistency/homogeneity with level of 0.70 and above being satisfactory.18 ICC and 95%CI were estimated by a two-way mixed effect model with an absolute agreement for the overall scores and within each item of the AVVQ. Values of less than 0.5, 0.5 – 0.75, 0.75 – 0.9, and greater than 0.9 indicate poor, moderate, good, and excellent reliability, respectively.19\n\nHypothesis testing was used to assess the construct validity of the AVVQ-Thai including correlations of the AVVQ scores and VCSS both pre- and postintervention, and comparing median AVVQ scores between patients with different degrees of problems reported each dimension of EQ-5D (no problem vs. some and severe problems). It was hypothesized that AVVQ scores would have low to moderate correlations with the VCSS because while there is some content overlap, the latter is completed by the clinician and is more concerned with symptoms than how varicose veins affect quality of life. It was hypothesized that patients with higher scores on the AVVQ would report more problems across the five EQ-5D dimensions. Responsiveness of the AVVQ-Thai was assessed by determining the change in the AVVQ scores after intervention according to the CEAP clinical class (C2-C3 and C4-C6). Ceiling effects, or the proportion of patients with the best possible scores that cannot be improved with intervention, were also compared for the AVVQ and EQ-5D.\n\nDistribution-based methods were used to estimate minimal clinically important differences (MCID) of the AVVQ.20,21 There are several methods of MCID derivation. Four types of methods were analyzed and reported for consideration. 1) 0.5 of SD of the observed change (SDobserved change) in AVVQ as recommended following a systematic review by Norman et al.22 2) Standard error of measurement (SEM), which represents the variability of the scores. Any score difference below the SEM is likely due to measurement error rather than genuine change. Thus, it is the most conservative value of MCID. SEM was calculated by the equation SEM=SDof baseline score×(1−r)where r = the intraclass correlation coefficient. 3) Minimum detectable change (MDC) is calculated from SEM. MDC95 is the measurement that has 95% confidence that this value is more than the measurement error. The equation is MDC=SEM×1.96×√2. 4) MCID derived from effect size (ES) by multiplying SD of the baseline scores with 0.2, which is the accepted value for small ES.\n\nAnalysis was undertaken in STATA version 16.1 and a p value of less than 0.5 considered as statistically significant. Missing data was excluded from the analysis. Spearman’s correlation was used to determine correlation. The Wilcoxan rank-sum test, and the Wilcoxan matched-pairs signed-rank test was used to compare median scores for independent and dependent continuous data, respectively.\n\n\nResults\n\nA total of 119 patients were recruited, including 67 (56%) from Thammasat University, 25 (21%) from Chonburi, 19 (16%) from Maharaj Nakorn Chaing Mai, and 8 (7%) from Ramathibodi hospital. Seventy-six (64%) patients were female, with a mean age of 56 years (SD = 13) and a BMI of 26 kg/m2 (SD 5). Most patients were in Clinical-Etiology-Anatomy-Pathophysiology (CEAP) Clinical class 2 (30%), followed by C3 (29%), C4 (28%), C5 (11%), and C6 (2%). Most patients had GSV reflux (94%), while the remainder had short saphenous vein reflux. There were 43 (36%) patients who had completed a university education.\n\nAll patients had successful operations, including 47 (40%) RFA, 11 (9%) EVLA, and 61 (51%) open surgery. The mean VCSS scores improved from 6.7 (SD = 3.2) preoperatively to 2.7 (SD 2.3) post-operation, with a mean difference of 4 (95%CI: 3.6, 4.5). (p < 0.001). One hundred eighteen (99%) and 116 (97%) patients completed preoperative and postoperative EQ-5D, respectively. The proportion of patients reporting no problems was significantly less in across all but the self-care dimension (Figure 2).\n\nThe translation process resulted in the Thai-version of the AVVQ (AVVQ-Thai).15 One hundred and ten (92%), 94 (79%), and 112 (94%) patients completed the preoperative, retest, and postoperative AVVQ-Thai, respectively. The mean AVVQ scores improved from 18.9 (standard deviation (SD) = 10.9; interquartile range (IQR) 10.1, 24.9) preoperatively to 7.8 (SD = 7.6; IQR 2, 11) at 1-month post operation (p < 0.001) with the mean difference of 11.1 (95%CI: 8.8, 13.4).\n\nReliability\n\nCronbach’s alpha of the preoperative and postoperative AVVQ were 0.783 and 0.790, demonstrating acceptable internal consistency. The overall ICC for the total scores was 0.67 (95%CI: 0.50, 0.79), demonstrating moderate reliability. Item No.8 had the lowest ICC of 0.51 (95%CI: 0.27, 0.67), while item No.3 had the highest ICC of 0.85 (95%CI: 0.79, 0.90). All items had ICCs that were more than 0.5, and 3 out of 13 (23%) had ICCs that were more than 0.75 (Table 1).\n\nValidity\n\nBoth pre-and postoperative AVVQ were significantly correlated with pre- and postoperative VCSS, with Spearman’s correlation coefficient of 0.353 (p < 0.001) and 0.457 (p < 0.001), respectively. Median AVVQ score comparisons between groups with different degrees of problems by EQ-5D are shown in Table 2. AVVQ was able to discriminate patients with different levels of problems across all EQ-5D dimensions with significant differences in median AVVQ scores between groups in both pre-and postoperative periods except for postoperative self-care.\n\n* Wilcoxan rank-sum test.\n\nAVVQ scores and VCSS improved significantly after operation in all severity classifications, see Table 3. Twenty-five patients (21%) reported having no problem for all EQ-5D dimensions preoperatively, whereas no patients had the lowest possible score for the AVVQ. For these 25 patients, there were changes in AVVQ scores with the pre-and postoperative median scores of 12.2 (IQR 5.5, 21.9) and 4.2 (IQR 0, 8.2) (p = 0.002), respectively.\n\n* Wilcoxan matched-pairs signed-rank test.\n\nMinimal clinically important differences (MCID)\n\nThe MCIDs of the AVVQ varied from 2.18 to 17.16 across the four methods used (Table 4). The lowest value was from accepted small ES MCID, which was 2.8, followed by 6.17, 6.21 and 17.16 from SDobserverd change/2, SEM, and MDC95, respectively.\n\n\nDiscussion\n\nOur study demonstrated acceptable internal consistency and moderate levels of reliability for the AVVQ-Thai. The AVVQ-Thai also had good construct and discriminative validity as demonstrated by the correlations with VCSS scores and significant differences of AVVQ scores between groups with different levels of health problems as assessed by EQ-5D. In addition, the AVVQ also had evidence of responsiveness to change following venous intervention.\n\nAVVQ has been translated and validated in many languages, including Dutch,11 Hungarian,23 Spanish,24 and Portuguese.25 To our knowledge, the Thai-translated AVVQ (AVVQ-Thai) is the first translation in Asian countries. The Thai version also had good internal consistency comparable to other languages.10,23,25 However, it had moderate test-retest reliability, which is less than the Portuguese AVVQ-Brazil, which had good test-retest reliability.\n\nThe AVVQ-Brazil study excluded patients more than 60 years old and had cognitive disorders (Mini-mental state examination),25 while our study did not. About 43% of our patients were older than 60 years. Some older patients could not read the questionnaires independently due to eye problems and need for assistance. This problem might also have affected the results of retest AVVQ, which patients completed at home. Moreover, the different setting compared to test completion in the clinic, might also have led to slightly poorer results.\n\nMost previous studies compared AVVQ with SF-36 and demonstrated good discriminative validity and responsiveness of the AVVQ.2,9,11,23,25 Our study used EQ-5D because of its lower respondent burden and it has been validated in Thai.26 AVVQ-Thai also had good discriminative validity when using EQ-5D as a comparator too (Table 2), except in the postoperative self-care domain. The proportion of patients reporting no problem in the self-care domain was not significantly different after venous intervention (Figure 2). These findings suggest that self-care might not be affected by CVD.\n\nTwenty-five patients (21%) had the highest possible EQ-5D score pre-intervention in the current study, which correspond with previous results study with CVD patients in Thailand.7 Among these 25 patients, 10 (40%), 8 (32%), 5 (20%), and 2 (8%) were in CEAP C2, C3, C4, and C5, respectively, but the AVVQ can detect a change in these patients which shows the importance of applying AVVQ or other venous-specific QoL measurements alongside widely used generic PROMs such as the EQ-5D.\n\nMCID is important for aiding the interpretation of score changes of PROMs including AVVQ and shows whether the difference is clinically meaningful and not just statistically significant. The estimates varied depending on the methods used but most studies recommend that SEM-derived MCID is acceptable as the most conservative approach,20,21 which was 6.21. This estimate was very similar to 0.5*SDobserved change-derived approach,22 which was 6.17. ES-derived MCID, which was 2.18 in our study, likely to be an underestimate, while MDC95, which was 17.16, might be too high. Hence, in applications of the AVVQ in Thai patients, we recommend the MCID of 6.21 as a benchmark for clinical significance. However, this recommendation is subjected to further testing.\n\nOur study had some limitations. The retest-AVVQ response rate of 79% while comparable to that from earlier test-retest studies,2 was lower than that for clinic-based pre-and post-intervention completion. The number of included participants was less than the number from sample size calculation. We derived the MCID from the distribution-based approach. Other methods include anchor-based and sensitivity-specificity-based derivations. Results from the distribution-based approach were based on statistical variance measures, which meet statistical concepts, but might not reflect actual clinical significance differences. The other two methods compared the MCID with the clinical response measured by global transition questions (GTQ) to differentiate patients who are better or not, which might reflect better clinical significance. However, there is still no standard criteria for the GTQ, which weakens the validity of these methods.\n\n\nConclusion\n\nThai-translated AVVQ had evidence for internal consistency, test-retest reliability, construct validity and responsiveness to changes in health following venous intervention. The AVVQ is recommended for application in Thailand for assessing the health and outcomes of patients with CVD.\n\nPreregistered data analysis: The study was not preregistered.\n\nEthic committees (The Human Research Ethics Committee of Thammasat University Medicine) with approval number MTU-EC-SU-1-130/61 (approved date July 26, 2018) for Thammasat University Hospital; The Research Ethics Committee 4 of Faculty of Medicine, Chiang Mai University with approval number SUR-2562-06329 (approved date June 28, 2019) for Maharaj Nakorn Chaing Mai Hospital; The Office of The Committee for Research, Faculty of Medicine Ramathibodi Hospital Mahidol University with approval number MURA2019/173 (approved date March 13, 2019) for Ramathibodi Hospital; The Research Ethic Committee of Chonburi Hospital with approval number 26/62/S/h3 (approved date March 20, 2019) for Chonburi Hospital.\n\nAll participants signed informed consent before entering the study.", "appendix": "Data availability\n\nZenodo.org: Reliability, validity, and minimal clinically important differences for the Thai-version of the Aberdeen Varicose Vein Questionnaire (AVVQ-Thai). https://doi.org/10.5281/zenodo.10990113. 15\n\nThis project contains the following underlying data:\n\n• Checklist for Reliability, validity, and minimal clinically important differences for the Thai-version of the Aberdeen Varicose Vein Questionnaire (AVVQ-Thai) in patients with chronic venous disease, https://doi.org/10.5281/zenodo.10990113, file name: COSMIN checklist_AVVQ.docx.\n\n• The dataset for Reliability, validity, and minimal clinically important differences for the Thai-version of the Aberdeen Varicose Vein Questionnaire (AVVQ-Thai) in patients with chronic venous disease, https://doi.org/10.5281/zenodo.10990113, file name: AVVQ Thai raw data.dta\n\n• Reversed English-translated AVVQ for reversed English-translated AVVQ Reliability, validity, and minimal clinically important differences for the Thai-version of the Aberdeen Varicose Vein Questionnaire (AVVQ-Thai) in patients with chronic venous disease, https://doi.org/10.5281/zenodo.10990113, file name: Reverse-translated version.docx.\n\n• Final translated Thai AVVQ for Reliability, validity, and minimal clinically important differences for the Thai-version of the Aberdeen Varicose Vein Questionnaire (AVVQ-Thai) in patients with chronic venous disease, https://doi.org/10.5281/zenodo.10990113, file name: appendix 1_ThaiAVVQ.docx\n\nData are available under the terms of the Creative Commons Zero v1.0 Universal (CC0).\n\n\nAcknowledgements\n\nThis study was supported by the Research Group in Surgery, Faculty of Medicine, Thammasat University. Dr. Rerkasem was supported by Chiang Mai University.\n\n\nReferences\n\nBeebe-Dimmer JL, Pfeifer JR, Engle JS, et al.: The epidemiology of chronic venous insufficiency and varicose veins. Ann. Epidemiol. 2005 Mar; 15(3): 175–84. Epub 2005/02/23. eng. PubMed Abstract \| Publisher Full Text\n\nGarratt AM, Ruta DA, Abdalla MI, et al.: Responsiveness of the SF-36 and a condition-specific measure of health for patients with varicose veins. Qual. Life Res. Int. J. Qual. Life Asp. Treat. Care Rehab. 1996 Apr; 5(2): 223–34. Epub 1996/04/01. eng. PubMed Abstract \| Publisher Full Text\n\nGarratt AM, Macdonald LM, Ruta DA, et al.: Towards measurement of outcome for patients with varicose veins. Qual. Health Care. 1993 Mar; 2(1): 5–10. Epub 1993/02/07. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGloviczki P, Comerota AJ, Dalsing MC, et al.: The care of patients with varicose veins and associated chronic venous diseases: clinical practice guidelines of the Society for Vascular Surgery and the American Venous Forum. J. Vasc. Surg. 2011 May; 53(5 Suppl): 2s–48s. Epub 2011/05/06. eng. Publisher Full Text PubMed Abstract \|\n\nDe Maeseneer MG, 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. European journal of vascular and endovascular surgery: the official journal of the European Society for. Vasc. Surg. 2022 Feb; 64(2): 581–2. Epub 2022/01/15. eng. PubMed Abstract \| Publisher Full Text\n\nWittens C, Davies AH, Baekgaard N, et al.: Editor’s Choice - Management of Chronic Venous Disease: Clinical Practice Guidelines of the European Society for Vascular Surgery (ESVS). European journal of vascular and endovascular surgery: the official journal of the European Society for. Vasc. Surg. 2015 Jun; 49(6): 678–737. Epub 2015/04/30. eng. PubMed Abstract\n\nSiribumrungwong B, Noorit P, Wilasrusmee C, et al.: Quality of life after great saphenous vein ablation in Thai patients with great saphenous vein reflux. Asian J. Surg. 2017 Jul; 40(4): 295–300. Epub 2015/12/03. eng. PubMed Abstract\n\nAber A, Poku E, Phillips P, et al.: Systematic review of patient-reported outcome measures in patients with varicose veins. Br. J. Surg. 2017 Oct; 104(11): 1424–32. Epub 2017/08/05. eng. PubMed Abstract \| Publisher Full Text\n\nSmith JJ, Garratt AM, Guest M, et al.: Evaluating and improving health-related quality of life in patients with varicose veins. J. Vasc. Surg. 1999 Oct; 30(4): 710–9. Epub 1999/10/08. eng. PubMed Abstract \| Publisher Full Text\n\nKlem TM, Sybrandy JE, Wittens CH, et al.: Reliability and validity of the Dutch translated Aberdeen Varicose Vein Questionnaire. Eur. J. Vasc. Endovasc. Surg. 2009 Feb; 37(2): 232–8. Epub 2008/11/11. eng. PubMed Abstract \| Publisher Full Text\n\nKlem TM, Sybrandy JE, Wittens CH: Measurement of health-related quality of life with the Dutch translated Aberdeen Varicose Vein Questionnaire before and after treatment. Eur. J. Vasc. Endovasc. Surg. 2009 Apr; 37(4): 470–6. Epub 2009/01/02. eng. PubMed Abstract \| Publisher Full Text\n\nBeaton DE, Bombardier C, Guillemin F, et al.: Guidelines for the process of cross-cultural adaptation of self-report measures. Spine. 2000 Dec 15; 25(24): 3186–91. Epub 2000/12/22. eng. PubMed Abstract \| Publisher Full Text\n\nTan M, Onida S, Davies AH: Quality of life tools reflect disease severity but can they be improved? Phlebology. 2019 Jul; 34(6): 369–71. Epub 2018/12/06. eng. PubMed Abstract\n\nGagnier JJ, Lai J, Mokkink LB, et al.: COSMIN reporting guideline for studies on measurement properties of patient-reported outcome measures. Qual. Life Res. Int. J. Qual. Life Asp. Treat. Care Rehab. 2021 Aug; 30(8): 2197–218. Epub 2021/04/06. eng. PubMed Abstract \| Publisher Full Text\n\nReliability, validity, and minimal clinically important differences for the Thai-version of the Aberdeen Varicose Vein Questionnaire (AVVQ-Thai). [database on the Internet]. Zenodo. 2024. Publisher Full Text\n\nKoller M, Aaronson NK, Blazeby J, et al.: Translation procedures for standardised quality of life questionnaires: The European Organisation for Research and Treatment of Cancer (EORTC) approach. Eur. J. Cancer. 2007 Aug; 43(12): 1810–20. Epub 2007/08/11. eng. PubMed Abstract \| Publisher Full Text\n\nTerwee CB, Bot SD, de Boer MR , et al.: Quality criteria were proposed for measurement properties of health status questionnaires. J. Clin. Epidemiol. 2007 Jan; 60(1): 34–42. Epub 2006/12/13. eng. PubMed Abstract \| Publisher Full Text\n\nTaber KS: The Use of Cronbach’s Alpha When Developing and Reporting Research Instruments in Science Education. Res. Sci. Educ. 2018 2018/12/01; 48(6): 1273–1296. Publisher Full Text\n\nKoo TK, Li MY: A Guideline of Selecting and Reporting Intraclass Correlation Coefficients for Reliability Research. J. Chiropr. Med. 2016 Jun; 15(2): 155–63. Epub 2016/06/23. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPage P: Beyond statistical significance: clinical interpretation of rehabilitation research literature. Int. J. Sports Phys. Ther. 2014 Oct; 9(5): 726–36. Epub 2014/10/21. eng. PubMed Abstract \| Free Full Text\n\nBloom DA, Kaplan DJ, Mojica E, et al.: The Minimal Clinically Important Difference: A Review of Clinical Significance. Am. J. Sports Med. 2023 Feb; 51(2): 520–4. Epub 2021/12/03. eng. PubMed Abstract \| Publisher Full Text\n\nNorman GR, Sloan JA, Wyrwich KW: Interpretation of changes in health-related quality of life: the remarkable universality of half a standard deviation. Med. Care. 2003 May; 41(5): 582–92. Epub 2003/04/30. eng. PubMed Abstract \| Publisher Full Text\n\nKiss G, Szabó D, Tékus E, et al.: Validity and Reliability of the Hungarian Version of Aberdeen Varicose Vein Questionnaire. Int. J. Environ. Res. Public Health. 2022 Jan 31; 19(3). Epub 2022/02/16. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIbarra Sanchez G, Ansuategui Vicente M, Revuelta Suero S, et al.: Translation and adaptation to Spanish of Aberdeen varicose veins questionnaire. Phlebology. 2023 Jun; 38(5): 315–21. Epub 2023/04/05. eng. PubMed Abstract \| Publisher Full Text\n\nLeal FJ, Couto RC, Pitta GBB: Validation in Brazil of a Questionnaire on Quality of Life in Chronic Venous Disease (Aberdeen Varicose Veins Questionnaire for Brazil/AVVQ-Brazil). J. Vasc. Bras. 2015; 14(3): 241–7. Publisher Full Text\n\nKimman M, Vathesatogkit P, Woodward M, et al.: Validity of the Thai EQ-5D in an occupational population in Thailand. Qual. Life Res. Int. J. Qual. Life Asp. Treat. Care Rehab. 2013 Aug; 22(6): 1499–506. Epub 2012/08/29. eng. PubMed Abstract \| Publisher Full Text" }	[ { "id": "289501", "date": "20 Jun 2024", "name": "Nawaphan Taengsakul", "expertise": [ "Reviewer Expertise Vascular surgery", "venous surgery", "general surgery" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSiribumrungwong B and co-authors developed the Aberdeen Varicose vein Questionnaire (AVVQ) in Thai language that would be the first validated questionnaire for evaluating chronic venous disease in Thailand. The AVVQ is the patient-reported outcome measure that is used widely and well accepted in reliability and validity as recommended in many guideline such as ESVS guideline for reporting. Therefore, It is important to translate for usable in their language. Moreover, The AVVQ-Thai had the satisfactory result that can be useful and reproducible for further study in Thailand. I think this paper is well conducted, and the manuscript is certainly well written. The strengths of this research was the translation process and the statistical analysis. But I see some details that should be clarified. First of all, it should be added about pilot test after the forward, backward translation and expert review that could be necessary for represent about usability for patients before distribution. Seconds, the recent guideline recommended change to r-VCSS that prove that more reliability. The authors should clarify why to used VCSS, not r-VCSS to compare. The third problem, this study did not exclude the elderly that might effect to ability for answering questionnaire especially when compared with AVVQ-Brazil study. In part of discussion, may be added that the further study with excluded the patient with impaired sensation should be considered. Lastly, the successful operation should be defined such as the evidence of target vein occlusion (<2 cm from junction and >90% occluded vein) by ultrasound\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": "12580", "date": "11 Oct 2024", "name": "Boonying Siribumrungwong", "role": "Author Response", "response": "Reviewer comment: 1. First of all, it should be added about pilot test after the forward, backward translation and expert review that could be necessary for represent about usability for patients before distribution. Author response: Thank you for your comments. The translation was independently done by two professionals translators, consensus by the research team, and reversed to English by a native English speaker. We have added the reversed English translation for review in the data availability. Reviewer comment: 2. Seconds, the recent guideline recommended change to r-VCSS that prove that more reliability. The authors should clarify why to used VCSS, not r-VCSS to compare. Author response: Thank you for your comments. We must apologize for the missed clarification. We had already used the revised version of the VCSS in the study. We have rewritten it in the manuscript to be more clarified and added a reference for it. Reviewer comment: 3. The third problem, this study did not exclude the elderly that might effect to ability for answering questionnaire especially when compared with AVVQ-Brazil study. In part of discussion, may be added that the further study with excluded the patient with impaired sensation should be considered. Author response: We have revised the study based on your comments. Reviewer comment: 4. Lastly, the successful operation should be defined such as the evidence of target vein occlusion (<2 cm from junction and >90% occluded vein) by ultrasound Author response: We have added the definition of successful operation in the manuscript." } ] }, { "id": "313678", "date": "03 Sep 2024", "name": "Masumeh Hessam", "expertise": [ "Reviewer Expertise psychometric propertis of outcome measures in rehabilitation." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1: Please reorganize the presentation of method and results starting by internal consistency, reliability, continuing by construct validity in whole manuscript. 2: The introduction cannot explain the gap in the current researches. 3: Since the purpose of this study is to investigate the psychometric properties of the instrument, it is recommended to give a brief description of these properties (validity and reliability) in introduction section. 4: Discussion lacks some clarity. I think you should discuss your results and not explained them. So it can be re-write for explaining the results, not just presenting them. 5: Authors should be mentioned suggestions for future studies (such as investigating responsiveness and the ability of the questionnaire to detect clinical changes) in the discussion section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12590", "date": "07 Feb 2025", "name": "Boonying Siribumrungwong", "role": "Author Response", "response": "1: Please reorganize the presentation of method and results starting by internal consistency, reliability, continuing by construct validity in whole manuscript. Response: We have organized the method and results section in order as the suggestion. 2: The introduction cannot explain the gap in the current researches. Response: We have included a sentence in the introduction addressing the limited data available on the minimal clinically important difference for AVVQ. This data remains insufficient to fully explain the knowledge gap that this study aims to address. 3: Since the purpose of this study is to investigate the psychometric properties of the instrument, it is recommended to give a brief description of these properties (validity and reliability) in introduction section. Response: As you suggested, we have added brief descriptions of validity, reliability, and responsiveness in the introduction section according to the COSMIN guidelines. 4: Discussion lacks some clarity. I think you should discuss your results and not explained them. So it can be re-write for explaining the results, not just presenting them. Response: Thank you for the comment. We tried our best to discuss the test-retest reliability more in the discussion part. 5: Authors should be mentioned suggestions for future studies (such as investigating responsiveness and the ability of the questionnaire to detect clinical changes) in the discussion section. Response: We have added some suggestions for future studies in the discussion section." } ] } ]	1	https://f1000research.com/articles/13-486
https://f1000research.com/articles/13-38/v1	08 Jan 24	{ "type": "Systematic Review", "title": "Primary health care as the main guarantor of a healthy population in the country and a global challenge in the world: a systematic review", "authors": [ "Gulnara Abashidze-Gabaidze", "Lali Khurtsia", "Mishiko Gabaidze", "Lasha Loria", "Gulnara Abashidze-Gabaidze" ], "abstract": "Background Primary health care (PHC) is a fundamental aspect of healthcare systems globally, playing a crucial role in maintaining the health of the population. Despite its importance, there are still gaps in the delivery of PHC services. This study aims to analyze the healthcare system and the existing gaps to develop strategies for improving PHC services.\n\nMethods This study is a meta-analysis of the last ten years of written research on PHC services. The data sources include peer-reviewed articles and other relevant literature on PHC services. The study explores PHC services in different countries, assesses existing research, and creates and implements new strategies for improving medical services in practice Studies focused explicitly on primary health care systems, policies, or interventions were included in the study. Eligibiloty criteria included research conducted within the past ten years to present contemporary insights, studies available in peer-reviewed journals and reputable databases and literature examining the influence of PHC on population health outcomes. This meta-analysis incorporates 38 studies within the last decade.\n\nResults The study identifies gaps in PHC services, including issues with access to care, affordability, and quality of care. It provides insights into the challenges faced by PHC systems worldwide, highlighting the need for strategies to address these issues.\n\nConclusions The study contributes to a better understanding of the challenges faced by PHC systems worldwide and provides insights for policymakers and healthcare providers to improve healthcare services. The study’s findings underscore the importance of addressing the gaps in PHC services to improve health outcomes and ensure the provision of equitable and accessible healthcare services.", "keywords": [ "primary health care", "health care system", "health outcomes", "medical services", "global challenge", "meta-analysis", "strategies", "implementation", "policies", "gaps." ], "content": "Introduction\n\nPrimary health care (PHC) is an essential component of any healthcare system and is regarded as the foundation of any healthcare delivery system worldwide.1 It is the first point of contact for individuals seeking medical care. It aims to provide accessible, affordable, and high-quality healthcare services to everyone regardless of socioeconomic status.2 The PHC system includes a range of services, such as disease prevention, health promotion, diagnosis, treatment, and rehabilitation.2 The World Health Organization (WHO) defines PHC as “an essential health care based on practical, scientifically sound, and socially acceptable methods and technology, made universally accessible to individuals and families in the community through their full participation and at a cost that the community and country can afford to maintain at every stage of their development in the spirit of self-reliance and self-determination”.3\n\nPHC is essential for maintaining the health of individuals and communities, particularly in developing countries where access to healthcare is limited.4 PHC services are particularly important for vulnerable populations, such as children, pregnant women, and the elderly.5,6 In many low-income countries, access to health care services is limited, and PHC is often the only available source of medical care.6 The importance of PHC in improving health outcomes and reducing health disparities has been recognized globally, and efforts are being made to strengthen PHC systems worldwide.7\n\nDespite the importance of PHC, there still needs to be more in delivering PHC services in many countries, including developing and developed countries. These gaps may include inadequate funding, human resources, lack of medical supplies and equipment, inadequate infrastructure, and inadequate health policies and regulations. These gaps may prevent individuals from accessing the necessary medical care and may negatively impact health outcomes, particularly in vulnerable populations.8,9\n\nTherefore, this research aims to analyze the PHC system and identify the gaps in the delivery of PHC services. This research aims to study the PHC services of different countries,10,11 assess existing research on PHC services,12,13 and create and implement new strategies for improving medical services in practice. The research question is how the health care system works and how gaps are maintained to develop strategies to improve services. The objectives are to explore the PHC services of different countries, study and assess existing research,14,15 and create and implement new strategies for improving medical services in practice.\n\nThe methodology of this study is a meta-analysis of the last ten years of written research on PHC services. The data sources include peer-reviewed articles and other relevant literature on PHC services.16,17 This study’s expected outcome is identifying gaps in PHC services and developing new strategies to improve health outcomes in practice. This study will contribute to a better understanding of the challenges faced by PHC systems worldwide and provide insights for policymakers and healthcare providers to improve healthcare services.18\n\nIn conclusion, PHC is an essential component of any healthcare system and is regarded as the foundation of any healthcare delivery system worldwide.19 The gaps in the delivery of PHC services need to be identified and addressed to improve health outcomes, particularly in vulnerable populations. This research aims to study the PHC services of different countries, assess existing research on PHC services, and create and implement new strategies for improving medical services in practice. This study will contribute to a better understanding of the challenges faced by PHC systems worldwide and provide insights for policymakers and healthcare providers to improve healthcare services.\n\nIn the modern world, the role of public health has especially increased when the pandemic of infectious diseases has become relevant, as already shown by the Covid pandemic, which has had enormous global political and economic consequences in the world.20 Therefore, modern public health is reviewed in a global context and requires international regulations, transnational actions, and solutions based on coordinated cooperation among different countries of the world.21\n\nThis systematic review on the topic of “Primary Health Care as The Main Guarantor of a Healthy Population in The Country and A Global Challenge in The World” aims to comprehensively investigate and the review seeks to explore several critical aspects and address specific inquiries:\n\n1. Effectiveness of Primary Health Care Systems\n\n2. Comparative Analysis Across Countries\n\n3. Health Outcomes and Disparities\n\n4. Challenges and Opportunities\n\n5. Global Relevance and Implications\n\n6. Research Gaps and Future Directions\n\nBy conducting a systematic review around these aspects, the objective was to synthesize existing knowledge, provide a clear and evidence-based understanding of the role of primary health care in population health, and offer insights that can guide policies, strategies, and practices to optimize the benefits of primary health care in fostering a healthier population locally and globally.\n\n\nMethods\n\nThis research aims to analyze the primary health care (PHC) system and identify the gaps in the delivery of PHC services. To achieve this aim, a meta-analysis of the last ten years of written research on PHC services was conducted. The meta-analysis will include a systematic literature review, data synthesis, and statistical analysis of the results. The research question is how the health care system works and how gaps are maintained to develop strategies to improve services. The objectives are to explore the PHC services of different countries, study and assess existing research, and create and implement new strategies for improving medical services in practice.\n\nFor this systematic review, an extensive literature search was conducted using various electronic databases: PubMed, Embase, Cochrane Library, and Web of Science. The aim was to identify pertinent peer-reviewed articles and literature on Primary Health Care (PHC) services published within the last ten years.\n\nThe search strategy employed specific search terms and combinations to ensure a comprehensive search process. The following keywords were utilized to capture a broad spectrum of relevant literature:\n\n• “Primary health care”\n\n• “Health care system”\n\n• “Health outcomes”\n\n• “Medical services”\n\n• “Global challenge”\n\n• “Meta-analysis”\n\n• “Strategies”\n\n• “Implementation”\n\n• “Policies”\n\n• “Gaps”\n\nEach database search employed unique search strings and combinations tailored to its algorithm. Filters and limits, such as publication date restrictions, were applied where necessary to focus the search on the relevant time.\n\nHowever, due to space limitations in this section, a concise overview of the search strategy is provided. The detailed search strategies, including specific search strings, filters, and limits used for each database, will be made available upon request, or included in the supplementary materials, as requested by the editorial team.\n\nFollowing the comprehensive literature search, 38 articles were identified and reviewed, meeting the inclusion criteria based on the search strategy and relevance to the systematic review’s objectives.\n\nInclusion and exclusion criteria\n\nThe literature search for this systematic review specifically targeted peer-reviewed articles and other relevant literature that extensively discussed and provided insights into Primary Health Care (PHC) services and their delivery mechanisms. The aim was to encompass scholarly works that comprehensively addressed PHC systems, policies, interventions, and their impact on population health outcomes. Inclusion was based on the relevance of the content to the study’s objective of analyzing and synthesizing information related to PHC’s role in fostering a healthy population. The selected studies were expected to contribute substantial data and insights pertinent to the meta-analysis conducted in this review.\n\nExclusion criteria\n\nConversely, articles falling outside the scope of addressing the designated topic or failing to furnish relevant data essential for the meta-analysis were excluded. This entailed excluding studies that did not directly delve into the realm of PHC services or failed to provide substantial and pertinent information aligned with the study’s objectives. Additionally, articles not published in the English language were excluded from this review to ensure the consistency and comprehensiveness of the analysis conducted within the confines of accessible and comprehensible literature.\n\nThe rationale behind these criteria was to focus on scholarly works that significantly contributed to the understanding of PHC services and their impact on population health outcomes while ensuring a level of uniformity and accessibility by restricting the language of publication to English.\n\nData extraction\n\nThe data extraction process involved screening the titles and abstracts of articles retrieved from the literature search. Full-text articles that met the inclusion criteria were considered for data extraction. We discussed the PHC services provided, identified gaps and improvement strategies from the retrieved articles.\n\nOutcomes sought\n\n• For this systematic review, data were sought for several specific outcomes related to Primary Health Care (PHC) services, including but not limited to:\n\n• Health outcomes: Measures encompassing various health indicators, such as mortality rates, disease prevalence, quality of life assessments, and healthcare utilization metrics.\n\n• Service delivery gaps: Identification of gaps in access, affordability, and quality of PHC services as reported in the literature.\n\n• Implementation strategies: Insights into strategies adopted for PHC implementation, including community involvement, infrastructure improvements, and healthcare workforce development.\n\n• It is important to note that while efforts were made to collect all results compatible with each outcome domain in each study, certain limitations existed due to varied reporting standards across studies. Methods used to decide which results to collect involved prioritizing outcomes based on relevance to the study’s objectives and the availability of clear and comprehensive data.\n\nOther variables sought\n\n• Participant and intervention characteristics: Data sought encompassed demographic information (age, gender), geographic location, intervention types, and characteristics of PHC systems studied.\n\n• Funding sources: Information regarding funding sources for the studies under review was sought to ascertain any potential biases or conflicts of interest.\n\n• Assumptions about missing or unclear information were made cautiously. In cases of missing or ambiguous data, assumptions were made based on available contextual information and considering the impact of such missing data on the overall analysis and interpretation of results.\n\nIn conducting the systematic review, a comprehensive evaluation of potential biases within the included studies was undertaken using established criteria relevant to the respective study designs. The risk of bias assessment aimed to ensure the reliability and validity of the synthesized evidence.\n\n1. Publication bias mitigation: To minimize publication bias, efforts were made to include both published and unpublished studies. Comprehensive search strategies across multiple databases and the inclusion of grey literature aimed to capture a wide array of research, reducing the likelihood of bias due to selective publication.\n\n2. Selection bias considerations: The inclusion and exclusion criteria were explicitly defined to limit selection bias. The rationale behind study selection was based on pre-defined criteria to ensure a representative sample of studies addressing primary health care, thus reducing the risk of bias related to specific populations or study types.\n\n3. Quality and consistency assessment: Studies included in the review underwent a rigorous quality assessment process. The Cochrane Risk of Bias Tool (or other appropriate tool based on study designs) was applied to assess individual study quality. This involved examining domains such as randomization, blinding, allocation concealment, and other relevant aspects to gauge the risk of bias in each study.\n\n4. Reporting biases: Efforts were made to identify and address reporting biases by scrutinizing available data, looking for discrepancies between reported and unreported findings within the included studies.\n\nThrough this systematic and methodical approach, the review aimed to provide an accurate and comprehensive synthesis of the available literature, accounting for potential biases within individual studies to strengthen the validity of the collective conclusions.\n\nData synthesis and analysis includes identifying gaps in PHC service delivery. Data were synthesized through a narrative synthesis of findings from articles included in the systematic review. The findings were summarized according to the provided medical services, identified gaps and improvement strategies.\n\n\nResults\n\nThe meta-analysis of the last ten years of written research on primary health care (PHC) services revealed that while the PHC system is crucial in ensuring a healthy population, there are significant gaps in its delivery across countries.22 These gaps significantly impact the health outcomes of individuals and communities, and the PHC system needs to be strengthened to address them effectively.\n\nThe review identified a range of PHC services provided across different countries, including preventive services, such as vaccinations, health education, and screening and curative services, such as treatment for acute and chronic conditions. Despite the variation in the services provided, several gaps were identified in delivering PHC services across countries. These gaps included inadequate staffing, limited access to essential medicines, insufficient funding, inadequate infrastructure, and inadequate training for health workers.22,23\n\nOne of the significant gaps identified in the delivery of PHC services was inadequate staffing.24 Many countries need more health workers, particularly in rural and remote areas with inadequate health facilities. The shortage of health workers affects the quality and accessibility of PHC services and leads to long waiting times, reduced patient satisfaction, and poor health outcomes. In addition, the shortage of health workers exacerbates the burden of communicable and non-communicable diseases, contributing to a high mortality rate.25\n\nAnother significant gap identified in the delivery of PHC services was limited access to essential medicines.26 Many PHC facilities in low- and middle-income countries face shortages of essential medicines, which affects the quality of care and health outcomes. The lack of essential medicines often leads to inappropriate treatment, prolonged illness, and complications, which significantly impact the quality of life of patients and their families.\n\nInsufficient funding was another gap identified in the delivery of PHC services.1 Many countries need more funding for the PHC system, which affects the quality and availability of services. The lack of funding leads to adequate infrastructure, adequate staffing, and limited access to essential medicines and medical equipment. As a result, patients face long waiting times, reduced patient satisfaction, and poor health outcomes.\n\nInadequate infrastructure was also identified as a gap in the delivery of PHC services.15 Many PHC facilities need more basic amenities, such as clean water, electricity, and adequate sanitation facilities, affecting care quality and safety. The lack of infrastructure often leads to poor hygiene, increased risk of infection, and reduced patient comfort, which affects patient satisfaction and health outcomes.27,28\n\nFinally, inadequate training for health workers was identified as a gap in the delivery of PHC services.29 Many health workers need more skills and knowledge to provide quality care, particularly in managing non-communicable diseases. The lack of training leads to poor diagnosis, inappropriate treatment, and reduced patient satisfaction, which affects health outcomes.\n\nWith the help of primary care services, patients are under constant monitoring and the doctor observes the patient throughout his life. As a result, the doctor has complete information about the patient’s disease, how it developed and how it is developing. This allows the doctor to better manage the disease. Another distinctive feature of primary care is the comprehensiveness of care because the family doctor cares not only for the patient’s physical, but also for his spiritual and social well-being. Health care is a complex system that also has a kind of coordination function.\n\nThe family doctor coordinates the full service of the patient, and he is not only a doctor but also a supporter, guide and coordinator who can protect patients and help them make the right choice during medical care. Through the doctor’s coordination, the patient receives the appropriate service at the appropriate time and place.30\n\nThe systematic review commenced with an initial search across electronic databases (PubMed et al. Library and Web of Science) to identify relevant articles. A total of [57 articles] records were identified through the search process. Following removing duplicates, [47 articles] unique records underwent title and abstract screening. Subsequently, [38 articles] full-text articles were assessed for eligibility based on predefined inclusion criteria.\n\nThroughout the review process, studies that appeared to meet the inclusion criteria were assessed; however, [14 articles] studies were excluded due to -irrelevant study design, inadequate data.\n\nThe systematic review included [38 articles] studies that met the predefined inclusion criteria. Each included study’s characteristics, including participant demographics, study design, interventions, and outcomes measured.\n\nPresentation of outcomes\n\nThe review synthesized data from included studies of gaps in PHC services. Critical gaps identified encompassed inadequate staffing, limited access to essential medicines, insufficient funding, inadequate infrastructure, and insufficient training for health workers.\n\n\nDiscussion\n\nThe gaps identified in the delivery of PHC services significantly impact the health outcomes of individuals and communities, especially in low- and middle-income countries. This study, however, has limitations. Firstly, the literature search was confined to articles published in English, potentially excluding relevant information published in other languages. Secondly, the quality of the included articles might have constrained the meta-analysis findings, urging caution in their interpretation.\n\nDespite these limitations, the study conducted a meta-analysis over the past decade, examining written research on healthcare services utilizing peer-reviewed articles and pertinent literature on PHC services. The study’s primary objective was to identify PHC service gaps and propose strategies to improve health outcomes.\n\nComprehensive and coordinated strategies targeting the root causes are imperative to address these identified gaps effectively. Policy interventions addressing staffing shortages, increased funding for the PHC system, infrastructure enhancement, and adequate training and support for healthcare workers are critical.\n\nA pivotal strategy involves bolstering health systems, necessitating the formulation of policies and programs enhancing the quality, accessibility, and affordability of health services. Achieving this may entail appropriate financing mechanisms, robust health governance systems, bolstered health workforce, and refined health information systems.\n\nFurthermore, integrating PHC services into the broader health system is another crucial strategy. This integration can bridge gaps and synergize efforts, ensuring more comprehensive and efficient healthcare delivery.\n\nIn conclusion, while this study sheds light on the gaps in PHC services and aims to offer strategies for improvement, acknowledging the study’s limitations is essential in interpreting its findings and implementing potential solutions.\n\n\nConclusion\n\nPrimary health care (PHC) is crucial in ensuring a healthy population and addressing global health challenges. However, there are significant gaps in the delivery of PHC services across countries, which significantly impact the health outcomes of individuals and communities.\n\nOur study revealed several gaps in the delivery of PHC services, including inadequate staffing, limited access to essential medicines, insufficient funding, inadequate infrastructure, and inadequate training for health workers.31,32 These gaps affect the quality and accessibility of PHC services, and lead to long waiting times, reduced patient satisfaction, and poor health outcomes.\n\nTo address these gaps effectively, comprehensive, and coordinated strategies are needed that address the underlying causes of these gaps. These strategies should include policies to address staffing shortages, increase funding for the PHC system, improve infrastructure, and provide training and support for health workers.30,32\n\nStrengthening health systems is a key strategy for addressing the gaps in PHC services. This involves the development of policies and programs that improve the quality, accessibility, and affordability of health services. This can be achieved through the development of appropriate financing mechanisms, the establishment of effective health governance systems, the expansion of the health workforce, and the improvement of health information systems.33\n\nIntegrating PHC services into the broader health system is another strategy for addressing the gaps in PHC services. Integration involves coordinating services across distinct levels of care and involving different stakeholders, including governments, healthcare providers, and communities. This can help to improve the quality and accessibility of services, reduce duplication and fragmentation of services, and enhance the efficiency and effectiveness of the health system.34,35\n\nIn conclusion, this study highlights the importance of PHC services in ensuring a healthy population and addressing global health challenges. It identifies significant gaps and challenges facing the PHC system and provides strategies for improving PHC services in practice. These strategies are essential for achieving universal health coverage and addressing the Sustainable Development Goals related to health. Implementing these strategies requires the commitment and collaboration of all stakeholders, including governments, healthcare providers, and communities, to deliver high-quality, accessible, and affordable PHC services for all.36,37\n\n\n\n1. Increase funding for primary health care: Adequate funding is essential for delivering quality primary health care services. Governments should increase their investment in the primary health care system, allocate sufficient resources, and ensure they are used efficiently and effectively. This would enable the system to address the gaps in the delivery of PHC services and ensure that all individuals have access to quality healthcare services.\n\n2. Expand the health workforce: The shortage of trained health workers is a significant barrier to delivering quality primary health care services. Governments should develop policies and programs that increase the number of health workers in the system, improve their skills, and ensure they are deployed effectively. This would improve the availability and accessibility of primary health care services, particularly in underserved areas.\n\n3. Strengthen health information systems: Accurate and reliable health information is essential to deliver primary health care services effectively. Governments should invest in developing and strengthening health information systems that capture relevant health data and enable effective monitoring and evaluation of the PHC system. This would provide policymakers and healthcare providers with the information they need to make informed decisions and improve the quality of healthcare services.\n\n4. Promote community participation: Community participation is essential for effectively delivering primary health care services. Governments should promote community participation in designing, delivering, and monitoring PHC services. This would enable the system to be more responsive to communities’ health needs and preferences and ensure that services are designed to meet their needs.\n\n5. Foster intersectoral collaboration: Health is influenced by a range of factors, including social, economic, and environmental determinants. Governments should foster intersectoral collaboration across different sectors to address the underlying causes of health inequities and promote health equity. This would involve working with different sectors, such as education, housing, and transportation, to create supportive environments for health and improve the social determinants of health.\n\n6. Embrace technological innovations: Technological innovations, such as telemedicine and electronic health records, can potentially transform the delivery of primary health care services. Governments should embrace these innovations and invest in their development and implementation. This would enable the system to be more efficient, effective, and responsive to the needs of patients.\n\n7. Foster international collaboration: Primary health care is a global challenge that requires international collaboration and cooperation. Governments should collaborate, share best practices, and learn from each other’s experiences to improve the delivery of primary healthcare services. This would enable countries to work together to address global health challenges and achieve universal health coverage.\n\n8. In order to promote the development of the Institute of Family Physicians, it is necessary to ensure the normal payment of primary health care personnel. It is advisable to introduce a combined method of primary care, which will increase their care.\n\n9. Primary health care is the foundation of the health care system, the health quality of the population, access to services, effective spending of scarce funds allocated for health care significantly depend on the health care system. management and analysis of the epidemiological situation, and establishment of a healthy lifestyle. The main criterion of public health priority lies. primarily in the cost efficiency of preventive measures\n\nIn conclusion, delivering quality primary health care services is essential for ensuring a healthy population and addressing global health challenges. Governments must prioritize developing and implementing policies and programs that address the gaps in delivering PHC services and ensure that all individuals have access to quality healthcare services. This requires a commitment to collaboration, innovation, and investment in the PHC system to achieve universal health coverage and address the Sustainable Development Goals related to health.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: PRISMA-S checklist for ‘Primary Health Care as The Main Guarantor of a Healthy Population in The Country and A Global Challenge in The World” a systematic review’, https://doi.org/10.6084/m9.figshare.24846126.v1. 38\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\nMacinko J, Starfield B, Shi L: The contribution of primary care systems to health outcomes within Organization for Economic Cooperation and Development (OECD) countries, 1970–1998. Health Serv. Res. 2003; 38(3): 831–865. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Primary Health Care. Published October 23, 2020. Reference Source\n\nWorld Health Organization: Declaration of Alma-Ata. May 8, 2023. Reference Source\n\nWorld Health Organization: The World Health Report 2018: Primary Health Care (Now More Than Ever).2018. Reference Source\n\nStarfield B: Primary Care: Balancing Health Needs, Services, and Technology. New York, NY: Oxford University Press; 2020.\n\nBhutta ZA, Ali S, Cousens S, et al.: Alma-Ata: Rebirth and revision 6 Interventions to address maternal, newborn, and child survival: What difference can integrate primary health care strategies make? Lancet. 2008; 372(9642): 972–989. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Declaration of Astana. Global Conference on Primary Health Care.2018. Reference Source\n\nShi L, Singh DA: Essentials of the US Health Care System. Jones & Bartlett Learning; 2017.\n\nJanamian T, Jackson CL, Glasson N, et al.: A systematic review of the challenges to implementation of the full extent of the expanded role of nurses in general practice. J. Adv. Nurs. 2016 May; 72(5): 1024–1036.\n\nMendis S, Al Bashir I, Dissanayake L, et al.: Gaps in capacity in primary care in low-resource settings for implementation of the WHO PEN package of non-communicable diseases interventions. Glob. Health. 2018 Dec; 14(1): 87.\n\nDrennan VM, Halter M, Brearley S, et al.: Investigating the contribution of physician assistants to primary care in England: a mixed-methods study. Health Services and Delivery Research. 2016 Feb; 4(5): 1–176.\n\nKarimy M, Araban M, Mousavifar SA, et al.: Developing indicators for evaluation of primary health care system in iran: a Delphi method study. Med. J. Islam Repub. Iran. 2017; 31: 86.\n\nRahman MM, Yoshida Y, Saito E, et al.: An assessment of the quality of care for non-communicable diseases in rural Bangladesh. BMC Health Serv. Res. 2019 Dec; 19(1): 1.\n\nJacobs B, Hill P, Bigdeli M, et al.: From data to policy: good practices and cautionary tales. Lancet Glob. Health. 2017 Jul 1; 5.\n\nShi L, Singh DA: Essentials of the US health care system. Jones & Bartlett Publishers; 2015.\n\nAtun R, de Jongh T , Secci F, et al.: Integration of targeted health interventions into health systems: a conceptual framework for analysis. Health Policy Plan. 2010; 25(2): 104–111. Publisher Full Text\n\nWorld Health Organization: Primary health care on the road to universal health coverage: 2019 monitoring report.2018.\n\nKringos DS, Boerma WG, Bourgueil Y, et al.: The European primary care monitor: structure, process, and outcome indicators. BMC Fam. Pract. 2013; 14(1): 1–11.\n\nVerulava T, Jorbenadze A: DEVELOPMENT OF PUBLIC HEALTH IN GEORGIA: CHALLENGES AND POLICY ISSUES. Arch. Balk. Med. Union. 1 Jun 022; 57(2): 179–184. Publisher Full Text\n\nAtun R, de Jongh T , Secci FV, et al.: Integration of targeted health interventions into health systems: a conceptual framework for analysis. Health Policy Plan. 2013; 28(8): 1–11.\n\nDzau VJ, Kirch D, Nasca T: Preventing a parallel pandemic—A national strategy to protect clinicians’ well-being. N. Engl. J. Med. 2020; 383(6): 513–515. PubMed Abstract \| Publisher Full Text\n\nMacinko J, Starfield B, Shi L: The contribution of primary care systems to health outcomes within Organization for Economic Cooperation and Development (OECD) countries, 1970-1998. Health Serv. Res. 2003; 38(3): 831–865. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBerwick DM: A user’s manual for the IOM’s “quality chasm” report. Health Aff. 2002; 21(3): 80–90. PubMed Abstract \| Publisher Full Text\n\nStarfield B: Primary care: An increasingly important contributor to effectiveness, equity, and efficiency of health services. SESPAS report 2012. Gac. Sanit. 2012; 26(Suppl 1): 20–26. PubMed Abstract \| Publisher Full Text\n\nMoher D, Liberati A, Tetzlaff J, et al.: Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement. PLoS Med. 2009; 6(7): e1000097. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Primary health care.2018. Reference Source\n\nEpping-Jordan JE, Pruitt SD, Bengoa R, et al.: Improving the quality of health care for chronic conditions. Qual. Saf. Health Care. 2004; 13(4): 299–305. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKruk ME, Gage AD, Arsenault C, et al.: High-quality health systems in the Sustainable Development Goals era: Time for a revolution. Lancet Glob. Health. 2018; 6(11): e1196–e1252. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Global strategy on human resources for health: Workforce 2030.2016. Reference Source\n\nVerulava T, Jorbenadze A: Primary Health Care Reforms in Georgia: The Experience and Challenges. Arch. Balk. Med. Union. 1 Dec 2022; 57(4): 384–389. (6 pages) Balkan Medical Union. Publisher Full Text\n\nCameron A, Ewen M, Ross-Degnan D, et al.: Medicine prices, availability, and affordability in 36 developing and middle-income countries: A secondary analysis. Lancet. 2009; 373(9659): 240–249. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Primary Health Care.2021. Reference Source\n\nKringos DS, Boerma WG, Bourgueil Y, et al.: The strength of primary care in Europe: an international comparative study. Br. J. Gen. Pract. 2013; 63(616): e742–e750. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShi L, Macinko J, Starfield B, et al.: The relationship between primary care, income inequality, and mortality in US states, 1980-1995. J. Am. Board Fam. Pract. 2003; 16(5): 412–422. PubMed Abstract \| Publisher Full Text\n\nStarfield B: Politics, primary healthcare, and health: was Virchow, right? J. Epidemiol. Community Health. 2012; 66(10): 927–932. Publisher Full Text\n\nUnited Nations: Universal Health Coverage.2019. Reference Source\n\nWorld Health Organization: World Health Statistics 2019: Monitoring Health for the SDGs.2019. Reference Source\n\nAbashidze-Gabaidze G, Khurtsia L, Gabaidze M, et al.: PRISMA checklist.pdf. figshare. 2023. Publisher Full Text" }	[ { "id": "263484", "date": "15 May 2024", "name": "Nia Roberts", "expertise": [ "Reviewer Expertise Information specialist", "who is only able to comment on the appropriateness of the search methods." ], "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'm unable to assess the search methods employed in the conduct of this review as they are not reported in sufficient detail. The search strategies need to be available in full, In addition, the numbers need to be reported in a PRISMA flowchart indicating how many papers were retrieved in total, duplicates excluded, total screened on title/abstract, total screened full-text and reasons for exclusion.\nThe authors consistently indicate that they have conducted a meta-analysis, but the results are presented as a narrative synthesis. I would have expected more papers to have been included to support the findings in the narrative synthesis, however, without view of the search process I can't decide whether relevant research might have been missed.\nThe authors indicate that a risk of bias assessment was undertaken, however, I don't see a table reporting the assessment for each study.\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? No\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) No", "responses": [ { "c_id": "12636", "date": "17 Oct 2024", "name": "Gulnara Abashidze-Gabaidze", "role": "Author Response", "response": "Ms. Nia Roberts, we are deeply grateful for your time and valuable advice. Your suggestions have been instrumental in strengthening our article. We have carefully considered your feedback and implemented your recommendations to the best of our ability. As you requested, we have included detailed information about the study characteristics in Table N1. Additionally, Figure N1 (PRISMA diagram) and the PRISMA checklist are provided to ensure the transparency of our narrative synthesis. We are sincerely thankful for your expert guidance, which will help us to improve our writing in the future." } ] }, { "id": "272310", "date": "17 May 2024", "name": "Richard Baker", "expertise": [ "Reviewer Expertise primary care and population mortality" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverview Congratulations to the authors for making the case that primary health care is key to the effectiveness of health systems. Round the world, primary health care needs strengthening both to improve population health and to increase the efficiency of health services. Although others have reviewed the effects of primary health care, this new study investigates gaps in care, in the lack of staff, shortages of funding, poor access to medicines, inadequate facilities and infrastructure, and inadequate training. The identification of these problems, shared by many countries, is important, and this constitutes a powerful message for policymakers – if they aim to improve the health of the people they are responsible for, they must strengthen primary health care. Specific comments The paper might be adjusted in a few ways to make it more accessible. 1. The Introduction covers a lot of relevant issues. Would it be worth saying something about primary health care in Georgia, if one aim of the paper is to inform the health system in George? Also, it is not clear why public health is given a paragraph on page 3. How does this fit in to the case for primary health care? 2. It would be better to use the term systematic review rather than meta-analysis. Meta-analysis implies a quantitative or statistical approach to combining the findings; the paper is does not involve a statistical analysis and is really a systematic review. A narrative synthesis (page 6) is not a meta-analysis. 3. The methods are generally well described and they indicate a careful approach was taken. It would be helpful to present more on the search strategy – would it be possible to include an example of the search strategy in a supplementary file? 4. A PRISMA chart would be helpful, and could be included in the supplementary materials (https://www.bmj.com/content/372/bmj.n71). This would help readers understand at what stage and why papers were excluded from the review. A very wide range of outcomes was included, and this could have led to a vast quantity of papers – how were they reduced down to the number in the review? 5. Care appears to have been taken in assessing the risk of bias in included studies. A standard format was used, for example. 6. The Results section needs to be re-ordered to first present basic information on the studies identified and the characteristics of those included. This information could be presented in a series of Tables that should show the country of origin, the outcomes of interest, and the findings of the assessment of risk of bias. Once this information has been reported, the findings can then be described. The findings themselves are interesting; the addition of tables describing the findings of each paper should help to explain the basis for the broad statements of the Results section. 7. The discussion section mentions the strengths and limitations of the study, and sets out a series of conclusions. There is some repetition across the discussion/ conclusions/ recommendations, and some editing would help. The conclusions and recommendations themselves are all reasonable. 8. The discussion might include a paragraph on how the review’s findings reflect those of other recent reviews of primary health care. This would help to show support the findings. I hope the authors continue to conduct studies in this field. They have wishes for good luck in such an undertaking.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? 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": "12621", "date": "14 Oct 2024", "name": "Gulnara Abashidze-Gabaidze", "role": "Author Response", "response": "Thank you, Mr. Baker, for your thorough review and valuable feedback. Your insights have been instrumental in strengthening this article and ensuring its quality. I appreciate your time and expertise Our primary objective was to collaborate with other countries, including Georgia, to gain insights from their experiences in PHC. In response to the World Health Organization's call, we aimed to unite countries in a global effort to address this disease. By forming an international partnership and fostering mutual cooperation, we sought to share knowledge and best practices. I appreciate your thoughtful feedback. While I believe I could have further refined this text, I've found this experience invaluable for my future writing endeavors. Thank you for your guidance. I've added a table describing the findings of each paper, which I think will help explain the rationale behind the broad statements in the results section. Are sufficient details of the methods and analysis provided to allow replication by others? The data for each article reviewed during the analysis, including study characteristics, are presented in Table N1. Figure N1 (PRISMA diagram of study selection) and the PRISMA checklist are used to enhance the transparency of the narrative synthesis. Your feedback has been invaluable in strengthening this article. Thank you again." } ] } ]	1	https://f1000research.com/articles/13-38
https://f1000research.com/articles/13-1204/v1	10 Oct 24	{ "type": "Research Article", "title": "The development of novel score model as a predictor of in-hospital mortality of adult cardiac surgery patients in Indonesia", "authors": [ "Juni Kurniawaty", "Budi Yuli Setianto", "Supomo Supomo", "Yunita Widyastuti", "Cindy Elfira Boom", "Budi Yuli Setianto", "Supomo Supomo", "Yunita Widyastuti", "Cindy Elfira Boom" ], "abstract": "Introduction In recent years, the number of cardiac surgeries has been on the rise. Several predictive models have been developed to assess the risk of mortality for these patients. EuroSCORE II, a widely used model, demonstrates good discrimination and calibration for the European population, but its accuracy may vary in the Indonesian population. The purpose of this study was to develop a scoring model tailored to Indonesian population, which may have better accuracy in assessing in-hospital mortality risk among adult cardiac surgery patients.\n\nMethod A retrospective study was conducted using medical records of adult cardiac surgery patients from four participating hospitals. Potential risk factors were included as variables and analyzed using bivariate and multivariable logistic regression with the L-backward method. Bootstrapping was applied to enhance the model’s validity. Receiver operating characteristic (ROC) curves were created for each model, and the area under the curve (AUC) was calculated to assess discrimination ability, while the Hosmer-Lemeshow test was used to evaluate calibration.\n\nResults We extracted data from 4,875 patients, with a mean age of 50.41 years, and most patients were men (63.1%). The majority of patients were in NYHA class I-II. The in-hospital mortality rate was 6.5%. From 62 potential variables, 13 variables were included in the final model. Our new model demonstrated strong discrimination and calibration (AUC 0.7564; Hosmer-Lemeshow p = 0.9510).\n\nConclusion The newly developed scoring model exhibited good discrimination and calibration, making it a promising tool for predicting in-hospital mortality in adult cardiac surgery patients in Indonesia.", "keywords": [ "in-hospital mortality", "cardiac surgery", "model building", "risk prediction", "retrospective study" ], "content": "Introduction\n\nThe trend of cardiac surgery is showing an increase in Indonesia. Cardiac surgery procedures have shown an increase from year to year in Indonesia.1 Cardiac surgery has been regarded as one of the most expensive surgical procedures in a hospital and is associated with high mortality and morbidity rates.2 To minimize perioperative mortality, patient selection has been advocated, using risk assessment systems developed over the last decades. Decision-making for surgery requires more than just clinical experience and intuition. This decision-making process is highly complex, and scoring systems were developed as a way to objectively assess patient conditions, determine patient mortality risk profiles, and improve patient outcomes.3\n\nSeveral risk stratification models have been developed for cardiac surgery patients. The three most commonly used scoring systems are the European System for Cardiac Operative Risk Evaluation (EuroSCORE) II,4 Society of Thoracic Surgeons (STS) score,2 and Parsonnet score.5 EuroSCORE II has been validated in various population settings and remains the standard for many institutions.6 Among the various scoring systems, EuroSCORE II is the most frequently studied in Indonesia. Results from several studies in Indonesia have found that EuroSCORE II shows good discriminatory but weak calibration performance.7–9\n\nExisting risk models shows suboptimal performance in Indonesia population. These models generally predict outcomes more accurately in the settings where they were initially developed. Socio-economic conditions, living standards, health resources, and geographic and ethnic characteristics may affect the applicability of these models in different regions.10 In clinical practice, most predictive scores show lower accuracy when validated on new population. The two common possible explanations for this are that the predictive scores were not adequately developed as well as major differences between the populations in which they were developed and validated.11\n\nTo this date, there is no known risk stratification model that has been developed from a local database or with characteristics that align with the Indonesia population. The main issue that we faced in Indonesia is the lack of a widely applicable scoring system for assessing in-hospital mortality risk in cardiac surgery patients. We propose to develop a mortality risk model for cardiac surgery patients from local database derived from the Indonesian population.\n\n\nMethods\n\nWe conducted a retrospective study using medical record data from adult cardiac surgery patients who underwent procedures at four tertiary referral hospitals in Indonesia (Dr. Sardjito General Hospital in Yogyakarta, Harapan Kita National Heart Center Hospital in Jakarta, Dr. Kariadi General Hospital in Semarang, and Abdoel Wahab Sjahranie Regional Hospital in Samarinda). The subjects were adult patients (aged 18 to 85 years) who underwent cardiac surgery procedures between January 1, 2016, and December 31, 2020. Heart transplant patients, aortic dissection patients, and patients with incomplete primary medical records were excluded from the study. It was estimated that between 75 and 3500 subjects were required for each potential predictor. Thus, a minimum of 3500 subjects were required for this study. This study complies with the Declaration of Helsinki and received ethical approval from the Medical and Health Research Ethics Committee of the Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia on October 30, 2019 (No: KE/FK/1277/EC/2019)\n\nThe selection of potential predictors and definitions for each variable was conducted through a focused group discussion. Selected candidate variables were based on variables present in EuroSCORE II, CARE, Parsonnet, STS scores. We also considered other risk factors that not included in existing scores but proven or considered strongly associated with post-cardiac surgery mortality risk, and potentially suitable as candidate variables in model development.\n\nThe statistical analysis began with bivariate analysis using t-tests for normally distributed numeric variables; otherwise, Mann-Whitney tests were performed. Chi-square tests were performed for categorical variables. Candidate variables with p < 0.25 or clinically significant associations that cannot be ignored, such as age and gender, and occurrence rates exceeding 1% of the total sample size, were included in multivariate analysis. Multivariate analysis was performed using logistic regression with backward elimination method. Models with significant variables underwent bootstrapping. Odds ratios (OR) and 95% confidence intervals (CI) were calculated from bootstrapped coefficients. ROC (receiver operating characteristic) curves were constructed for each model, and the AUC (area under the curve) values were assessed and compared to determine the discriminative performance of each model. The final model is the best fit model for in-hospital mortality. Model calibration was tested using the Hosmer-Lemeshow test, comparing the model’s predicted mortality with actual mortality. A risk prediction model with a p-value > 0.05 is considered well-calibrated. The analysis was performed using STATA 15 software.\n\n\nResults\n\nA total of 4,940 samples from 4 participating hospitals met the initial inclusion criteria. Of these, 65 subjects were excluded (53 patients with aortic dissection and 12 patients with incomplete primary outcome data), resulting in a final sample size of 4,875 patients (Figure 1).\n\nCompared to the EuroSCORE II database, our population was younger, with median age of 50.4 years, with higher proportion of female patients (36.9 %), and more patients had NYHA class I-II,. The in-hospital mortality rates for cardiac surgery patients at Dr. Sardjito General Hospital, Dr. Kariadi General Hospital, Abdoel Wahab Regional Hospital, and Harapan Kita National Heart Center were 8.6% (74 patients), 8.7% (113 patients), 9.3% (30 patients), and 4.18% (101 patients), respectively. These translated into overall mortality rate of 6.5%, which is higher than the mortality rate in the EuroSCORE II database. The demographic characteristics of the study subjects are shown in Table 1.\n\nOf the 62 variables included in bivariate analysis, 36 variables had p < 0.25. The L-backward multivariable logistic regression analysis was performed and 19 variables were retained. These 19 variables were used as base model for our model building process.\n\nAfter L-backward multivariable logistic regression analysis was performed, we further selected variables with p < 0.05 or with high β coefficient Model selection was based on AUCs of ROC curves and AIC values. The final model consisted of 13 variables (Table 2).\n\nOur final model had an AUC of 0.7564 for the ROC curve (Figure 2), indicating good discriminative performance (AUC > 0.7). Goodness-of-fit test with the Hosmer-Lemeshow (HL) test was used to evaluate the calibration of the model. The p-value for the HL test of the new scoring model in this study was p = 0.9510, indicating good calibration (Table 3).\n\n\nDiscussion\n\nThe purpose of this study was to develop a model that can be widely applied across various hospitals in Indonesia and integrated into local data collection and management systems. From this study, we proposed the following logistic regression formula intended for predicting in-hospital mortality for cardiac surgery patients:\n\nWhere e = 2.718, β0 (constant of the logistic regression equation) = -6.424, βi is the coefficient of variable Xi, and so forth: 1.501 (history of PCI), 1.473 (history of cardiac surgery), 1.286 (severe musculoskeletal and neurological disorders), 1.225 (Hemoglobin < 12 mg/dL), 0.987 (BMI < 18.5 kg/m2), 0.928 (two or more procedures), 0.814 (LVEF ≤ 30%), 0.711 (CPB), 0.701 (left main disease), 0.443 (moderate to severe tricuspid regurgitation), 0.412 (TAPSE < 17 mm), 0.352 (creatinine clearance < 50 ml/min), 0.038 (age). Several variables in the new scoring model were not present in EuroSCORE II, these include history of PCI, hemoglobin < 12 g/dL, BMI < 18.5 kg/m2, left main disease, TAPSE < 17 mm, and moderate to severe tricuspid regurgitation.\n\nIn a retrospective study of 6,504 CABG patients, PCI was an independent predictor for in-hospital mortality (3.6% in patients with PCI vs 2.3% in patients without PCI).12 Another study also found PCI as predictor of in-hospital mortality and major adverse cardiac events (MACEs), with the negative impact being more pronounced in certain groups, such as patients with diabetes mellitus and triple-vessel coronary artery disease (CAD 3 VD).13 In contrast, a multi-center study of 34,316 CABG patients from 16 institutions found no significant association between history of previous PCI and mortality rates, though it did observe higher rates of major complications and longer hospital stays in the PCI group.14 The history of percutaneous coronary intervention (PCI) is associated with a poor prognosis in cardiac surgery patients due to various factors. The presence of a stent necessitates the surgeon to perform anastomosis on more distal and thinner branches of the coronary arteries, which increases the likelihood of graft occlusion. Another possibility is that multiple coronary interventions affect the natural blood flow in patients with collateral vessels, leading to microinfarctions in the myocardium. Patients who receive PCI with stenting typically have significant atherosclerosis, though not as advanced as those requiring surgical treatment. However, in the event of PCI failure, these patients require surgical revascularization, by which point their atherosclerosis may be more advanced and widespread. Additionally, stents have been linked to endothelial irregularities, which may lead to adverse cardiovascular outcomes, complicating coronary anastomosis and potentially impacting graft patency.15\n\nOver the past two decades, several observational studies have shown a relationship between preoperative anemia and postoperative adverse outcomes.16 Anemia is clinically significant, and its prevalence increases in patients undergoing heart surgery. Patients undergoing cardiac surgery may be more susceptible to the effects of preoperative anemia, since these patients have limited cardiac reserves, while surgery itself and CPB has been associated with significant blood loss and hemodilution.17 Low hemoglobin levels has been linked to higher mortality and morbidity in older adults, as well as in patients with congestive heart failure and coronary artery disease, especially during acute coronary syndrome. These groups of patients have high perioperative risk due to their existing comorbidities, and the presence of severe coronary artery disease may exacerbate id. CABG patients are particularly sensitive to the effect of low hemoglobin levels due to their limited coronary reserves.18–20\n\nObesity is well-known as a risk factor for developing cardiovascular diseases, and patients with a high BMI are frequently seen among those undergoing heart surgery (77% of the total patients).21 However, it is suggested that overweight and obese patients undergoing heart surgery had a better survival advantage compared to patients with a BMI < 18.5 kg/m2, normal weight patients, and morbidly obese patients.22 The term “obesity paradox” reflects the relationship between obesity, compared to normal weight, and decreased mortality rates. This paradoxical relationship has been demonstrated in diabetes, end-stage renal disease, hypertension, congestive heart failure, coronary artery disease (CAD), and peripheral artery disease.23,24 Excess adipose tissue provides benefits during illness and stress. Individuals with low BMI lack the reserves to tolerate the effects of weight loss, as seen in obese patients, contributing significantly to mortality.25–27 A BMI < 18.5 kg/m2 may result from malnutrition and cachexia or comorbid conditions. It may also indicate underlying serious illnesses. Moderate obesity provides a protective effect in patients undergoing heart surgery and in the general population.28\n\nLeft main coronary artery disease (LMCAD) has been associated with poor outcomes of cardiac surgery procedures. This is largely because the left main coronary artery supplies a major portion of the heart muscle. Blockage in this artery may severely reduce blood flow to a large area of the heart, especially the left ventricle, which is responsible for pumping oxygen-rich blood throughout the body.29 The critical nature of this artery’s function in supplying a large portion of the heart underscores why LMCAD is linked to increased morbidity and mortality in cardiac surgery patients.30\n\nIt is suggested that the mortality rate in patients with right ventricular dysfunction is 3.5 to 4.2 times higher compared to patients normal right ventricle.31 The tricuspid annular plane systolic excursion (TAPSE) is a crucial echocardiographic parameter that plays a significant role in assessing cardiac function. TAPSE is a measure of the longitudinal motion of the tricuspid annulus towards the apex of the heart during systole, reflecting right ventricular systolic function.32 In the context of cardiac surgery, TAPSE serves as an essential indicator of right ventricular performance and can provide valuable insights into postoperative outcomes and potential complications. TAPSE assessment can offer insights into the impact of surgical interventions on right ventricular function and overall cardiac performance.33\n\nFunctional tricuspid regurgitation is often secondary to pulmonary hypertension, which causes right ventricular remodeling, tricuspid annulus dilation, papillary muscle displacement, and tricuspid valve leaflet tethering. The progression of tricuspid regurgitation is linked to a specific pattern of right ventricular remodeling, most prominently at the mid-ventricular level, with minimal changes in ventricular length accompanied by increased right ventricular sphericity. Persistent progression of tricuspid regurgitation is a sign of poor outcomes. In patients with pulmonary arterial hypertension hospitalized for right-sided congestive heart failure, the degree of tricuspid regurgitation is an independent predictor of poor outcomes.34\n\nThis study utilized a multicenter setting from four tertiary hospitals in Indonesia that serve as tertiary referral centers for cardiac surgery and have relatively adequate postoperative intensive care. This resulted in an adequate sample size while minimizing the influence of non-patient factors during and after surgery that could affect postoperative outcomes. However, limitations of this study should be considered. It only analyzed variables or conditions with a high incidence in the sampled population, potentially missing other variables that may impact mortality outcome but were not included in the new scoring model. The study also excludes patients with aortic dissection. This exclusion was necessary because the number of patients with aortic dissection was very small, and including them would obscure the influence of other candidate variables with higher incidence rates. Thus, the results of this study cannot be extrapolated to patients with aortic dissection. The study uses retrospective data, which complicates data control. Prospective data collection was not feasible due to the time and effort required. Additionally, the study included data from only four hospitals, raising the question of whether the results can be applied to other hospitals. The included hospitals have different characteristics and are expected to represent other hospitals in Indonesia. Nevertheless, further studies with prospective data samples are needed to validate the results of this study.\n\n\nConclusion\n\nThe new scoring model, consisting of 13 variables, has relatively accurate discrimination and calibration performances, making it potentially applicable to open-heart surgery patients in Indonesia. External validation of the new scoring model is necessary before it can be applied as a prediction score for cardiac surgery patients in Indonesia. Further study using prospective data and evaluating mortality rates over a longer period, such as 30-day, 90-day, and 1-5 year mortality, is recommended.\n\n\nDeclaration\n\nEthical approval was obtained from the Medical and Health Research Ethics Committee of the Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia on October 30, 2019 (No: KE/FK/1277/EC/2019). The ethics committee waived the informed consent requirement for this study due to its retrospective design based on patient medical records.", "appendix": "Data availability\n\nOSF: The Development of Novel Score Model as a Predictor of In-hospital Mortality of Adult Cardiac Surgery Patients in Indonesia. https://doi.org/10.17605/OSF.IO/E72MB 35\n\nThis project contains the following underlying data:\n\n- Data file: study database.xlsx\n\n- study database.dta\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nOSF: STROBE checklist for The Development of Novel Score Model as a Predictor of In-hospital Mortality of Adult Cardiac Surgery Patients in Indonesia. https://doi.org/10.17605/OSF.IO/E72MB 35\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThis article is partially based on author’s doctoral dissertation work at Universitas Gadjah Mada, Yogyakarta, indonesia.\n\n\nReferences\n\nRumah Sakit Jantung dan Pembuluh Darah Harapan Kita: Laporan tahunan badan layanan umum rumah sakit jantung dan pembuluh darah harapan kita tahun 2016. Rumah Sakit Jantung dan Pembuluh Darah Harapan Kita; 2017 [cited 2017 Dec 20]. Reference Source\n\nD’Agostino RS, Jacobs JP, Badhwar V, et al.: The Society of Thoracic Surgeons Adult Cardiac Surgery Database: 2018 Update on Outcomes and Quality. Ann. Thorac. Surg. 2018 Jan; 105(1): 15–23. PubMed Abstract \| Publisher Full Text\n\nChand M, Armstrong T, Britton G, et al.: How and why do we measure surgical risk? J. R. Soc. Med. 2007 Nov 1; 100(11): 508–512. Publisher Full Text\n\nNashef SAM, Roques F, Sharples LD, et al.: EuroSCORE II. Eur. J. Cardiothorac. Surg. 2012 Apr; 41(4): 734–745. discussion 744–745. Publisher Full Text\n\nParsonnet V, Dean D, Bernstein AD: A method of uniform stratification of risk for evaluating the results of surgery in acquired adult heart disease. Circulation. 1989 Jun; 79(6 Pt 2): I3–I12. PubMed Abstract\n\nPrins C, de Villiers JI , Botes L, et al.: Cardiac surgery risk-stratification models. Cardiovasc. J. Afr. 2012 Apr; 23(3): 160–164. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPramodana B: Validation of EuroSCORE II as a postoperative cardiac surgery mortality prediction model in RSCM. Jakarta: Universitas Indonesia; 2016.\n\nWidyastuti Y, Boom CE, Parmana IAM, et al.: EuroSCORE II for prediction of in-hospital mortality after open heart surgery in Indonesia. Morocco: 2016.\n\nRahman FA: Validation of EuroSCORE II as predictor of postoperative mortality of cardiac surgery patient in Dr Sardjito Hospital. Yogyakarta: Universitas Gadjah Mada; 2016.\n\nRabbani MS, Qadir I, Ahmed Y, et al.: Heart valve surgery: EuroSCORE vs. EuroSCORE II vs. Society of Thoracic Surgeons score. Heart Int. 2014 Dec; 9(2): 53–58. PubMed Abstract \| Publisher Full Text\n\nToll DB, Janssen KJM, Vergouwe Y, et al.: Validation, updating and impact of clinical prediction rules: a review. J. Clin. Epidemiol. 2008 Nov; 61(11): 1085–1094. PubMed Abstract \| Publisher Full Text\n\nHassan A, Buth KJ, Baskett RJF, et al.: The association between prior percutaneous coronary intervention and short-term outcomes after coronary artery bypass grafting. Am. Heart J. 2005 Nov; 150(5): 1026–1031. PubMed Abstract \| Publisher Full Text\n\nBonaros N, Hennerbichler D, Friedrich G, et al.: Increased mortality and perioperative complications in patients with previous elective percutaneous coronary interventions undergoing coronary artery bypass surgery. J. Thorac. Cardiovasc. Surg. 2009 Apr; 137(4): 846–852. PubMed Abstract \| Publisher Full Text\n\nMehta GS, LaPar DJ, Bhamidipati CM, et al.: Previous percutaneous coronary intervention increases morbidity after coronary artery bypass grafting. Surgery. 2012 Jul; 152(1): 5–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLisboa LAF, Mejia OA, Dallan LA, et al.: Intervenção Coronariana Percutânea prévia como fator de risco para Revascularização Miocárdica. Arq. Bras. Cardiol. 2012 Jul; 99(1): 586–595. PubMed Abstract \| Publisher Full Text\n\nPadmanabhan H, Siau K, Curtis J, et al.: Preoperative Anemia and Outcomes in Cardiovascular Surgery: Systematic Review and Meta-Analysis. Ann. Thorac. Surg. 2019 Dec; 108(6): 1840–1848. PubMed Abstract \| Publisher Full Text\n\nKlein AA, Collier TJ, Brar MS, et al.: The incidence and importance of anaemia in patients undergoing cardiac surgery in the UK - the first Association of Cardiothoracic Anaesthetists national audit. Anaesthesia. 2016 Jun; 71(6): 627–635. PubMed Abstract \| Publisher Full Text\n\nKarkouti K, Wijeysundera DN, Beattie WS: Risk Associated With Preoperative Anemia in Cardiac Surgery: A Multicenter Cohort Study. Circulation. 2008 Jan 29; 117(4): 478–484. Publisher Full Text\n\nKulier A, Levin J, Moser R, et al.: Impact of preoperative anemia on outcome in patients undergoing coronary artery bypass graft surgery. Circulation. 2007 Jul 31; 116(5): 471–479. PubMed Abstract \| Publisher Full Text\n\nMiceli A, Romeo F, Glauber M, et al.: Preoperative anemia increases mortality and postoperative morbidity after cardiac surgery. J. Cardiothorac. Surg. 2014 Dec [cited 2019 May 13]; 9(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLavie CJ, Milani RV, Ventura HO: Obesity and cardiovascular disease: risk factor, paradox, and impact of weight loss. J. Am. Coll. Cardiol. 2009 May 26; 53(21): 1925–1932. Publisher Full Text\n\nBanack HR, Kaufman JS: The obesity paradox: understanding the effect of obesity on mortality among individuals with cardiovascular disease. Prev. Med. 2014 May; 62: 96–102. PubMed Abstract \| Publisher Full Text\n\nMortasawi A, Arnrich B, Rosendahl U, et al.: Is age an independent determinant of mortality in cardiac surgery as suggested by the EuroSCORE? BMC Surg. 2002 Oct 7; 2: 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStamou SC, Nussbaum M, Stiegel RM, et al.: Effect of body mass index on outcomes after cardiac surgery: is there an obesity paradox? Ann. Thorac. Surg. 2011 Jan; 91(1): 42–47. Publisher Full Text\n\nJohnson AP, Parlow JL, Whitehead M, et al.: Body Mass Index, Outcomes, and Mortality Following Cardiac Surgery in Ontario, Canada. JAHA. 2015 Jul 17; 4(7): e002140.\n\nLavie CJ, De Schutter A, Patel DA, et al.: Body Composition and Survival in Stable Coronary Heart Disease. J. Am. Coll. Cardiol. 2012 Oct; 60(15): 1374–1380. Publisher Full Text\n\nSyrakas CA, Neumaier-Prauser P, Angelis I, et al.: Is extreme obesity a risk factor for increased in-hospital mortality and postoperative morbidity after cardiac surgery? Results of 2251 obese patients with BMI of 30 to 50. Thorac. Cardiovasc. Surg. 2007 Dec; 55(8): 491–493. PubMed Abstract \| Publisher Full Text\n\nBenedetto U, Danese C, Codispoti M: Obesity paradox in coronary artery bypass grafting: myth or reality? J. Thorac. Cardiovasc. Surg. 2014 May; 147(5): 1517–1523. Publisher Full Text\n\nLee CW, Chang M: A Simple, Effective, and Durable Treatment Choice for Left Main Coronary Artery Disease. J. Am. Coll. Cardiol. Intv. 2016 Jun; 9(11): 1112–1114. PubMed Abstract \| Publisher Full Text\n\nYe Y, Yang M, Zhang S, et al.: Percutaneous coronary intervention versus cardiac bypass surgery for left main coronary artery disease: A trial sequential analysis. Medicine. 2017 Oct; 96(41): e8115. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTowheed A, Sabbagh E, Gupta R, et al.: Right Ventricular Dysfunction and Short-Term Outcomes Following Left-Sided Valvular Surgery: An Echocardiographic Study. J. Am. Heart Assoc. 2021 Feb 16; 10(4): e016283. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen X, Ma Y, Deng Z, et al.: Prediction of Early Postoperative Major Cardiac Events and In-Hospital Mortality in Elderly Hip Fracture Patients: The Role of Different Types of Preoperative Cardiac Abnormalities on Echocardiography Report. CIA. 2020 May; 15: 755–762. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan I, Shahbaz A, Iqbal M, et al.: Correlation of tricuspid annular plane systolic excursion with poor outcome in surgery for rheumatic heart valvular disease. ARYA. Atherosclerosis. 2019 Jul 14 [cited 2024 Jul 3]; 15(3): 130–135. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMedvedofsky D, Aronson D, Gomberg-Maitland M, et al.: Tricuspid regurgitation progression and regression in pulmonary arterial hypertension: implications for right ventricular and tricuspid valve apparatus geometry and patients outcome. Eur. Heart J. Cardiovasc. Imaging. 2017 Jan; 18(1): 86–94. PubMed Abstract \| Publisher Full Text\n\nBoom CE, Kurniawaty J, Widyastuti Y, et al.: The Development of Novel Score Model as a Predictor of In-hospital Mortality of Adult Cardiac Surgery Patients an in Indonesia. OSF Registries. 2024 [cited 2024 Sep 27]. Reference Source" }	[ { "id": "340392", "date": "27 Nov 2024", "name": "Amr Arafat", "expertise": [ "Reviewer Expertise Cardiothoracic surgery- Statistical analysis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article “The Development of Novel Score Model as a Predictor of In-hospital Mortality of Adult Cardiac Surgery Patients in Indonesia\" presents a study aimed at developing a novel scoring model to predict in-hospital mortality for adult cardiac surgery patients in Indonesia. This research addresses a significant gap in existing predictive models, particularly the EuroSCORE II, which, while effective in European populations, has shown suboptimal performance in Indonesian settings. The study is relevant. The increasing number of cardiac surgeries in Indonesia and the associated high mortality rates highlight the need for localized predictive models The sample size is accepted and the predictors used are comprehensive. By focusing on an Indonesian population, the study addresses the limitations of existing models that do not consider the socio-economic and health resource contexts specific to Indonesia.\nComments to improve the manuscript The abstract is limited. The results section lacks numbers and does not give an overview on the significant variables. While the introduction provides context, it could benefit from a more extensive review of existing models, particularly those developed in similar settings or populations. Discussing previous studies in Indonesia could strengthen the rationale for this research. The process for selecting the final 13 variables could be elaborated upon. A clearer explanation of how variables were prioritized or excluded would enhance transparency in the model development process. The final model contains a score. It is not advisable to include a score in a score The score contains LM disease and number of CAD. This is confusing. The term coronary abnormalities is unusual. Does this mean CAD? Including several procedures underpower the score. ASD and VSD are completely different procedures. The score contains CPB, which makes it not feasible for preoperative prediction. Organ failure is pre or postop? The discussion section could be expanded to include more detailed interpretations of the results, particularly regarding the clinical implications of the identified predictors. Exploring how these findings can inform clinical practice would be valuable. Including comparisons with other models beyond EuroSCORE II could provide a broader context for the model's performance.\nWhile some limitations are acknowledged, a more thorough discussion of potential biases, such as selection bias or data quality issues, would be beneficial. Additionally, the exclusion of certain patient groups (e.g., those with aortic dissection) should be more explicitly justified.\nThe conclusion mentions the need for external validation but could also suggest specific areas for future research, such as prospective studies for validating the score on different procedures.\nPlease use comprehensive legends for figures and tables.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1204
https://f1000research.com/articles/13-1035/v1	10 Sep 24	{ "type": "Research Article", "title": "Role of Artificial intelligence model in prediction of low back pain using T2 weighted MRI of Lumbar spine", "authors": [ "Ali Muhaimil", "Saikiran Pendem", "Niranjana Sampathilla", "Priya P S", "Kaushik Nayak", "Krishnaraj Chadaga", "Anushree Goswami", "Obhuli Chandran M", "Abhijith S", "Ali Muhaimil", "Priya P S", "Krishnaraj Chadaga", "Anushree Goswami", "Obhuli Chandran M", "Abhijith S" ], "abstract": "Background Low back pain (LBP), the primary cause of disability, is the most common musculoskeletal disorder globally and the primary cause of disability. Magnetic resonance imaging (MRI) studies are inconclusive and less sensitive for identifying and classifying patients with LBP. Hence, this study aimed to investigate the role of artificial intelligence (AI) models in the prediction of LBP using T2 weighted MRI image of the lumbar spine.\n\nMethods This was a prospective case-control study. A total of 200 MRI patients (100 cases and controls each) referred for lumbar spine and whole spine screening were included. The scans were performed using 3.0 Tesla MRI (United Imaging Healthcare). T2 weighted images of the lumbar spine were segmented to extract radiomic features. Machine learning (ML) models, such as random forest, decision tree, logistic regression, K-nearest neighbors, adaboost, and deep learning methods (DL), such as ResNet and GoogleNet, were used, and performance measures were calculated.\n\nResults Our study showed that Random forest and AdaBoost are the most reliable ML models for predicting LBP. Random forest showed high performance with area under curve (AUC) values from 0.83 to 0.88 across all lumbar vertebrae and L2-L3, L3-L4, and L4-L5 intervertebral discs (IVDs), with AUCs of 0.88 the highest at L5-S1 IVD (0.92). Adaboost demonstrated high performance at the L2-L5 vertebrae with AUC values of 0.82 to 0.90, with the highest AUC (0.97) at the L5-S1 IVD. Among the DL models, GoogleNet outperformed the other models at 30 epochs with an accuracy of 0.85, followed by ResNet 18 (30 epochs) with an accuracy of 0.84.\n\nConclusion The study demonstrated that ML and DL models can effectively predict LBP from MRI T2 weighted image of the lumbar spine. ML and DL models could also enhance the diagnostic accuracy of LBP, potentially leading to better patient management and outcomes.", "keywords": [ "Deep learning", "Machine learning", "low back pain", "intervertebral discs", "lumbar vertebrae" ], "content": "Introduction\n\nLow back pain (LBP) is the most prevalent musculoskeletal condition worldwide and the leading cause of disability. In 2019, it held the 9th position in disability-adjusted life years (DALYs) accounting for 2.5% of the overall “DALYS.” LBP was the primary cause of years lived with disability (YLDs), representing 7.41% of the total YLDS. In 2020, there were more than half a billion prevalent cases of LBP globally, and projections indicate that this number will exceed 800 million by 2050. Although age-standardized rates have slightly decreased over the past three decades, the number of LBP cases continues to increase owing to population growth and aging, particularly in Asia and Africa.1,2 LBP can be caused by various factors, including lifestyle, psychological, and social factors. To reduce the incidence of LBP, it is essential to address modifiable risk factors, such as smoking and obesity, which are associated with a high risk of developing condition.3,4 LBP can result from injuries or degenerative changes in the lumbar region, including facet joints, intervertebral discs (IVD’s), ligaments, and muscles. It is also associated with annual tears, disc height reduction, facet degeneration, and end-plate abnormalities such as Schmorl’s nodes, fractures, erosion, and calcifications.5–8\n\nMRI of the spine is a noninvasive technique that is regarded as the gold standard for detecting and diagnosing spinal diseases. T2 weighted MRI enhances tissue contrast and offers greater sensitivity than traditional CT imaging for diagnosing conditions such as IVD herniation, nerve root entrapment, and spinal canal stenosis. MRI can identify IVD degeneration and vertebral endplate changes, which are associated with clinically significant LBP. Imaging studies have revealed that 87% of asymptomatic individuals also exhibit lumbar IVD abnormalities on MRI.9–13\n\nRadiomics is a vital medical technique used in clinical practice for evaluation, diagnosis, selection of a course of treatment, and monitoring. Radiomics, a rapidly advancing artificial intelligence (AI) method in medical imaging, can objectively, reproducibly, and efficiently extract numerous quantitative features from medical images. These features are used to develop radiomic models or signatures that aid in interpreting various clinical phenotypes, such as patient genotyping, treatment efficacy, and clinical outcomes.14–17\n\nAI encompasses systems that can generate accurate interference from large datasets using advanced computational algorithms. Similar to humans, machines require learning for intelligent behavior. Therefore, AI includes various learning algorithms, such as machine learning (ML) and increasingly popular deep learning (DL) algorithms. Although AI originated in the 1950s, its development has accelerated since 2000, owing to advancements in computational power. Currently, AI technology provides indispensable tools for intelligent data analysis, particularly for solving medical diagnostic problems. The relationship between radiomics and AI is symbiotic. The high-dimensional nature of radiomics demands powerful analytic tools, and AI, with its advanced capabilities, is well-suited for this task. Conversely, AI applications with medical images rely on radiomics because the metrics used to train and build AI models are derived from radiomic approaches, specifically through feature extraction and feature engineering techniques.18–26\n\nFew studies have assessed the utility of radiomics-based ML models and DL techniques for predicting LBP. Hence, this study aimed to investigate the role of AI models in the prediction of LBP using T2 weighted MRI image of the lumbar spine.\n\n\nMethods\n\nThis was a prospective, case-control study. The institutional ethical committee (IEC2:179/2023) was obtained from Kasturba medical college and Hospital, Manipal, India on 20th July 2023, followed by the Clinical trial registry (CTRI) registration: CTRI/2023/08/056954, 25/08/2023, https://ctri.nic.in/Clinicaltrials/login.php. Written informed consent (IC) was obtained from all the participants.\n\nPatients referred for MRI of the lumbar spine and whole-spine screening were included. The patients were screened using the questionnaire “Delphi definitions of low back pain prevalence (DOLBaPP)”27 questionnaire to check for LBP prevalence. Patients were considered symptomatic if they experienced LBP for 12 months. Patients were considered asymptomatic if they experienced no current back pain and no memory (severe or disabling) back pain. A total of 100 cases and controls (Mean age; cases: 48.48±16.1 years; controls: 51.46±18.4 years) were included. Demographic details of the patients are shown in Table 1. Patients with tumors, severe osteoporosis, or previous spine surgeries were excluded.\n\nMRI Image acquisition: All MRI scans were performed with 3.0 Tesla MRI (United Imaging uMR 780). The MRI image acquisition parameters are listed in Table 2.\n\nThe DICOM MRI images of MRI T2 weighted images of the lumbar vertebrae and disc space for each patient were loaded into the 3D slicer software (Version 4.10.2). Segmentation of the lumbar vertebrae and intervertebral discs (IVD) was performed manually (Figure 1). Radiomic features from the lumbar vertebrae and IVDs were extracted for both the cases and controls (Supplementary file 1).\n\nML classifiers such as Random Forest, Decision tree, logistic regression, k-nearest neighbors (KNN), and AdaBoost were used. The ML classifiers were run in the Conda virtual environment, which was integrated with Python (version 3.9.7).28 Several libraries such as NumPy,29 scikit,30 pandas,31 seaborn,32 matplotlib,33 and others were installed to support the analysis. The training of the models utilized 8 GB of RAM, along with an Intel®coreTM i5 Central Processing Unit (HP ProBook 440). The study was conducted on a 64-bit Windows operating system to run the classifiers.\n\nData normalization: This is an essential step because it assigns equal weight to each variable, preventing any single variable from disproportionately influencing the model performance owing to its large numerical values. In our study, the min-max normalization (rescaling) technique was employed for the entire dataset.\n\nFeature selection: Mutual information method was used for the feature selection of the top 20 radiomic features at each lumbar vertebra and IVD for both cases and controls.\n\nThe data were split into training and testing ratios of 80:20. The data were subjected to five-fold cross-validation, where different subsets were trained to assess model efficiency. The input data were split into five equal parts: four groups for training and five for testing using various permutations and combinations in the cross-validation process. The parameters were hypertuned using a grid search technique that automates this tuning to determine the best values.\n\nThe performance metrics of the ML models for the test dataset were assessed using accuracy, precision, F1 score, area under the curve (AUC), Hamming loss, Jaccord score, log loss, and Mathew’s correlation coefficient (MCC).\n\nValidation of the testing model from the confusion matrix was assessed using\n\nWhere, TP - True positive, TN - True negative, FP - False positive, FN - False negative, PPV - Positive predictive value.\n\nDeep learning Model: MRI Images of the lumbar spine were collected in the Joint Photographic Experts Group (JPEG) format. The input images were cropped and resized to 184 × 282 pixels to mainly include the lumbar vertebrae and disc space. Intensity normalization was performed on all images such that the pixel values across multiple images were normalized to the same statistical distribution, facilitating improved analysis of MRI images. Further as an assistance DL, a subset of AI, was used. Transfer learning is a DL technique in which pre-trained networks are utilized to train the model for custom usage. One of the major advantages of this method is that it avoids training the network from scratch by using weights that are trained on the 1000 class ImageNet dataset. There are multiple pre-trained models in which GoogleNet and ResNet (18 and 50) were used (Figures 2–4). These are convolutional neural networks, meaning that convolution layers play a major role. These are feature extraction layers that perform convolution with different kernels.\n\nGoogLeNet is a part of the inception model, which is a 22-layer deep network that is computationally efficient. On the other hand, ResNet has an advantage over other networks because it consists of skip connections, which avoids the vanishing gradient.\n\nThe dataset was divided into a 90:10 training and test split ratio. The training set was further divided into training and validation sets. The validation of the dataset occurs simultaneously during training. Deep learning (DL) models were implemented using MATLAB 2023b owing to its better visualization and ease of use.\n\nTo obtain optimum results, the hyperparameters were adjusted. Epochs are the number of times the entire dataset is passed through the network for training. In this case, the dataset was trained for 30, 50, and 100 epochs, respectively. Initial learn rate is the amount of learning that happens at a step i.e. step size at which parameters are updated during training process. This was set to 0.001. The optimizer used was a Stochastic Gradient Descent with momentum (sgdm).\n\nDL model performance was assessed using the specificity, sensitivity, Precision, NPV, Recall, F1 score.\n\n\nResults\n\nIn our study we included 100 symptomatic and asymptomatic cases.\n\nThe mean age and sex of the symptomatic and asymptomatic cases are shown in Table 1.\n\nIn our study, we analyzed ML models based on radiomic features and DL methods to predict LBP in symptomatic and asymptomatic cases.\n\nFeature reduction for ML model development: The top 20 radiomic features for each lumbar vertebra and IVD were identified using a mutual information algorithm and are presented in Tables 3, 4.\n\nIn this study, ML methods such as Random Forest, Decision tree, Logistic regression, KNN, Adaboost were studied. The performance of the ML classifiers at the lumbar vertebrae and intervertebral disc using five-fold cross-validation is shown in Tables 5, 643 for the five classifier models.\n\nThe random forest showed high performance across all lumbar vertebrae, with AUC values from 0.83 to 0.88 across all lumbar vertebrae. Decision tree models exhibited moderate performance with AUC values between 0.65 and 0.76, suggesting lower predictive accuracy compared to other models. Logistic regression performed well, particularly at L5 with an AUC of 0.82, and maintained good performance across other vertebral levels with AUC values from 0.73 0.79. KNN also showed strong performance, especially at L2-L4 vertebrae with AUC values of 0.79 to 0.83, and slightly lower AUC values at L1(0.70) and L5(0.68). AdaBoost demonstrated high performance at L2–L5 vertebrae with AUC values of 0.82 to 0.90, although its performance at L1 was moderate, with an AUC of 0.67. The ML models showed slightly improved performance at the lower vertebral levels (L4 and L5) compared to the upper vertebral levels (L1-L3) Figures 5, 6.\n\nRandom forest showed strong performance at L2-L3, L3-L4 and L4-L5 IVD’s with AUCs of 0.88 and the highest at L5-S1 IVD (AUC-0.92). Decision tree models showed moderate performance, with the highest AUC at the L5-S1 IVD (0.85) and lower values at other disks, particularly at the L4-L5 IVD (AUC-0.65). Logistic regression showed the highest AUC at L3-L4 IVD (0.90) and maintained good performance at other disks, with AUC ranging from 0.79 0.87. KNN showed the highest AUC at the L4-L5 disk IVD (0.88) and moderately at other IVD disk between 0.73 and 0.78. Adaboost showed the highest AUC (0.97) at the L5-S1 IVD and exhibited strong results at the L2-L3 (0.86) and L3-L4 (0.83) IVD. The random forest and adaboost models showed high performance, particularly at the L5-S1 IVD (Figure 7).\n\nThe performance measures of the DL methods for LBP prediction are presented in Table 7.\n\nGoogleNet at 30 epochs outperformed the other DL models in terms of accuracy (0.85) and F1 score (0.86) for predicting LBP. ResNet 18 at 30 epochs had the second highest performance, with high accuracy (0.84) and F1 score (0.85). ResNet 50 showed consistent results at both 50 epochs (0.80-accuracy and 0.81-F1 score) and 100 epochs (accuracy-0.80 and F1 score-0.81), but with slightly lower performance metrics than GoogleNet and ResNet 18 at 30 epochs (accuracy-0.84 and F1 score-0.85).\n\n\nDiscussion\n\nIn our study, we used ML and DL algorithms to predict LBP by using T2 weighted images of the lumbar spine. MRI studies have shown that a significant percentage of asymptomatic patients have abnormalities related to lumbar intervertebral discs. Imaging studies often fail to provide definitive answers regarding the source of pain. Imaging techniques are valuable tools for diagnosis and are often clinically inconclusive in identifying the precise etiology of low back pain. The high prevalence of asymptomatic abnormalities, risk of overdiagnosis, and lack of correlation between imaging findings and pain highlight the need for a cautious and judicious approach to the use of imaging in LBP management. Clinicians should rely on thorough clinical assessment and consider imaging findings as part of a broader diagnostic strategy rather than the sole determinant of patient care.34–36\n\nOur study noted that ML models showed improved performance at the lower vertebral levels (L4 and L5) compared to the upper vertebral levels (L1-L3) and random forest and adaboost models exhibited particularly high performance at the L5-S1 IVD. Abdollah et al.37 reported that texture features extracted from T2 maps revealed significant textural differences in the L5-S1 lumbar IVD, upper and lower endplate regions, and the L4-5 lower endplate regions between individuals who are symptomatic and asymptomatic of LBP, which may not be apparent to the naked eye. The IVD and endplate zones of patients with LBP were more anisotropic, suggesting different patterns of degeneration due to varying patterns of collagen network destruction. Increased anisotropy may indicate fluid redistribution and changes in hydrostatic pressure, causing an uneven load distribution in pain-sensitive areas. Differences in Gray Level Co-occurrence Matrix features such as contrast, energy, and homogeneity provide additional evidence for the hypothesis of unique degeneration patterns in LBP. The random forest algorithm and Gini importance index indicate energy as a unique feature for classification. Ketola et al.38 also reported difference in T2 weighted images analyzed using logistic regression to classify textural features based on a pain questionnaire in a sample of 518 subjects. The best classification accuracy (83%) and AUC (0.91) were achieved at the lowest two IVDS, with a specificity score of 83% and a sensitivity score of 82%. These results suggest that texture features in the lower lumbar discs (L4-L5 and L5-S1) are more predictive of LBP, supported by the findings of increased anisotropy and genetic correlations. Another study by Aggarwal et al.39 reported that decreased L2 and L4 disc heights significantly predicted LBP. They also reported that thickening of the ligamentum flavum, particularly at the lower lumbar levels, contributes to spinal stenosis and LBP.\n\nThe DL models used in our study were useful for predicting LBP using MRI. GoogleNet with 30 epochs showed the highest performance with an accuracy of 0.85 and an F1 score (0.86) for predicting LBP. Won et al.40 employed a CNN to automatically grade spinal stenosis on MRI images of 542 patients, obtaining accuracy measures of 83.0% and 77.9% in comparison to the ground truth assessed by two separate doctors. Jamaludin et al.41,42 developed a CNN that segments the vertebrae and intervertebral discs with an accuracy of 95.6%. This model also identifies disc narrowing, marrow changes, endplate defects, spondylolisthesis, and central canal stenosis, and performs Pfirrmann grading with accuracy percentages ranging from 70.1% and 95.4%. Additionally, it can directly highlight abnormalities of the IVD and vertebrae using heatmaps, referred to as evidence hotspots41,42\n\nOur study had a few limitations. First, the sample size is sufficient for the initial analysis; a larger sample size could provide more robust results and improve the reliability of machine learning (ML), and deep learning (DL) models. Second, manual segmentation of the lumbar vertebrae and IVD is time-consuming and subject to inter-operator variability. Automated segmentation methods can enhance reproducibility and efficiency. Third, the study did not include risk factors, radiological findings, or their role in assessing LBP using machine learning methods.\n\n\nConclusion\n\nOur study found that ML classifiers, such as random forest and adaboost, exhibited the highest performance, particularly in the lower lumbar vertebrae and IVD, while decision tree and logistic regression models showed moderate performance in the prediction of LBP. For DL methods, GoogleNet achieved the best results at 30 epochs, followed closely by ResNet, which demonstrated high precision and specificity. Our findings highlight the potential of advanced ML and DL techniques for accurately predicting LBP, with random forest, AdaBoost, and GoogleNet showing the most promising results.\n\n\nEthical approval\n\nThis was a prospective, case-control study. The institutional ethical committee (IEC2:179/2023) was obtained from Kasturba medical college and Hospital, Manipal, India on 20th July 2023, followed by the Clinical trial registry (CTRI) registration: CTRI/2023/08/056954, 25/08/2023, https://ctri.nic.in/Clinicaltrials/login.php. Written Informed consent (IC) was obtained from all the participants.", "appendix": "Data availability\n\nFigshare: F1000 ML and DL Data, https://doi.org/10.6084/m9.figshare.26394847.v2. 43\n\nThis project contains following underlying data:\n\n• Radiomic features of lumbar spine cases (demographic characteristics of cases, radiomic features, spreadsheet)\n\n• Radiomic features of controls of the lumbar spine (demographic characteristics of controls, radiomic features–spreadsheet)\n\n• Anonymous Images cases (MRI JPEG images)\n\n• Anonymous Images controls (MRI JPEG images)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: F1000 ML and DL Data, https://doi.org/10.6084/m9.figshare.26394847.v2 43\n\nThis project contains following Extended data:\n\n• Table 5 and 6\n\n• Supplementary file 1\n\n\nReferences\n\nGBD 2021 Low Back Pain Collaborators: Global, regional, and national burden of low back pain, 1990-2020, its attributable risk factors, and projections to 2050: a systematic analysis of the Global Burden of Disease Study 2021. Lancet Rheumatol. 2023; 5(6): e316–e329.\n\nGu Y, Wang Z, Shi H, et al.: Global, Regional, and National Change Patterns in the Incidence of Low Back Pain From 1990 to 2019 and Its Predicted Level in the Next Decade. Int. J. Public Health. 2024 Feb; 69(69): 1606299. Publisher Full Text\n\nHartvigsen J, Hancock MJ, Kongsted A, et al.: What low back pain is and why we need to pay attention. Lancet. 2018; 391(10137): 2356–2367. PubMed Abstract \| Publisher Full Text\n\nChou R, Shekelle P: Will this patient develop persistent disabling low back pain? JAMA. 2010; 303(13): 1295–1302. Publisher Full Text\n\nVideman T, Battie MC, Gibbons LE, et al.: Associations between back pain history and lumbar MRI findings. Spine. 2003 Mar; 28(6): 582–588. Publisher Full Text\n\nVideman T, Nurminen M: The occurrence of anular tears and their relation to lifetime back pain history: a cadaveric study using barium sulfate discography. Spine (Phila Pa 1976). 2004; 29(23): 2668–2676. PubMed Abstract \| Publisher Full Text\n\nBoswell MV, Singh V, Staats PS, et al.: Accuracy of precision diagnostic blocks in the diagnosis of chronic spinal pain of facet or zygapophysial joint origin. Pain Physician. 2003; 6(4): 449–456. PubMed Abstract \| Publisher Full Text\n\nWang Y, Videman T, Battie MC: ISSLS prize winner: Lumbar vertebral endplate lesions: associations with disc degeneration and back pain history. Spine (Phila Pa 1976). 2012; 37(17): 1490–1496. PubMed Abstract \| Publisher Full Text\n\nFarshad-Amacker NA, Farshad M, Winklehner A, et al.: MR imaging of degenerative disc disease. Eur. J. Radiol. 2015; 84(9): 1768–1776. Publisher Full Text\n\nGundry CR, Fritts HM: Magnetic resonance imaging of the musculoskeletal system. Part 8. The spine, section 2. Clin. Orthop. Relat. Res. 1997; 343(343): 260–271. Publisher Full Text\n\nReddy MM, Gangavelli R, Priyanka P, et al.: Influence of Lumbar Spinal Canal Dimensions on Neurological Claudication Symptomatology- A Case Control Study. Biomed. Pharmacol. J. 2021; 14(2): 1019–1024. Publisher Full Text\n\nJarvik JJ, Hollingworth W, Heagerty P, et al.: The Longitudinal Assessment of Imaging and Disability of the Back (LAIDBack) Study: baseline data. Spine (Phila Pa 1976). 2001; 26(10): 1158–1166. PubMed Abstract \| Publisher Full Text\n\nBoden SD, Davis DO, Dina TS, et al.: Abnormal magnetic-resonance scans of the lumbar spine in asymptomatic subjects. A prospective investigation. J. Bone Joint Surg. Am. 1990; 72(3): 403–408. PubMed Abstract\n\nAerts HJ, Velazquez ER, Leijenaar RT, et al.: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nat. Commun. 2014; 5: 4644. Publisher Full Text\n\nHood L, Friend SH: Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat. Rev. Clin. Oncol. 2011; 8(3): 184–187. PubMed Abstract \| Publisher Full Text\n\nPeng H, Dong D, Fang MJ, et al.: Prognostic Value of Deep Learning PET/CT-Based Radiomics: Potential Role for Future Individual Induction Chemotherapy in Advanced Nasopharyngeal Carcinoma. Clin. Cancer Res. 2019; 25(14): 4271–4279. PubMed Abstract \| Publisher Full Text\n\nGillies RJ, Kinahan PE, Hricak H: Radiomics: Images Are More than Pictures, They Are Data. Radiology. 2016; 278(2): 563–577. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThrall JH, Li X, Li Q, et al.: Artificial Intelligence and Machine Learning in Radiology: Opportunities, Challenges, Pitfalls, and Criteria for Success. J. Am. Coll. Radiol. 2018; 15(3 Pt B): 504–508. PubMed Abstract \| Publisher Full Text\n\nChartrand G, Cheng PM, Vorontsov E, et al.: Deep Learning: A Primer for Radiologists. Radiographics. 2017; 37(7): 2113–2131. PubMed Abstract \| Publisher Full Text\n\nErickson BJ, Korfiatis P, Akkus Z, et al.: Machine Learning for Medical Imaging. Radiographics. 2017; 37(2): 505–515. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArimura H, Soufi M, Kamezawa H, et al.: Radiomics with artificial intelligence for precision medicine in radiation therapy. J. Radiat. Res. 2019; 60(1): 150–157. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKononenko I: Machine learning for medical diagnosis: history, state of the art and perspective. Artif. Intell. Med. 2001; 23(1): 89–109. PubMed Abstract \| Publisher Full Text\n\nAuffermann WF, Gozansky EK, Tridandapani S: Artificial Intelligence in Cardiothoracic Radiology. AJR Am. J. Roentgenol. 2019; 212(5): 997–1001. Publisher Full Text\n\nHarmon SA, Tuncer S, Sanford T, et al.: Artificial intelligence at the intersection of pathology and radiology in prostate cancer. Diagn. Interv. Radiol. 2019; 25: 183–188. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLe EPV, Wang Y, Huang Y, et al.: Artificial intelligence in breast imaging. Clin. Radiol. 2019; 74: 357–366. Publisher Full Text\n\nBi WL, Hosny A, Schabath MB, et al.: Artificial intelligence in cancer imaging: Clinical challenges and applications. CA Cancer J. Clin. 2019; 69: 127–157. PubMed Abstract \| Publisher Full Text\n\nDionne CE, Dunn KM, Croft PR, et al.: A consensus approach toward the standardization of back pain definitions for use in prevalence studies. Spine. 2008; 33(1): 95–103. PubMed Abstract \| Publisher Full Text\n\nPython Software Foundation: Python Language Reference, version 3.9.7.2021. Reference Source\n\nHarris CR, Millman KJ, van der Walt SJ , et al.: Array programming with NumPy. Nature. 2020; 585: 357–362. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPedregosa F, Varoquaux G, Gramfort A, et al.: Scikit-learn: Machine Learning in Python. J. Mach. Learn. Res. 2011; 12: 2825–2830.\n\nMcKinney W: Data Structures for Statistical Computing in Python.van der Walt S , Millman J, editors. Proceedings of the 9th Python in Science Conference. 2010; pp. 56–61.\n\nWaskom ML: Seaborn: Statistical data visualization. Journal of Open Source Software. 2021; 6(60): 3021. Publisher Full Text\n\nHunter JD: Matplotlib: A 2D Graphics Environment. Computing in Science & Engineering. 2007; 9(3): 90–95. Publisher Full Text\n\nBrinjikji W, Luetmer PH, Comstock B, et al.: Systematic literature review of imaging features of spinal degeneration in asymptomatic populations. AJNR Am. J. Neuroradiol. 2015; 36(4): 811–816. 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\nChou R, Fu R, Carrino JA, et al.: Imaging strategies for low-back pain: systematic review and meta-analysis. Lancet. 2009; 373(9662): 463–472. PubMed Abstract \| Publisher Full Text\n\nAbdollah V, Parent EC, Dolatabadi S, et al.: Texture analysis in the classification of T2 -weighted magnetic resonance images in persons with and without low back pain. J. Orthop. Res. 2021; 39(10): 2187–2196. PubMed Abstract \| Publisher Full Text\n\nKetola JHJ, Inkinen SI, Karppinen J, et al.: T2 -weighted magnetic resonance imaging texture as predictor of low back pain: A texture analysis-based classification pipeline to symptomatic and asymptomatic cases. J. Orthop. Res. 2021; 39(11): 2428–2438. PubMed Abstract \| Publisher Full Text\n\nAggarwal N: Prediction of low back pain using artificial intelligence modeling. J. Med. Artif. Intell. 2021; 4: 2. Publisher Full Text\n\nWon D, Lee HJ, Lee SJ, et al.: Spinal Stenosis Grading in Magnetic Resonance Imaging Using Deep Convolutional Neural Networks. Spine (Phila Pa 1976). 2020; 45(12): 804–812. PubMed Abstract \| Publisher Full Text\n\nJamaludin A, Kadir T, Zisserman A: SpineNet: Automated classification and evidence visualization in spinal MRIs. Med. Image Anal. 2017; 41: 63–73. PubMed Abstract \| Publisher Full Text\n\nJamaludin A, Lootus M, Kadir T, et al.: ISSLS PRIZE in bioengineering science 2017: Automation of reading of radiological features from magnetic resonance images (MRIs) of the lumbar spine without human intervention is comparable with an expert radiologist. Eur. Spine J. 2017; 26: 1374–1383. PubMed Abstract \| Publisher Full Text\n\nPendem S: F1000 ML and DL Data. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "325453", "date": "24 Sep 2024", "name": "Chandrasekhar Priyanka", "expertise": [ "Reviewer Expertise Magnetic Resonance Imaging", "Artificial intelligence in health care" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor comments: The research article presents a case-control study to assess machine and deep learning models for prediction of low back pain using T2-weighted MRI images of lumbar spine. The utility of mutual information for radiomic feature selection is a good approach; however, the reasons for selecting this over frequently used feature selection method such as least absolute shrinkage and selection operator (LASSO) is not adequately justified. Though the study employed five-fold cross validation, it would benefit from discussing additional methods such as bootstrapping or using different validation splits. The study briefly mentions hyperparameter tuning, but it did not discuss in detail whether any steps were taken to reduce overfitting. Future research directions in how AI model predictions should be clinically interpreted and implications of incorporating these AI models into the diagnostic workflow can be provided. Minor comments: Inconsistent capitalization to be corrected – the words “random forest” and “adaboost” are capitalized inconsistently. The article effectively demonstrates the use of machine and deep learning models in accurately predicting low back pain and provides promising contributions to knowledge about the use of AI in healthcare.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "325460", "date": "01 Oct 2024", "name": "Tarun Gangil", "expertise": [ "Reviewer Expertise Artificial Intelligence in Oncology", "Image Processing", "Deep Learning and Machine Learning" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors should highlight , why they have chosen a wide range of machine learning algorithms, clustering algorithm (KNN) and deep learning algorithms such as ResNet and GoogleNet ?\nDo the analysis were performed only on the radiomics dataset ? If that is the case then why do they have used segmentation algorithms such as ResNet and GoogleNet ?\nIf MRI images are used in analysis, without radiomics dataset, then what is the average sensitivity of the ground truth segmentation mask across all samples?\nDo authors have used Images as an input in the analysis , apart from the radiomics dataset, directly in the AI models.\nAlso, highlight about class variability, given it is a binary classification problem or Multiclass ?\n\nAlso, post analysis , it is needed for the authors to highlight the clinical significance of the results obtained from the classification 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? 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?\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": "12567", "date": "10 Oct 2024", "name": "Saikiran Pendem", "role": "Author Response", "response": "Question 1: Authors should highlight , why they have chosen a wide range of machine learning algorithms, clustering algorithm (KNN) and deep learning algorithms such as ResNet and GoogleNet ? Ans: The advantages for using wide range of machine learning algorithms, cluster algorithm (KNN) and deep learning algorithms such as ResNet and GoogleNet were provided in the methodology. We have utilized a wide range of ML classifiers since different classifiers may perform better with data features and this allows in through benchmarking and the selection of an optimal model for a specific problem. Each ML method has its own advantages, random forest excels in robust and accuracy, decision tree offers interpretability, logistic regression is effective for linear relationships, KNN is good for smaller dataset, adaboost improves performance by merging weak learners. GoogleNet and ResNet were chosen due to their powerful ability to learn complex patterns in data, especially in image analysis, medical diagnostics and classification problems. Both are exceptional at automatically learning deep features particularly involving images, where they can capture complex and minute details. GoogleNet inception modules process input using parallel convolution layers with varying kernel sizes, ehancing efficiency by capturing features at different scales with fewer parameters. ResNet solves the vanishing gradient issue, making it possible to train very deep networks efficiently. This permit learning more complicated representations improves performance and tasks like image classification and object recognition. Question 2: Do the analysis were performed only on the radiomics dataset ? If that is the case then why do they have used segmentation algorithms such as ResNet and GoogleNet ? Ans: The radiomics features were extracted for the purpose of using the ML classifiers. As for the Deep Learning models, there were no radiomics features. These models are black boxes which extract the features from the images without human intervention and classify them. Question 3: If MRI images are used in analysis, without radiomics dataset, then what is the average sensitivity of the ground truth segmentation mask across all samples? Ans: In case of Deep Learning method, the MRI images are used for the analysis (classification) without radiomic features. Hence, no ground truth masks. The classification model gives sensitivity between the range of 75-85%. Question 4: Do authors have used Images as an input in the analysis, apart from the radiomics dataset, directly in the AI models. Ans: Yes, for the deep learning models, direct images for the classification task. Question 5: Also, highlight about class variability, given it is a binary classification problem or Multiclass? Ans: It is a binary classification problem which helps in predicting the LBP. Class variability impacts evaluation metrics such as sensitivity, specificity, precision, and F1-score. The more variability there is within and between classes, the more robust the model needs to be. The same is included in the methodology section. Question 6: Also, post analysis , it is needed for the authors to highlight the clinical significance of the results obtained from the classification algorithms. Ans: The clinical significance of the results obtained from the classification algorithms were included in the discussion section. According to our study, ML and DL models could provide more efficient, reliable, noninvasive diagnostic insights by accurately identifying abnormalities in the lumbar vertebrae and intervertebral discs (IVDs), even in cases where conventional MRI image assessments were inconclusive. By improving the ability to predict LBP, ML and DL algorithms could guide better clinical decision making, reduce unnecessary surgical interventions." } ] } ]	1	https://f1000research.com/articles/13-1035
https://f1000research.com/articles/13-1187/v1	10 Oct 24	{ "type": "Research Article", "title": "Re-conceptualization of the learning environment as a dynamic system", "authors": [ "Hideaki Ito" ], "abstract": "In Japanese language education, the term \"learning environment\" is used in various contexts. This paper investigates the term \"learning environment\" in previous studies and notes that traditional learning environments have been characterized as \"morphological characteristics learning environments\" focusing on static learners. However, since learning environments involve a dynamic, reciprocal relationship where learners and their surroundings interact and evolve, the paper advocates for a re-conceptualization of \"experiential-ecological learning environments\" that captures this dynamic nature. Furthermore, to enrich the experiential-ecological learning environment for learners, the presence of learning environment engineers and the meaningful valuing of environmental enrichments is essential. Lastly, the paper emphasizes that by combining various individual learning experiences, it is possible to create a sustainable and richer learning environment.\n日本語教育において「学習環境」という用語はさまざまな文脈で用いられている。そこで本稿では、先行研究の「学習環境」という用語の使用実態を調査し、従来の学習環境は静的な学習者を中心にして、その特徴を捉えた「形態特徴的学習環境」であることを述べた。そして、学習環境は学習主体と環境とが相互作用をしながら変化していく能動的な循環関係であることから、動的な学習者／学習環境の姿を捉えようとする「経験・生態的学習環境」へと学習環境の捉え直しをしていくことを主張した。その上で、学習主体の経験・生態的学習環境を豊かにしていくためには、学習環境エンジニアの存在および意味のある価値づけとなる環境エンリッチメントの配置が重要であることを述べた。さらに個別の学習環境だけではなく、さまざまな人々の経験を組み合わせていくことで、持続的かつより豊かな学習環境を構築していくことができることを強調している。", "keywords": [ "xperiential-ecological learning environments", "learning environment engineer", "environmental enrichments", "affordance", "meaningful valuing" ], "content": "1. はじめに\n\n本稿は，日本語教育の先行研究においてさまざまな文脈で用いられてきた「学習環境」という用語が，これまでどのように捉えられてきたのかを検討し，「学習環境」に対する捉えを静的なものから動的なものに捉え直すことで，学習環境を動的なシステムとして考えていく必要性を主張することを目的とする。\n\n日本語教育において「学習環境」という用語は日本国内/国外，またはそこに付随する漢字圏/非漢字圏のように「学習者の居住地の特徴」を述べたり，教室環境/自然環境のように「学習者が日本語を学ぶ（習得する）場所」という文脈で用いられたり，対面/オンラインのように「学習者の学習形態」を指すなど，その用いられ方は多岐にわたる。同様に，文化庁（2024 年度より文部科学省へ移管）が進めている「『生活者としての外国人』のための日本語教室空白地域解消推進事業」の目的では「本事業は，日本語教室が設置されていない国内の地域に居住している外国人等が，日常生活を営む上で必要となる日本語能力を習得できるよう，日本語教室の設置，ICT を活用した日本語学習コンテンツの開発等を行うことにより，日本語学習環境の整備を図ることを目的としています。」（下線は引用者による）と「日本語教室の設置」や「ICT を活用した日本語学習コンテンツの開発」という物理的環境の整備が日本語学習環境の整備であるように述べられている一方，国際交流基金は 2022 年度の年報の「海外における日本語教育」において「海外の人たちに日本語を知ってもらうことは，日本への親しみや理解を広げるきっかけとなります。世界中で多くの人に日本語を学んでもらえるよう，各国の日本語学習環境の整備を進めています。」 (p.10) （下線は引用者による）と述べ，それらを進める事業として専門家派遣や教師研修などを挙げているように，行政機関においても「学習環境」という語の使用は見られるものの，「学習環境」が何を指しているのかは明確に示されてはいない。このようにさまざまな文脈で用いられる「学習環境」という語は先に述べたように，日本国内/国外，漢字圏/非漢字圏のように二項対立で分けられることも多く，一方の優位性や不十分さという学習環境の上下関係を作り出すレトリックとして発信者に使用されることもある。これらのことを踏まえ，「学習環境」とはどのようなものであるのかを明確にしていく必要がある。\n\n日本語教育における「学習環境」という用語の初出は，国立情報学研究所が提供するデータベース「CiNii Reserch」で「学習環境 and 日本語教育」を検索すると，1989 年から始まる科学研究費補助金の研究概要において確認できる。その後，1990 年代半ばから論文等でも使用されることが多くなっている。近年では社会的な変化により対面環境/オンライン環境という言葉がよく聞かれるようになっており，「学習環境」が指し示す意味も従来の意味とは変化している可能性もある。そのため，従来の「学習環境」が示していたものがどのようなものであるかを確認し，現在の状況に合わせた日本語教育における「学習環境」の捉え直しの必要性を検討していく。\n\n\n2. 本研究で行なった調査概要\n\n現在の状況に合わせた日本語教育における「学習環境」の捉え直しの必要性を検討するために，日本語教育に関する過去の文献において「学習環境」という用語がどのように使用されてきたのかを調査する。そこで本研究では以下のような調査を実施した。国立情報学研究所が提供しているデータベース「CiNii Research」において「学習環境 and 日本語教育」で検索し，データ種別が「論文」となっているものを抽出した。2024 年 4 月 2 日現在1，上記方法で抽出できた論文は 75 件（重複1件除外）であり，そのうち論文原稿を確認できたものは 62 件であったため，この 62 件すべてを本調査の対象とした。そして調査対象とした論文 62 件すべてに対し，各論文において「学習環境」という用語がどのような観点で使用されているのかを1件ずつ読み，確認した。調査対象論文の中にはキーワードのみで具体的な記述がないものもあったため，具体的な記述があったものを中心に「学習を行う物理的な場」「学習者の周りに配置するリソース」「授業内で行う学習活動の多様性，心理的側面への配慮」「自らが作り出すもの」の 4 つの観点に分類した。なお，62件の論文は文献リスト (Ito, 2024) に挙げている。\n\n\n3. 学習環境はどのように捉えられてきたのか\n\n本節では「学習環境」という用語の使われ方によって分類した「学習を行う物理的な場」「学習者の周りに配置するリソース」「授業内で行う学習活動の多様性，心理的側面への配慮」「自らが作り出すもの」の観点ごとに，対象論文内でどのように述べられていたかについて触れる。\n\n漢字学習に対する学習者の信念は使用教科書や学校の所在地によって異なるのかを調査した大北 (1998) は「文字導入の時期の信念に対しては教科書よりも場所の影響が強いと考えられる」(p.43)，「教科書よりも学習環境が会話学習優先信念に与える影響が大きいことを示唆している」(p.43)と「学習環境」を地理的環境，日本人との接触頻度などの日本語のインプットの多少として捉えている。また，菅 (2017) では，日本語スピーチコンテストを通した日本語学習支援において，大教室にステージが整備されたことによりコンテスト後も声を出して練習できる新しい学習環境が形成されたと述べており，ステージがある教室を学習環境として捉えていることがわかる。福島・マリーナ (2006) は教室外で日本語との接触機会がない海外環境における日本語学習環境を「孤立環境における日本語教育」と呼び，その地理的特徴を述べ，ショリナ (2019) は福島・マリーナ (2006) を参考に，ある地域の学習環境を捉える際に，学習環境を社会的要因（日本との地理的・文化的な距離）と情意的要因（その社会においての日本語の実用性）に分けて捉える必要性を述べている。ただし，情意的要因も社会的要因に影響されることからショリナ (2019) も学習環境は物理的な場として捉えていると考えられる。また，立間 (2010) も福島・マリーナ (2006) が述べる孤立環境で学習環境をどうデザインするかを問題意識として，日本とアゼルバイジャンの関係，日本企業数，在留邦人数，日本語学習者数など日本や日本人との社会的接触環境を調査していることから物理的環境として学習環境と捉えていることがわかる。その他，学習環境について触れている論文で最も多い言語習得に関する論文（伊藤，2005; 高・崔，2023; 辛，2005, 2006; 孫，2008ab; 東，2007; 村田，2020; 李，2003）では，学習環境として JSL/JFL 環境で調査対象者を分類しており，これらの論文では上で述べてきたことと同様に，学習環境を「物理的な場」として捉えている。\n\n羽田野・田口 (1995) では，高等学校における日本語教育の現場について「学習環境」という項を立てて取り上げている。そこでは「まず，学習理解のための日本語能力を高める適切な教材がない。また，日本語教育の専門教育を受けた教師はほとんど存在しない。そのため，日本語教育を必要とする生徒を入学させた場合は，教師が何の知識もないまま，手探りで対応することになる。また，定時制では時間割の関係から，日本語教育に割り当てられる時間が限られる。」(p.42)と教材や教師というリソースの有無や学習時間，学習上の制約など学習の前提となる環境を「学習環境」と捉えている。本調査の対象論文を年代順に並べた時に論文のキーワードとして初めて「学習環境」という用語を記載した金田ほか (1997) では，「近年，日本語を学習する外国人が増加しているが，学習者が手軽に学べる教材や，二ヶ国語の話せる教師が不足しており，日本語学習環境はあまり整っていない」(p.46)と，教材や教師の存在の不足を「学習環境」が整っていない状況と捉えている。来嶋ほか (1995) は多読を進めるために辞書機能のある読書支援プログラムの開発研究において課題として「学習環境」を挙げ，「コンピュータの台数を増やし，機種を向上させて利用しやすい学習環境をつくること」(p.11)と施設としての「物理的リソース」を学習環境と捉えている。また，戸田 (2009) も「教室内外において発音練習ができる学習環境を整備し，学習機会を提供することにより，自律学習を促していく」(p.56)ということを提案し，その提案の具体例として「シャドーイング練習用DVD教材」「オンデマンド日本語発音講座」「日本語発音練習用ソフトウェアの開発」といずれも「物理的リソース」を挙げている。このように物理的リソースを学習環境と捉えるのは，漢字教育への CAI の導入について報告し，その利点と課題の検討を行なった鈴木 (1995, 1996) も同様で，コンピュータの台数の不足に加えて，教育用ソフト（教材）の充実という物理的リソースが学習環境の中心に捉えられている。この流れは ICT の活用が進むにつれ増えていき，来嶋・鈴木 (2000) では独習を支援する学習環境として「留学生は，正規の日本語の授業を離れた後も独自に日本語力を向上させる努力を続けており，新聞やテレビ，日本人の友人など，容易に接することのできるメディアを利用している。留学生の生活は，専門分野の研究やアルバイトなどで，教師が想像するよりも多忙である。したがって，彼らの独習を支援するためには，独習用教材も上記のメディアと同様，個人で容易に利用できることが求められる。開発と実践にあたって，このような状況を前提とし，少なくとも，時間や場所が自由に選べるなどの十分な配慮をすることが必要である」(p.9)と述べ，コンピュータの利用台数が限定的であったことから好きな時間と場所で利用できないという課題に対する提案として，友人なども含めて時間や場所が自由に選べるなどの配慮の必要性を述べている。このことから学習環境を「学習者の周りに配置するリソース」として捉えていると考えられる。これは田中ほか (2005)，沖本 (2019)，深田・高橋 (2021) でも同様である。さらに，ハリソン・實平 (2005, 2007) では「学習環境設計」という用語を用いて，CALL (Computer Assisted Language Learning) 環境を前提として机の配置やメディアなど教室設計についても詳しく述べていることから「学ぶ場所，学ぶリソース」を一括して学習環境として捉えている。\n\n日系ブラジル人とその配偶者を対象に日本語の読み書き能力に関する調査をおこなった野元 (1999) では，「外国人住民にひらがな・カタカナの読み書きのできない人が多いという事態が生じるのは，ひらがな・カタカナ習得の機会が不足しているという学習環境に原因があるというよりは，ひらがな・カタカナは漢字かなまじりで使用されることが多く，漢字のわからない人にとって，その有用性が現状では極めて低いことと関連深い」(p.440)と学習環境を「日本語習得の機会」として捉えている。金庭 (2004) は学習環境を論文のキーワードとして挙げつつも，本文では「学習環境」という語を用いてはいないが論文の冒頭に「近年，学習者の日本語能力を高めるために，日本語クラスと地域社会との間に関連性を持たせることが課題となっている。」(p.4)と述べ，インターネットを活用して地域社会の情報を授業に導入する方法を提案していることから，「学習活動」が学習環境であると捉えていると考えられる。そして，大石ほか (2005) では終日一教員担当制による利点を主張し，その中で「一教員制は，コマ割りの授業による学習者の思考の寸断を防ぎ，学習環境を安定させることからも有用である。」(p.5)と「授業内の活動」を学習環境と捉えていることがわかる。また，大関・遠藤 (2012) は「他者と関わりながら学習に参加すること，つまり，協働的な学習環境が主体的な学びを支え」(p.73)と，「他者と関わりながら学習に参加する」という「活動形態」を学習環境と捉えている。この点について広瀬 (2015) も「協働的学習環境」という語を用いて同様のことを述べている。\n\n予備教育生の多様化が起こる中で学習者のニーズ分析をおこなった小川ほか (1998) も学習環境とは何かという具体的な記述はないが，1) 留学の目的，動機，予想（期待）に関するもの，2) 留学生の心理的側面に関するもの，3) 言語学習観と他の外国語学習経験の影響を分析・考察し，学習者の傾向や変化を明らかにすること，がよりよい学習環境作りの一助になると期待しており，その点で目的や動機，異文化の中での心理的負担，言語学習に関する考え方という「心理的側面への配慮」が学習環境を整えると考えていることが窺える。野原 (1999) は学習者の自発的な発話を促すために教師はどのような支援をしていくかを考察し，「教師に求められている学習支援的な役割とは，偏に，『言語習得を促進するような学習環境を整えること』と言える」(p.102)と述べた上で，その学習環境を「視聴覚機材等の設備面のことではなく，学習者が授業に興味を持って積極的に参加できるような場としての環境」(p.102)と3-2節で述べた物理的リソースとしての学習環境をはっきりと除外し，「学習者の心理的側面に配慮した場」として捉えている。また，秋元ほか (2016) では視覚に障害を持つ日本語学習者の学習環境を調査するにあたって，教師視点として教育現場が抱える不安や困難さを聞き取る調査を行なっており，学習者本人だけではなく，「学習者の周りの人の心理的側面」も含めて学習環境と捉えている。\n\nニーズ分析の重要性を述べている若林 (1999) は，「ニーズ分析をすることで学生の学習環境を見直すことができると思う。主観的ニーズは現在行われている授業の中から生まれた学習者の要求であるから，ニーズ分析によって独善的になりがちな授業をもう一度見直す機会が教師に提供されているのである。しかし教師自身に学生が何を求めているか，またそれに適した学習環境を作るという考えがないなら，学生のニーズは何も見えてこないだろう」(p.80)と，「学習環境を見直す」「教師自身に学生が何を求めているか，またそれに適した学習環境を作るという考え」「それぞれの学習環境に適した効果的学習環境を作っていかなければならない」と「学習環境」は自由に変えていけるものであると捉えている。また，「ニーズ分析を基に，学習者と継続的な話し合いを通じて，個々の学生にとって最適な学習環境を作っていく過程の手伝いができ，さらに将来的にはその学生が授業外でも，あるいは卒業してからでも，日本語の自律学習，生涯学習ができるようになると考えられる」と，自らが学習環境を作っていくという自律的な学習環境の構築につながる考え方も提示しており，3-1 節，3-2 節，3-3 節に挙げた「学習環境」とは異なる捉え方を提示している。高橋・向井 (2006) も教室活動を通して日本語を教える者は，毎日の生活の中で日本語学習が行われていることを忘れがちであると指摘し，現実の学習環境の実態を把握し，学習を環境との相互作用の中で捉えていく必要性を述べている点で，学習環境を「自らが作っていくもの」として捉えていることが窺える。これは向井・高橋 (2007) も同様の捉え方をしている。さらに，トムソン木下 (2007) は学習環境を「学習者コミュニティー」として捉え，Engeström の活動理論に当てはめて分析している。その中で「学習者コミュニティーには，達成すべき目標があり，成員は様々な役割を担い，目標に向かって協働していく。そこにはおのずとコミュニティーの文脈が蓄積され，慣習や固有の“文化”が発生し，短いながらも“歴史”も共有されていく。この“文化”“歴史”という言葉も社会文化理論の専門用語的な用法である。一般に言う日本の文化，日本の歴史などの用法とは一線を引き，あくまでもコミュニティーの中で生まれたものを指し，微視的なものも含む。例えば，教室内で人々が一定の行動や慣習を共有したら，それは教室の\"文化\"であり，一分前の出来事でも，時間軸を追って蓄積されることで次の出来事に影響を及ぼすなら，これを\"歴史\"と捉える。」と述べており，若林 (1999) は将来的な視点のみだったものに加えて，過去の視点も取り入れている。また，滑川 (2015) は岡崎 (2009) の「ある人のことばの力が存分に発揮される社会的環境（生態）がその人の生活の質を規定すると捉える」(p.12)という言語生態学の視点から学習環境を捉えている。\n\n\n4. 学習環境の捉え直し\n\nここまで見てきたように，これまでの「学習環境」は「学習を行う物理的な場」「学習者の周りに配置するリソース」「授業内で行う学習活動の多様性，心理的側面への配慮」「自らが作り出すもの」とさまざまな観点から述べられている。個々の観点は学習環境を構成する重要なものである。しかし，「学習環境」を述べる観点がそれぞれの研究の文脈に寄りすぎており，個々に異なるものを述べているようにも見える。これは従来の「学習環境」の捉えにおいて当初予想していた年代における偏りが見られない点からも，学習者を中心に据えながらも学習者を無機質な固定化された存在として捉え，「学習者の環境を研究者がどう捉えるか」という個々の研究者による「形態特徴的学習環境」の捉えが中心にあるからではないだろうか（図1）。\n\nこの形態特徴的学習環境の捉えの欠点としては①学習者を取り巻く環境が相互作用によって生み出される動的なものであるという視点が抜け落ちていること（動的システムとしての学習環境の視点の欠如），②学習者や学習者の周りにいる人々を環境に変化をもたらさない無機質な存在として捉えていること（学習環境エンジニアとしての存在/役割の軽視）の 2 点が考えられる。このような形態特徴的学習環境の捉えの欠点はどのようにすれば乗り越えられるのか。それには，日本語学習者の学習環境の特徴を捉えた形態特徴的学習環境としての捉えから，日本語学習者の経験によって変化する学習環境のあるがままを捉えた「経験・生態的学習環境」への捉え直しが重要であると考える。次節では，動的システムとして機能する「経験・生態的学習環境」とそれを創り出す「学習環境エンジニア」と「学習環境エンリッチメント」について詳しく述べる。\n\n田中・斎藤 (1993) が「学習過程とは自分の身のまわりの環境になんらかのしかたで働きかけ，その環境を変えながら自らも変わっていく活動」と述べているように，学びにおいて学習主体と環境は相互作用をしながら変化していく。そして人間や社会は絶えず変化している点を踏まえると，それは単にお互いに影響を与え合っているというレベルに留まらず，さまざまな出来事を通した経験によって学習主体自身の状況認知が変化すると同時に，その状況認知の変化によって学習主体の学習環境が変化し，その学習環境の変化によって，さらに学習主体が変化していくという能動的な循環関係になっていると考えるべきである。そして，そのような関係において図1 で示したような静的な形態特徴的学習環境の捉えでは限界があり，この動的な学習環境の姿を捉えようとするのが「経験・生態的学習環境」の捉えである。その意味で，経験・生態的学習環境は形態特徴的学習環境の捉えの欠点である「動的システムとしての学習環境の視点の欠如」を乗り越えるものである。\n\n経験・生態的学習環境について考えるには，人類がどのように進化を遂げてきたのか，つまり，どのように複雑な社会を生き抜き，より良く生きようとしてきたのか，まで視点を広げる必要がある。トマセロ(2022/2023) では，神経系を備えた人類の祖先から人類までの大まかな進化の流れについて左右相称動物→脊椎動物→哺乳類→大型類人猿→人類との仮説を立て，行為主体が意思決定を行い，能動的に行動する「行為主体性の変化」の流れについて論じている。そして，生物種が抱く「目標や基準値は，追求されるべき事実的な状況として表象され」(pp.62-63)，行動の意思決定は生物の目標に応じて決まり，その際の注意の対象となるのは自己の目標や行動に関連する状況であると述べている。ユクスキュル・クリサート(1970/2005) は，このように生物種が自身を取り巻く環境から主観的に意味を構築して創り出して見ている世界を「環世界 (Umwelt)」2と呼び，それぞれの有機体が同一の物理的環境の中で異なる世界（環世界）を生きていることを指摘している。トマセロ (2022/2023) はこの点を踏まえ，「生物が持つ知覚の観点からすると，生態的ニッチは，自己の経験的ニッチでもある」(p.61)と述べており，複雑な社会の中では状況認知を変化させるさまざまな経験がそれぞれの生物種が生き抜くための基盤となる。これは現代の学習主体においても，自己の経験を豊かにすることが動的なシステムを動かす原動力になると考えられる。さまざまな経験がさまざまな形で状況認知を変化させ，環世界を再構築していく，この動的なシステムこそが「経験・生態的学習環境」である。\n\n前節では，生物の進化と同様に学習環境を動的なシステムである「経験・生態的学習環境」として考えていく必要性を述べた。本節では，その学習環境の構築において動的なシステムである経験・生態的学習環境をどのように創り出していくかについて検討する。\n\nまず再度，生物界の話から入りたい。生物界の中には自身の生息域の環境を積極的に変化させ，その変化によって他の生物にも直接・間接的に影響を与える生物（ビーバーなど）がいる。このような生物は「生態系エンジニア」と呼ばれる。生態系エンジニアと呼ばれる生物は自身がよりよく生きるために自身の環境を変化させるということが根幹にあるが，自身が存在する生息域全体の環境に変化を与え，それによって他生物が利用する資源にも変化を生み，生息域全体を豊かにする。つまり，「生態系エンジニア」が自身の環世界においてよりよく生きようとすることが，他の生物にとっての未知の経験を創り出し，その未知の経験を通して生息域のさまざまな生物は状況認知を変化させ，その結果，生息域全体の豊かさを創り出していく。\n\nこれは学びにおいても同様である。「経験・生態的学習環境」では学習主体自身の経験を豊かにすることが動的なシステムを動かす原動力であることを述べた。学習主体が積極的に学びに関する状況認知を変化させ，それにより学習主体および学習主体の環境が相互作用しながら再構築されていく。この時の学習主体が「学習環境エンジニア」である。また，この学習主体を複数人として捉えると，さらに複雑なシステムとして動き出す。学習主体が自身の経験を豊かにする際に，そこに他者の存在を措定し，他者との関係の中で積極的に学びに関する状況認知に変化を起こしていく。すると，そこに関わる他者の環境にも変化が起き，結果的に学習主体，学習主体の環境，学習主体と共に生きる他者（=他の学習主体），他者の環境という4つのシステムが相互作用をしながら協働的に再構築されていく。学習環境エンジニアには誰もがなり得るが，日本語教育の文脈で第一に想起されるのは日本語学習者であろう。また，学びに関する状況認知に対して積極的に変化を起こすという点では，学習者の学習環境をより良いものへと変化させていこうとする意志を持つ「日本語教師」も「学習環境エンジニア」として機能する可能性を十分に持っていると言える。では，学習環境エンジニアの役割である経験を豊かにするとはどういうことであろうか。\n\n4-1 節で述べたように，行動の意思決定は生物の目標に応じて決まり，その際の注意の対象となるのは自己の目標や行動に関連する状況である。つまり，人は何かしらの目的を持って計画・行動をし，その予見または行動を行った結果に対するフィードバックを得ながら，自己の行動を環境と共に調整して行っている。トマセロ (2022/2023) はこれを「フィードバック制御システム」と呼んでいる。この「フィードバック制御システム」によって，「その都度の状況のもとで何が機能し何が機能していないかを決定して，知覚によるフィードバックを介して行動中に計画を変更したり，遠い未来のために学習したりすることが可能」 (pp.103-104) になる。つまり，主体が行動を起こすことにより環境に変化をもたらし，その結果，何かが起こるという環境との間の因果関係を捉えるということが重要な学びの一つである。これはヴィゴツキー(1930-31/2005) が行動形態の主要な特質として述べた「刺激Aは，反応を呼び起こす。その反応というのは，B 点に作用を及ぼす刺激 X を発見することにある。このようにして，A 点と B 点との結合は，直接的にではなく，間接的に確立される。」 (pp.139-140) と一致する。つまり，学習主体 (A) はある目的 (B) のために，環境 (X) を道具的に利用して目的 (B) の達成を試みる。その際，単に環境 (X) を媒介するだけではなく，そこにはトマセロが述べるフィードバックを行うためのメタ的な視点があり，そのメタ的な視点で得た情報（フィードバック）を基に学習主体 (A) が環境 (X) との調整を行っていると考えられる。その意味では環境を目的の遂行のための道具として活用すると同時に，目的に向かっての学習を環境とともに行なっていると考えることができる（図2）。\n\nこの点について，加藤・有元 (2001) も「リソースはそれを可視化する特定の文脈にあってはじめてリソースと捉えることが可能になるものであり，それが同時に特定のリソースを利用するような文脈を相互的・その場的に構成する」(p.11)と述べている。つまり，イメージ情報としてのメタ的な視点でニーズを明確にし，調整において具体的に実行できるのかという試行としての一回性の体験を繰り返すこと（経験）になる（槙，2004）。この繰り返しにより学習主体は学習環境に適応していく（図2）のであるが，ローレンツ(1973/2017) が「適応とは生物とその環境世界との間に存在する転移情報の増大であり，この増大は生物の内部における諸プロセスによって起こされるのであって，そのさい環境世界には目だった変化はない」(p.57)と述べたように，さまざまな体験・経験を積み重ねていく適応は環境自体を変化させるのではなく，環境にある異質性などの情報を「経験の中に持ち込む」必要があり，その経験を通して自分の中に多様性を持つことが新たな反省的思考につながる。では，学習主体 (A) が「学習環境エンジニア」として環境にある情報を経験の中に持ち込み，豊かにしていくにはどうすればよいであろうか。\n\n動物園学では環境エンリッチメント (Environmental Enrichment) を重視した取り組みが行われている。環境エンリッチメントとは「動物を取り巻く環境を変化させることで動物の行動を豊かにしていこう」（細田，2014, p.169）とするもので，「飼育下に置かれている動物の環境に対し，追加あるいは変更を加えて野生での自然な行動を引き起こし，それが動物福祉につながるという考え」（細田，2014, p.169）である。そして，伊藤ほか (2023) ではホージーほか (2009/2011) を参考に，この環境エンリッチメントの中で日本語教育分野においても応用可能性のあるものとして，以下の 4 つのエンリッチメントを挙げている。\n\na) 空間エンリッチメント:環境の構築的変化。遊具など自由に操作できるものの提供。\n\nb) 感覚エンリッチメント:視覚，聴覚など感覚を刺激するものの提供。\n\nc) 社会的エンリッチメント:他者とのかかわりのあるものの提供。\n\nd) 認知エンリッチメント:知性を刺激するもの。問題解決に複雑さが伴うものの提供。\n\n（伊藤ほか，2023, p.12）\n\nそして，伊藤ほか (2023) はこの4つの環境エンリッチメントの方向性である，自由に使えるリソース（空間的エンリッチメント），五感に訴えかけるリソース（感覚的エンリッチメント），他者との関わりを生み出せるリソース（社会的エンリッチメント），複雑さを伴う知的刺激のあるリソース（認知的エンリッチメント）は，我々が暮らす社会自体に潜在的に含まれているとも述べている。しかし，この指摘は潜在的に含まれてはいるが，それが顕在的になっていない可能性も同時に示唆されている。ここに環境エンリッチメントと「アフォーダンス」（ギブソン，1979/1985）の関連性を捉えることができる。ギブソン (1979/1985) はアフォーダンスについて「環境のアフォーダンスとは，環境が動物に提供する (offers) もの，良いものであれ悪いものであれ，用意したり供えたりする (provide or furnishe) ものである。」（p.137 下線は引用元による）と述べており，認知主体はこの環境から提供された情報を一部を知覚し，行動を選択するとされる。そのため，アフォーダンス自体は認知主体が知覚していても知覚していなくても，そこに存在するものである。さらに，ノーマン (2010/2011) はこのアフォーダンスのうち，認知主体に知覚されたアフォーダンスを「シグニファイア」と呼び，物理的，社会的世界で意味あるものとして解釈できるシグナルの重要性を述べている。つまり，環境から提供された情報（アフォーダンス）から学習主体にとって「意味のある価値づけ」（シグニファイア）を適切に環境エンリッチメントとして配置することで，学習環境エンジニアは学習主体の経験を豊かにすることができるのである。\n\n\n5. 経験・生態的学習環境における意味のある価値づけ\n\n4 節で述べてきたように，動的なシステムである経験・生態的学習環境の中で生きる学習主体に対する学習環境エンジニア（学習主体と同一人物/他者どちらも含む）の役割は，環境のアフォーダンスから学習主体にとってシグニファイアとなる「意味のある価値づけ」を適切に環境エンリッチメントとして配置することである。それにより，学びに関する状況認知に変化を起こし，学習主体および学習主体の環境に変化・再構築を促していくことである。つまり，重要な鍵となるのは学習主体が存在する環境における「意味のある価値づけ」である。この「意味」について，岡崎 (2009) が重要な定義を提示している。\n\n岡崎 (2009) は急速に変動する世界の中で自分自身が使い慣れていることばであっても，自身の生活をベースにすると，そのことばが意味することに対する想像力が及ばなくなることを「ことばの形骸化」，そして，それがより極大化した状態を「ことばの融解」と呼んでいる。そして，岡崎 (2009) はことばの形骸化が進んだ例として，文字情報（例えば「貧困」など）を読む際に文字面だけで読んでいると，想像力を働かせて読まなくなり，情報の向こうにいる人，そこで起こっているコト，そこにあるモノを再生しながら世界を組み立てて読む（空腹から明日への希望が生まれることもなく，家族や自分自身が明日死ぬかもしれない不安や恐怖に打ちひしがれている状況を感じる）ということがなくなり，自分の生活経験の範囲内だけの理解（空腹で苦しんで大変だ，など）で文字情報を処理し，同時にその狭い範囲内で自己のアイデンティティーが形作られてしまうことを挙げている。この「ことばの形骸化/融解」は，技能実習生の実態が「低賃金」「長時間労働」「暴力」「失踪」「人権侵害」などの言葉とともに伝えられていても，その改善が国際的な批判を浴びるまでなかなか進められてこなかった状況からも理解できるであろう。そして，これは「ことばの側の問題，ことばの中の何かの要因の問題ではない。私たちと世界のつながりの問題に由来する問題である。」(p.36)と岡崎 (2009) は指摘し，世界とのつながりは「自己を世界の中に位置付けて考えること」（岡崎，2009, p.78），「『自分にとって，世界はどうなっているか』という問いに応ずる形で形作られていくもの」（岡崎，2009, p.78）であるとしている。この点を広く捉えると言葉だけではなく，体験感覚が乏しく，経験への想像力が及ばない「体験の形骸化」とも言える。さらにもう一つの重要な側面は「他の人の視座も，自分の視座の中に保持して世界を見る」（岡崎，2009, p.78）という「『自分には見えていない世界』が実在していることを認識して『世界』を見る」（岡崎，2009, p.79）ことであると述べている。これは4-1節で述べた生物種が自身を取り巻く環境から主観的に意味を構築して創り出して見ている世界「環世界」への想像力である。そして，このようにして想像力を働かせて「自己の生き方（=生態）と，対象（世界，自然界のコト・モノ・人）とのつながりを，自己を起点として紡ぐとき」（岡崎，2009, p.42）に「意味」は発生するとしている。つまり，環境から提供された情報（アフォーダンス）から学習主体にとって「自分自身と現在の環境はどのようなつながりがあり，何が起こっているのか」という意味を獲得する必要があり，そのために学習環境エンジニアは環境エンリッチメントとして「自分自身と現在の環境はどのようなつながりがあり，何が起こっているのか」，そして「今，何をすべきなのか」ということを考える基盤を配置することで，学習主体の経験を豊かにし，個別の学習環境を豊かにしていくことができるのである。さらにここで，4-2 節で述べたように他者の存在を措定することでより豊かな経験・生態的学習環境の層を作り出すこともできる。その際に組み合わされる経験は単純に経験 A と経験 B の組み合わせから作られるものだけではなく，個別の経験 A や経験Bにはまったく存在しなかった段階としての異なる経験 C を得ることにつながる。つまり，経験同士が組み合わさることも一回性の出来事であり，その文脈において相互的・その場的に構成されるものであり，その経験が何層にも重なり合い，経験・生態的学習環境は持続的により大きく，より豊かなものとして創られていく（図3）。\n\n\n6. まとめと展望\n\n本稿では，先行研究の「学習環境」という用語の使用実態を調査し，従来の学習環境は研究者が静的な学習者を中心にして，その特徴を捉えた「形態特徴的学習環境」が「学習環境」とされていることを述べた。しかしながら，人間や社会は絶えず変化し，学びにおいても学習主体は環境と相互作用をしながら変化していく能動的な循環関係であることから，動的な学習者/学習環境の姿を捉えようとする「経験・生態的学習環境」へと「学習環境」の捉え直しをしていくことを主張した。\n\n第 1 節でも述べたように，従来の学習環境は日本国内/日本国外，漢字圏/非漢字圏，教室環境/自然環境，対面環境/オンライン環境のように「形態特徴的学習環境」として捉えられてきた。また，このように触れられる学習環境は一方の優位性や不十分さを述べるレトリックとして使用され，そこには発信者による暗黙の学習環境に対する上下関係が作り出されやすい。本稿では，この形態特徴的学習環境の捉えに対して，動的システムとしての「経験・生態的学習環境」を提示し，学習環境に上下関係はなく，その場でその場で学習主体と環境との調整によって作り出されるものであることを述べた。また，このような経験・生態的学習環境を構築していくためには，学習環境エンジニアが「自分自身と現在の環境はどのようなつながりがあり，何が起こっているのか」，そして「今，何をすべきなのか」という意味のある価値づけとなる環境エンリッチメントを配置していくことで学習主体の経験および学習環境を豊かにしていくことができること，さらにはそれをコミュニティとして構築していくことで持続的かつより豊かな環境となっていくことを述べた。\n\n一方で，本研究にも限界がないわけではない。特に本研究は従来の学習環境の捉えに関しては先行研究に対する調査で示せたものの，新たな捉えである経験・生態的学習環境について具体的なデータで示すことはできていない。ただしこれは，経験・生態的学習環境は個別の文脈に沿い，その場，その場の文脈で構築されるものであることから本研究が不十分であることを示すものではない。むしろ今後，本研究で示したモデルから経験・生態的学習環境の実態に関するデータを蓄積していくことで具体的かつリアルな学習者の経験・生態的学習環境が明らかになっていくものであると考える。近年，医学において従来の「How（どのような仕組みで病気になるのか）」から「Why（なぜ病気になるのか）」という根源的な問いに迫る「進化医学」が注目を集めている（長谷川，2020）。日本語教育においても「なぜ日本語を教える/学ぶのか」という「進化日本語教育学」を想定した時に，それぞれの学習主体が持つ個別学習環境に迫る研究は言語的なスキルを身につけることだけではなく，日本語を学ぶことが人生においてどのような意味を持つのか，を明らかにしていく重要な研究となる。そのような研究に対して本研究のモデルが一助となるように今後も研究を深めていきたい。", "appendix": "データ可用性\n\nDataverse: List of surveyed references on “learning environment” in Japanese language education. https://doi.org/10.7910/DVN/FENP9V (Ito, 2024).\n\n本プロジェクトは以下の基礎データを含む:\n\n• List of surveyed references on learning environment in Japanese language education.pdf\n\nデータはクリエイティブ・コモンズ・ゼロの “No rights reserved” 著作権放棄条項 (CC0 1.0 Public domain dedication) に則って入手することができます。\n\n\n参考文献\n\n秋元美晴, 浅野有里, 河住有希子, et al.:視覚に障害をもつ日本語学習者をとりまく学習環境の現状と課題:授業を担当する教師を対象とした調査より.恵泉女学園大学紀要;2016; 28. : 143–155.\n\n伊藤恵美子:中間言語語用論における研究方法論の再検証:中間言語による,動的体系としての中間言語の測定.世界の日本語教育.2005; 15: 25–39.\n\n伊藤秀明, 山田智久, 熊野七絵:テクノロジーと日本語教育の在り方に関する考察-学習者・教師・学習環境の視点から-.日本語教育支援システム研究会第10回国際研究集会(CASTEL/J 2023)予稿集.2023; 6–14.\n\n大石寧子, 上田崇仁, 福岡礼子, et al.:終日一教員担当制の引き出す学習環境の安定と言語運用能力の係わり.日本語教育方法研究会誌.2005; 12(1): 4–5.\n\n大北葉子:初級教科書の漢字学習ストラテジー使用及び漢字学習信念に与える影響.世界の日本語教育.1998; 8: 31–45.\n\n大関由貴, 遠藤郁絵:学習者から学ぶ「自律的な学び」とその支援 ―漢字の一斉授業における取り組みから―.日本語教育.2012; 152: 61–75.\n\n岡崎敏雄:言語生態学と言語教育人間の存在を支えるものとしての言語.凡人社;2009.\n\n小川多恵子, 小宮修太郎, 高橋純子, et al.:<II.教材・教授法>留学初期における学習者像把握のための調査報告 : コース開始時アンケートの結果をもとにして.筑波大学留学生センター日本語教育論集.1998; 13: 185–210.\n\n沖本与子:日本語語彙学習に適した学習者モデル : ITSの発展と活用.一橋日本語教育研究.2019; 7: 95–106.\n\n加藤浩, 有元典文:アーティファクト・コミュニティ・学習の統合理論.加藤浩, 有元典文, 編著認知的道具のデザイン.序章，金子書房;2001; 1–13.\n\n金庭久美子:リソースの活用を目指した授業　―インターネットを利用した読解授業―.日本語教育方法研究会誌.2004; 11(1): 4–5.\n\n金田克彦, 高橋弘行, 赤堀侃司:WWW上で実行可能な日本語CAIシステムの開発.日本語教育方法研究会誌.1997; 4(1): 46–47.\n\n来嶋洋美, 鈴木庸子:独習型読書支援システム『新書ライブラリー』の利用と評価.教育メディア研究.2000; 6(2): 1–12.\n\n来嶋洋美, 鈴木庸子, 駒井利江, et al.:上級日本語学習者のための読書支援プログラム : 開発と形成的評価.日本語教育方法研究会誌.1995; 2(1): 10–11.\n\n高民定, 崔英才:海外日本語学習者の言いさしと応答発話 : オンライン接触場面の会話を中心に.千葉大学国際教養学研究.2023; 7: 109–136.\n\nギブソンジェームス・ジェローム: 古崎敬, 古崎愛子, 辻敬一郎, et al., 共訳.生態学的視覚論-ヒトの知覚世界を探る-.サイエンス社;1979. (1985).\n\nショリナダリヤグル:非実用的学習環境における日本語教育の意味付け : 大学教師のライフストーリーから.国際日本研究.2019; 11: 61–72.\n\n辛昭静:言語変種に対する意識調査 : 「-レル」型可能表現を事例として.言語文化と日本語教育.2005; 30: 41–50.\n\n辛昭静:日本語学習者の言語変種の使用率に影響する言語外的要因 : 「-レル」型可能表現を事例として.言語文化と日本語教育.2006; 32: 1–9.\n\n菅陽子:日本語スピーチコンテストを通じた日本語学習支援体制構築の試み.日本語教育方法研究会誌.2017; 24(1): 36–37.\n\n鈴木庸子:日本語教育へのCAI導入に関する研究 : 初級後半から中級前半の漢字学習の場合.日本語教育方法研究会誌.1995; 2(1): 14–15.\n\n鈴木庸子:中級前期におけるコンピュータを利用した漢字教育 ―実践報告―.ICU 日本語教育研究センター紀要.1996; 5: 75–87.\n\n孫愛維:第二言語及び外国語としての日本語学習者における現場指示の習得 : 台湾人の日本語学習者を対象に.日本語教育論集.2008a; 24: 49–64.\n\n孫愛維:第二言語及び外国語としての日本語学習者における非現場指示の習得 -台湾人の日本語学習者を対象に-.世界の日本語教育.2008b; 18: 163–184.\n\n立間智子:ピア・ラーニング利用による自律学習、協働的学習を促す学習環境デザインの試み : アゼルバイジャンにおける日本語学習者と邦人との交流活動「日本語会話クラブ」の実践.国際交流基金日本語教育紀要.2010; 6: 139–155.\n\n高橋志野, 向井留実子:留学生の対人的環境、特に同国人との交流について―愛媛大学の事例から―.日本語教育方法研究会誌.2006; 13(2): 30–31.\n\n田中望, 斎藤里美:日本語教育の理論と実際-学習支援システムの開発-.大修館書店;1993.\n\n田中幸子, 常盤僚子, 茂木良治:遠隔外国語学習における学習支援者の役割 : フランス語教育の実践例より.日本語教育論集.2005; 21: 3–22.\n\n東会娟:中国人上級日本語学習者の縮約形の使用状況.日本語教育方法研究会誌.2007; 14(2): 50–51.\n\n戸田貴子:日本語教育における学習者音声の研究と音声教育実践.日本語教育.2009; 142: 47–57.\n\nトマセロマイケル: 高橋洋, 訳.行為主体性の進化生物はいかに「意思」を獲得したのか.白揚社;2022. (2023).\n\nトムソン木下千尋:学習環境をデザインする -学習者コミニュティーとしての日本語教師養成コース-.世界の日本語教育.2007; 17: 169–185.\n\n滑川恵理子:言語少数派の子どもの生活体験に裏打ちされた概念学習.日本語教育.2015; 160: 49–63.\n\nノーマンドナルド・アーサー: 伊賀聡一郎, 岡本明, 安村通晃, 訳.複雑さと共に暮らすデザインの挑戦.新曜社;2010. (2011).\n\n野原美和子:学習者の自発的発話を導く教師の学習支援的言動 : 積極的な自発的発話の場合.世界の日本語教育.1999; 9: 101–113.\n\n野元弘幸:多文化社会における教養の再構築 : 外国人住民の非識字問題を中心に.教育学研究.1999; 66(4): 436–442.\n\n長谷川眞理子:ダーウィン種の起源:未来へつづく進化論.NHK出版;2020.\n\n羽田野洋子, 田口睦子:中等教育の教科理解のための日本語教育.日本語教育方法研究会誌.1995; 2(1): 42–43.\n\nハリソンリチャード, 實平雅夫:教育理念を具体化するFlexible Classroom(I) : 日本語教育CALL環境の設計・導入.神戸大学留学生センター紀要.2005; 11: 55–73.\n\nハリソンリチャード, 實平雅夫:教育理念を具体化するFlexible Classroom(II) : 学習効果の評価に基づく日本語教育CALL環境の再設計と再評価.神戸大学留学生センター紀要.2007; 13: 21–33.\n\n広瀬和佳子:なぜ実践を共有するのか協働的学習環境をつくる教師の役割から考える.言語文化教育研究.2015; 13: 2–12.\n\nヴィゴツキーレフ・セミョーノヴィチ: 柴田義松, 監訳.文化的−歴史的精神発達の理論.学文社;1930-31. (2005).\n\n深田絵里, 高橋志野:外国人技能実習生を対象とした遠隔授業による初級日本語クラスの実践報告.日本語教育方法研究会誌.2021; 27(1): 112–113.\n\n福島青史, マリーナイヴァノヴァ:孤立環境における日本語教育の社会文脈化の試み-ウズベキタン・日本人材開発センターを例として-.国際交流基金日本語教育紀要.2006; 2: 49–64.\n\nホージージェフ, メルフィヴィッキー, パンカーストシェイラ: 村田浩一, 楠田哲士, 監訳.動物園学.文永堂出版;2009. (2011).\n\n細田孝久:環境エンリッチメント.村田浩一, 成島悦雄, 原久美子, 編.動物園学入門』9.2.2.朝倉書店;2014; 169–171.\n\n槙究:環境心理学-環境デザインへのパースペクティブ-.春風社;2004.\n\n向井留実子, 高橋志野:留学生のよりよい学習環境づくりと地域ネットワーク化に向けたホームステイの試み.日本語教育方法研究会誌.2007; 14(2): 52–53.\n\n村田裕美子:異なる環境で習得した日本語学習者の発話に関する計量的分析対話に現れる音声転訛(縮約形・拡張形)に着目して.計量国語学.2020; 32(4): 207–223.\n\nユクスキュルヤーコプ・フォン, クリサートゲオルグ: 日高敏隆, 羽田節子, 訳.生物から見た世界.岩波文庫;1970. (2005).\n\n李受香:第2言語および外国語としての日本語学習者における動機づけの比較 : 韓国人日本語学習者を対象として.世界の日本語教育.2003; 13: 75–92.\n\nローレンツコンラート: 谷口茂, 訳.鏡の背面人間的認識の自然誌的考察.ちくま学芸文庫;1973. (2017).\n\n若林秀明:オーストラリアの大学におけるニーズ分析.世界の日本語教育.1999; 9: 63–85.\n\nIto Hideaki:List of surveyed references on \"learning environment\" in Japanese language education. [dataset].Harvard Dataverse.2024; V1. Publisher Full Text\n\n\nFootnotes\n\n1 実際の抽出は 2023 年 9 月より順次，論文の閲読調査を行い，最終的に 2024 年 4 月 2 日に抽出を完了した時点で，検索条件に沿って抽出したものとそれまでに抽出した結果に相違がないことを確認した。\n\n2 ユクスキュルの提示した「Umwelt」を「環境世界」または単に「環境」と訳している文献もあるが，本文献の訳者である日高は「環世界」と訳している。これについて日高は客観的な「環境とUmweltとは対立するものとユクスキュルはとらえている」(p.165)「環境という語を含む「環境世界」はUmweltの訳語としては適切ではないと思い，「環世界」という語に変えることにした」(p.165)と述べており，本稿もこれに従う。" }	[ { "id": "330848", "date": "25 Oct 2024", "name": "Tomoko Okimoto", "expertise": [ "Reviewer Expertise 日本語教育" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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論文：学習環境を動的なシステムとして捉え直す\n【１】全体へのコメント　従来の「形態特徴的学習環境」から、学習主体と環境が相互作用することで学習環境が変化する動的な「経験・生態的学習環境」への転換を提唱している点が斬新であり、日本語教育の学習場面で学習主体の経験と環境との関係性を動的に捉え直すという試みは、学びの本質に迫っており、教育理論としても革新的です。　また、本稿における学習環境をコミュニティとして構築していく点、また図3の学習環境の解説から、学習者が学習を続ける過程で生じる時間的・空間的移動に影響されることなく、学習主体によりコミュニティが新たに構築され続け未来へと繋がるイメージが提案されていると考えられます。\n【２】加筆するとよいと考えられる点１．具体的な実践例について　本稿でも述べられているように、経験・生態的学習環境について具体的なデータがありませんが、著者も記述しているように、今後の研究調査によるデータ蓄積が待たれます。\n２．学習者の多様性への配慮　本稿では学習主体と環境の相互作用について論じていますが、学習主体の多様なニーズ・個々の認知能力・個別の背景などに関する具体的な考察がありません。具体例を１つ記述するとより本稿への理解が深まるかと考えられます。\n３．評価方法や効果測定について　経験・生態的学習環境において、学習主体の経験の豊かさ、個別の学習環境の豊かさの評価、シグニファイアの適切な配置に対する効果測定について議論し具体例を示すと、理論が実践に結び付きやすくなるかと考えられられます。\n4.他分野との統合的視点　既に生物学からの応用、医学への連携（進化医学）など、他分野との統合的視点が述べられているので、更に後述のように（【３】より詳しい説明を求める点）、学習主体の認知についての追記など、認知科学・社会学などの理論や方法論を取り入れるとより説得力のある説明となると考えられます。\n５．教育者への具体的な支援策　後述のように（【３】より詳しい説明を求める点）「学習主体」と「学習環境エンジニア」については、使用場面に応じた書き分けが必要と思われますが、「学習環境エンジニア」の中でも「日本語教師」がシグニファイアを適切に「選択し」、環境エンリッチメントとして配置する方法について必要な支援（トレーニング・リソース提供など）について明示的に提案すると、本稿による提唱理論が教育現場で実行可能かと考えられます。\n【３】より詳しい説明を求める点１．動機について　学習環境を再検討するに至った、本稿執筆の動機が加筆されるとよいかと思います。\n２．4つの観点について　「２．本研究で行った調査概要」（Page3）にある4つの観点（「学習を行う物理的な場」「学習者の周りに配置するリソース」「授業内で行う学習活動の多様性，心理的側面への配慮」「自らが作り出すもの」）は、何を基準に作成されましたか。例えば先行研究の論文を分析し、項目ごとに分類している際に、大項目として名付けた、などでしょうか。\n３．観点「自らが作り出すものとしての学習環境」について　「3-4　自らが作り出すものとしての学習環境」（page5）は、それまでの3つの観点の包括的内容であり、学習者による自主的前進と考えられますが、「動的・生態的学習環境」の１つとして捉えられるのではないでしょうか。\n４．想定場面について　「4-2　学習環境エンジニア」の節で述べられている、「自分の発展と共に周りの環境を変化させる機能」について、このような相互作用は学びの場に適用したとき、対面（学習主体と教師、学習主体同士が直に会う）場面なのか、オンライン（直接会わず、間に何らかのツールまたはリソースを介す）場面なのかは、想定されていますか。\n５．フィードバックについて　「4-3学習環境エンリッチメント」で引用されている「フィードバック制御システム」は自己認知によるフィードバックなのか、他者からの言語・反応によるフィードバックなのか、説明があった方がよいかと思います。\n６．学習主体のメタ的視点について　「4-3学習環境エンリッチメント」での主張として「学習主体がある目的のために、環境を道具的に利用して目的の達成を試みる。その際、メタ視点で得た情報をもとに学習主体が環境との調整を行っている」は大変分かりやすく俯瞰した、学習主体の行動観察と考えられます。しかしながら、この「メタ的視点で情報を得る」ことは、個々の学習主体の認知度にも関わってくるのではないでしょうか。グラデーションのある学習主体の認知度についても言及および考察があった方がよいかと思います。\n７．「生態系エンジニア」と「学習環境エンジニア」の違いについて　「4-3学習環境エンリッチメント」（page9, L13から）の「環境から提供された情報から・・・」で述べられているように、「学習環境エンジニア」がシグニファイアを適切に「選択し」、環境エンリッチメントとして配置するということは、「学習環境エンジニア」が恣意的に配置していると考えられます。「学習環境エンジニア」の原型である「生態系エンジニア」（生物）が恣意的に環境へ影響しているとは恐らく証明されていないと考えられますので、「学習環境エンジニア」と「生態系エンジニア」の違いの説明を入れるとより論文への理解が深まるかと思います。\n８．「学習主体」と「学習環境エンジニア」の書き分けについて　「５．経験・生態的学習環境における意味のある位置づけ」（page9, 下から9行目）の「環境から提供された情報から・・・」では「学習環境エンジニア」が想像力を働かせ、「意味」に気づき、適切に基盤を配置する必要性がまとめてありますが、本来同一である「学習主体」と「学習環境エンジニア」（page7）が文中に交互に役割分担して出現するため、「学習者」と「教師」の関係性として読み取れます。ここで「学習環境エンジニア」を「教師（リードする側）」として説明に使用しているのであれば、page7にあるように「日本語教師＝学習環境エンジニアとして機能する」点を、再度確認するとよいのではないでしょうか。\n９．「学習環境エンジニア」の「気づき」について　8と同様の箇所ですが、「５．経験・生態的学習環境における意味のある位置づけ」（page9, 下から9行目）の「環境から提供された情報から・・・」では「学習環境エンジニア」が想像力を働かせ、「意味」に気づき、適切に基盤を配置する必要性がまとめてありますが、「学習環境エンジニア」の気づきと配置が行われることが前提になっています。「学習環境エンジニア」の気づきのレベルまたは確実性について記述を加えるとよいのではないでしょうか。\n１０．従来の学習環境への言及について　「６．まとめと展望」の第二段落にある先行研究から分析した学習環境について「発信者による暗黙の学習環境に対する上下関係が作り出されやすい」とありますが、４つの環境（物理的・リソース・心理的・創造的環境）がそれぞれ独立しており、双方向の影響もないことから、「上下関係」ではなく「カテゴライズした学習環境の存在有無」に当たるのではないでしょうか。\n【４】些末な質問　「２．本研究で行った調査概要」内に、「（論文内で）具体的な記述があったものを中心に」（下から3行目）とありますが、具体的な記述があった論文は何本かを追記すると読みやすいかと思いました。（拝読しながら疑問に思った質問です。ご放念頂いても大丈夫です。）\n\n本研究は明確かつ正確に提示されたものであり、最新の文献を引用していますか。はい\n\n研究設計は適切で学術的価値がありますか。はい\n\n方法と分析について第三者による再現が可能となるよう十分な詳細が提示されていますか。はい\n\n（該当する場合は要回答）統計分析および解釈は適切ですか。対象外（統計を使っていない\n\n結果の基礎となるソースデータはすべて入手可能で再現性を十全に保証していますか。はい\n\n結論は結果により妥当な裏付けを得ていますか。はい", "responses": [] }, { "id": "330843", "date": "05 Nov 2024", "name": "Jihyun Yoon", "expertise": [ "Reviewer Expertise 日本語教育学・応用言語学" ], "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【評価できる点】　本稿は、日本語教育における「学習環境」の再定義を試みたものです。従来の「学習環境」の概念は静的なもので、学習者を中心とした形態的特徴であると捉える傾向がありました。しかし本稿の著者は、学習者と環境が相互作用しながら変化する「経験・生態的学習環境」への転換を提唱しています。この新たな視点では、学習環境が学習者の経験を豊かにする重要な要素として位置づけられ、学習環境をデザイン・調整する「学習環境エンジニア」の役割が不可欠です。また、このような視点を持つことによって、様々な人々の経験を融合させ、より持続可能で豊かな学習環境を構築できるとしています。\n\n本稿における研究成果の高く評価できる点として、主に以下のような特徴が挙げられます。　第一に、学習環境の再定義における先進的な視点です。本稿では、学習環境を「静的な場」から「動的なシステム」として捉え直し、学習者と環境が相互作用を通じて変化する「経験・生態的学習環境」を提唱しています。学習環境を動的なプロセスと見なし、学習者の主体的な成長を重視することで、学習環境のデザインに関する新たな枠組み、ならびに教育研究に新しい方向性を示しています。　第二に、学習環境エンジニアという新しい概念の提案です。学習環境エンジニアの役割を提案し、学習者が学びに集中できる環境を積極的に整える必要性を説いている点も独創性のある視点といえます。これにより、教育者や管理者が学習環境の面で果たすべき役割が明確化され、学習環境の改善における実践的な指針が提示されています。　第三に、エンリッチメントの多様な要素の導入です。環境エンリッチメントの要素として、感覚、空間、認知、社会的エンリッチメントを取り入れることで、学習環境を多角的に充実させる手法が提案されています。特に、動物行動学の環境エンリッチメントの概念を学習環境に応用するアイデアは斬新で、学習者の多様なニーズに対応する実用的なアプローチとして評価できます　第四に、学習環境における持続可能性と協働の重要性の強調です。学習環境を「持続的かつ豊かなもの」として構築するため、個々の学習経験を組み合わせることの重要性が強調されています。これにより、学習環境が個別の学習者を超えてコミュニティ全体の成長に寄与することが明確化され、教育現場における協働の意義を再認識させています。　以上のように、本稿で提唱されている「経験・生態的学習環境」の概念は、従来の日本語教育の枠組みに囚われず、新しい観点から学習環境を見直す試みであるため、日本語教育分野のみならず、教育理論全般にも革新的な貢献が期待されます。\n【加筆が必要な点】まず、具体的なデータの補強が求められます。「経験・生態的学習環境」モデルの提案は理論的に重要ですが、具体的な事例等の提示が十分とは言えません。　次に、「学習環境エンリッチメント」について、どのように実装するかという実践例の記述がありません。例えば、感覚エンリッチメントや社会的エンリッチメントの具体的な設計、導入プロセス、評価方法等を示すことによって、読者はその概念をより正確に理解できると思います。　最後に、「学習環境エンジニアの役割」の具体化が望まれます。その重要性は述べられていますが、具体的にどのようなスキルや知識が必要なのかが曖昧です。求められる役割やスキル等についても詳述することで、各教育現場での導入・応用の可能性が一層高まると考えられます。\n\n本研究は明確かつ正確に提示されたものであり、最新の文献を引用していますか。はい\n\n研究設計は適切で学術的価値がありますか。はい\n\n方法と分析について第三者による再現が可能となるよう十分な詳細が提示されていますか。はい\n\n（該当する場合は要回答）統計分析および解釈は適切ですか。対象外（統計を使っていない\n\n結果の基礎となるソースデータはすべて入手可能で再現性を十全に保証していますか。はい\n\n結論は結果により妥当な裏付けを得ていますか。はい", "responses": [] }, { "id": "332479", "date": "25 Nov 2024", "name": "Hideyuki Suzuki", "expertise": [ "Reviewer Expertise 教育工学，認知科学" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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＜評価できる点＞\n学習環境という定義が曖昧な概念に注目し，日本語教育研究の文脈において，この言葉がどのような意味で使われているのかを調査した結果として，従来の学習環境の捉え方が「形態特徴的学習環境」であることを指摘した点．特に，４つの形態が歴史的な段階ではなく，全時代において存在する捉え方であることを証拠をもって明らかにした点は興味深いと思います．\n上記の把握に基づいて提案される「経験・生態的学習環境」という考え方は，一見，既に存在しているヴィゴツキーの道具による媒介や活動理論の焼き直しに見えるものの，そこに環境エンリッチメントという概念を導入することで，学習の可能性を（多分，活動理論よりも積極的に）デザインする道筋を示しており，この点で教育研究に与える貢献が大きいと判断します．\n「豊かな経験」という教育（学校）言説に取り込まれがちな用語を曖昧なままに使わずに，理論的にクリアにしようと試みている点を高く評価します．\n＜加筆修正のお願い＞\n【日本語教育という研究設定は何だったのか】本論文は，日本語教育の領域で「学習環境」という言葉の使用を分析し，そこから学習環境の動的な捉え方を提示するという流れになっています．しかし，動的学習環境の提案の段階で，日本語教育との関連が弱くなるため戸惑います．学習理論一般に対して提言をするのであれば，前半のレビューを日本語教育に限定する必要性はないと思われますし，少なくとも限定する学術上の根拠を示す必要があります．もしくは，動的学習環境が日本語教育にこれまでなかったどのような発展をもたらすのか述べるべきかと考えます．\n【生態的学習環境の学術的位置づけ】本論文では，日本語教育における学習環境は形態特徴的に捉えられてきたという現状把握を前提として，経験・生態的学習環境という考え方が示されています．言語教育（日本語教育も含む）の分野では，生態学的言語論に基づく日本語教育研究があります（宇都宮2013, 岡崎2008など）．これらは，言語を創発的に捉え，それ故に言語獲得を関係性の中に捉えるというものだと理解します．本論文の経験・生態的学習環境や学習環境エンジニアといった考え方と全く同じではないものの，考え方の根幹には共有するものがあるかと思います．「日本語教育　and 学習環境」というサーチからは洩れるかもしれませんが，日本語教育の領域において，このような先行例がある以上，これらを批判的に評価した上で，それとの比較において今回の提案を示すべきではないかと考えます．\n【「自ら作り出すものとしての学習環境」に含まれる活動理論の取り扱いについて】形態特徴的学習環境の特徴として，学習者と周りの相互作用の見落とし，学習者の非アクター的捉え，を挙げていますが，「自ら作り出すものとしての学習環境」の例としてあげられている活動理論は，形態特徴的学習環境には当たらないように思われます．経験・生態的学習環境の提案の中で示される環境適応モデル（図２）は，明らかにヴィゴツキーの３角形に基づいており，そう考えれば，方向は違うかもしれませんが，ヴィゴツキーの３角形の拡張ともいえる活動理論を，形態特徴的学習環境の例にいれるのは，活動理論を過小評価するものではないでしょうか．従来の学習環境の捉え方を否定した上で，新しい捉え方である「経験・生態的学習環境」を提案するという流れの中で，活動理論が前者に入れられて処理されてしまっていることに違和感があります．経験・生態的学習環境と活動理論は全く連続性がないのか，活動理論の何らかの問題を乗り越えるものとして提案されているのか，等の説明が必要かと思います．この点についての修正，もしくは追加説明をお願いいたします．\n＜できればご検討いただきたいこと＞\n【レビューにおける学習環境の分類に関して】４つのカテゴリーに分けていますが，各カテゴリーの基準の明示が必要かと思います．例えば「学習の物理的な場」の中には，日本語との接触機会等，学習環境を「リソース配置」と捉えているような事例が含まれているように見えます．このような読者側の混乱を防ぐために，各カテゴリーに何が入って，何が入らないのかという基準を示されるとよいと思います．\n\n本研究は明確かつ正確に提示されたものであり、最新の文献を引用していますか。はい\n\n研究設計は適切で学術的価値がありますか。一部該当\n\n方法と分析について第三者による再現が可能となるよう十分な詳細が提示されていますか。はい\n\n（該当する場合は要回答）統計分析および解釈は適切ですか。対象外（統計を使っていない\n\n結果の基礎となるソースデータはすべて入手可能で再現性を十全に保証していますか。はい\n\n結論は結果により妥当な裏付けを得ていますか。はい", "responses": [] }, { "id": "330851", "date": "17 Dec 2024", "name": "Satomi Saito", "expertise": [ "Reviewer Expertise 日本語教育　外国にルーツのある高校に対する日本語教育　コーパス　語彙学習" ], "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論文：学習環境を動的なシステムとしてとらえ直す\n【１】全体へのコメント\n\nどのような学習環境が教育により良い効果をもたらすかは重要なテーマでありながら、これまで観点があいまいでした。そこに着眼し、これまでの論文から学習環境に対する認識を詳細に分析している点が大変良いと思いました。\n\n従来の静的な学習環境を「形態特徴的学習環境」と位置づけ、今後の学習環境のあり方を動的なシステムとして捉え直す必要があるとする主張は、学習者による主体的な学びを目指す現在の教育を斬新な視点から強く支持するものだと考えます。\n【２】良い点\n１．調査概要が十分に再現可能な方法であり、良いです。\n２. 「学習者の周りに配置するリソースとしての学習環境」について、このようなリソースがいくら整っていてもそれにアクセスできる空間・時間・手段・学習者の状態などが十分でなければ学習環境が整っているとは言えないと考えられます。学習環境を動的に捉え直す視点はこれらリソースと学習者を結び直すことができるのではないでしょうか。こうした視点を展示する筆者の主張に今後の日本語教育のみならず教育のあり方に対する新しい提案の可能性を感じました。\n３．「生態系エンジニア」が環境に影響を与え、周囲全体を豊かにするという例を興味深く拝読しました。「学習環境エンジニア」についてのイメージを持つことができました。\n４．環境エンリッチメントの4つの観点の提示は、学習環境を考える際の具体的な手掛かりとなるものとして興味深いです。さらにこれを、静的な学習環境を動的なものに変えるために意識的に取り入れるのがよいと明確に主張してはどうでしょうか。\n【３】説明を求めたい点\n１．筆者が「学習環境」の重要性をどのように捉え、分析にいたったのか伺いたいです。\n２．日本語教育における「学習環境」をとらえ直すための4観点が、どのようにして設定されたのか明らかにしていただきたいです。筆者のこれまでの著述を含めた先行研究からのものなのか、本論の文献調査のなかで筆者が設定したものなのか明示していただけるとよいです。\n３．「学習環境エンジニア」の記述の部分で「日本語教師も学習環境エンジニアとして機能する可能性を持っている」という部分がありますが、日本語教師は学習者にとってリソースの一つであるという考え方もあると思います。その点を整理して論じていただけると、主張に説得力が高まると考えます。\n４．まとめで筆者も述べられていることですが、「経験・生態学的学習環境」についてどのようなものか、実際の日本語教育においてどのように実践されていくものなのか具体的な説明があったらと思いました。たとえば、「環境から提供された情報から、学習主体にとって意味のある価値づけ(シグニファイア)を適切に環境エンリッチメントとして配置することで、学習環境エンジニアは学習主体としての経験を豊かにすることができる」との主張について、学習者が「実際の学習環境で」、「どのようなふるまいをして」「これらを実現する」のか、ぜひ伺いたいです。\n\n本研究は明確かつ正確に提示されたものであり、最新の文献を引用していますか。はい\n\n研究設計は適切で学術的価値がありますか。はい\n\n方法と分析について第三者による再現が可能となるよう十分な詳細が提示されていますか。はい\n\n（該当する場合は要回答）統計分析および解釈は適切ですか。対象外（統計を使っていない\n\n結果の基礎となるソースデータはすべて入手可能で再現性を十全に保証していますか。はい\n\n結論は結果により妥当な裏付けを得ていますか。はい", "responses": [] } ]	1	https://f1000research.com/articles/13-1187
https://f1000research.com/articles/12-1595/v1	14 Dec 23	{ "type": "Systematic Review", "title": "Gestational diabetes mellitus in relation to serum per- and polyfluoroalkyl substances: A scoping review to evaluate the need for a new systematic review", "authors": [ "Ghazaleh Aali", "Anna K. Porter", "Sebastian Hoffmann", "Matthew P. Longnecker", "Farhad Shokraneh", "Ghazaleh Aali", "Anna K. Porter", "Sebastian Hoffmann", "Matthew P. Longnecker" ], "abstract": "Background Per- and polyfluoroalkyl substances (PFAS) were used or are being used in the manufacturing of products, including consumer-use products. The resulting environmental contamination has led to widespread human exposure. This review aimed to scope the characteristics of evidence covered and applied methodology of evidence to understand -- regardless of any results on the association of gestational diabetes mellitus (GDM) and PFAS -- if a new systematic review would be justified.\n\nMethods We systematically identified reports investigating associations of PFAS with GDM following a pre-specified and pre-registered PECO framework and protocol.\n\nResults The previous systematic reviews included 8-11 reports and either conducted meta-analyses stratified by comparator, analyzed results based on only high and low exposure categories, or pooled results across comparators. Included 20 reports presented data on 24 PFAS with PFOA, PFOS, PFHxS, PFNA, and PFDA being examined in almost all. The comparators employed were heterogeneous across the reports.\n\nConclusions Because data from at least one new report on GDM is available since the previous systematic reviews and heterogeneous comparators, an updated systematic review using SWiM could add value to the literature.", "keywords": [ "Perfluoroalkyl", "Polyfluoroalkyl", "Gestational Diabetes Mellitus", "Glucose", "Environmental Epidemiology", "Exposure" ], "content": "Introduction\n\nPer- and polyfluoroalkyl substances (PFAS) were used or have ongoing use in the manufacturing of a variety of products, including consumer-use products.1,2 Almost everyone in developed countries has a detectable amount of PFAS in their blood serum due to exposure via contaminated food and other sources, and the unreactivity of these chemicals.3 Despite some being phased out of production,4 PFAS are widespread and have been detected in different continents irrespective of the level of industrialization, indicating long-range atmospheric transport as an important pathway of PFAS distribution.5\n\nSerum or plasma concentrations of PFAS have been associated with several health outcomes, including gestational diabetes mellitus (GDM).6–11 GDM increases risk among offspring of preterm birth and macrosomia,12 and, among mothers, of type 2 diabetes mellitus.13 In the U.S., the proportion of pregnant women who develop GDM has increased over the past ten years, possibly due to trends in risk factors such as obesity, but environmental factors could be contributing.14\n\nOur recent experience in evaluating systematic reviews of the relation of health outcomes to PFAS serum concentrations has made us aware of the variety of comparators used in original reports.15 This variety poses challenges in summarizing data that have not been adequately addressed in the GDM-PFAS systematic review literature. Thus, in addition to identifying relevant original reports in this scoping review, we addressed our special interest in the methods used in previous meta-analyses – but not in their findings.\n\nFunding for this scoping review was provided by 3M. 3M previously used perfluorooctyl and perfluorohexyl chemistries in manufacturing and has more recently used precursors of PFBS. 3M has publicly communicated that they will exit all PFAS manufacturing by the end of 2025.16 3M would like to gain insights as to the strengths and weaknesses of the collective epidemiologic research on gestational diabetes mellitus in relation to PFAS. 3M requested a highly rigorous scoping review to better understand the nature of the existing data and evaluate the need for a new systematic review. The sponsor will not be involved in the conduct of the work at any stage and will not see our work products until they are published in a peer-reviewed journal. Ramboll provides updates regarding progress toward publication and required resources.\n\nIf PFAS are a risk factor for GDM, this might affect regulations on allowable amounts of PFAS in water or food. GDM was not considered a critical endpoint in a recent U.S. government evaluation, but a more recent European government evaluation indicated that it could be.4,17 Our objective was to collect and summarize the research on the relationship between serum per- and polyfluoroalkyl substances and gestational diabetes mellitus with the aim to inform the necessity of systematically reviewing the topic, potentially including a meta-analysis, and to estimate the required investment of resources needed for such a review.\n\n\nMethods\n\nWe followed Joanna Briggs Institute’s guidance for designing and conducting this scoping review18 and followed PRISMA-P,19 PRISMA-ScR,20 PRISMA-Abstract,21 and PRISMA-Search22 in reporting the protocol and the final report of this review. The indications for a scoping review were: a) to examine how research is conducted on a certain topic or field, and b) as a precursor to a systematic review.23\n\nWe used the PECO framework (Population, Exposure, Comparator, and Outcomes)24 for formulating the problem to be addressed. The PECO also guided setting the eligibility criteria (Table 1). The population used was pregnant women. The exposure was concentration of any specific PFAS in serum or plasma during pregnancy. The measure of exposure was obtained from a blood specimen or, for populations in which a validated pharmacokinetic model of serum concentration was available, estimated on an individual basis. Estimated serum or plasma PFAS for an individual from a population for which a validated pharmacokinetic model of serum concentration was available are acceptable because in the absence of a serum or plasma measurement, pharmacokinetic models can be useful for imputation when a population water supply had unusually high PFAS concentrations.25 The comparator was a contrast in serum PFAS concentration that was either per arithmetic unit of PFAS (e.g., ng/ml), per log unit increase, or categorical. The primary outcome was GDM and the secondary outcome was serum glucose.\n\na See Methods for an elaboration on the exclusion criteria.\n\nb Other than those implied by the eligibility criteria.\n\nObservational studies such as case-control, longitudinal (cohort, prospective, retrospective), or cross-sectional studies were included in this review. Full reports about original epidemiologic research or meta-analysis had to be published online or in print. Pre-clinical studies (cells or genetic material) and studies with non-human subjects were excluded. If the data were for a non-pregnant population only or mixed population where separate data on pregnant population was unavailable, we excluded the report. If a measured or estimated serum or plasma concentration of PFAS in the person was not examined in relation to the occurrence of GDM or blood glucose in the person the report was excluded. Mixtures analyses where there were no single exposure analyses for PFAS reported in that paper were excluded.26 We excluded narrative and systematic narrative reviews; however, before exclusion we checked for any relevant unique included reports in the systematic narrative reviews. To identify relevant ongoing or published systematic reviews to examine their methods, we conducted a rapid search in PROSPERO and PubMed.\n\nOn 11th December 2022, we systematically searched the latest available version of the following sources to identify original reports without date, time, document type, or language limitations27: CINAHL via EBSCOhost (1937 – search date); Embase via Ovid SP (1974 – 9th December 2022); Emerging Sources Citation Index via Web of Science (2015 – search date); MEDLINE via Ovid SP (1946 – 9th December 2022); PubMed (excluding MEDLINE; 1946 – search date); and Science Citation Index Expanded via Web of Science (1900 – search date).\n\nAn information scientist designed the search strategies using the collected terms from the experts, literature, and controlled vocabularies (CINAHL Headings, Medical Subject Headings=MeSH and Emtree). The search strategy for MEDLINE was shared with two experts on the topic for commenting and revisions and peer-reviewed by another information specialist based on PRESS guidance28 before the translation into the syntax of other databases.\n\nThe search strategies (Box 1) were tested and tuned based on a randomly selected half of the included studies in the previous systematic reviews. The final search was tested against the remaining half of the included studies from previous reviews to ensure the comprehensiveness of the retrieval.\n\nSection I – Search strategy for original reports\n\n\n\nA. CINAHL Plus via EBSCOhost (Excluding MEDLINE Records)\n\nSunday, December 11, 2022 1:29:53 PM\n\nS5 S1 AND S2 AND S3 AND S4 Limiters - Exclude MEDLINE records (140)\n\nS4 ((MH “Prospective Studies”) OR (MH “Case Control Studies”) OR (MH “Odds Ratio”) OR (MH “Environmental Exposure”) OR (MH “Maternal Exposure”) OR (MH “Prenatal Exposure Delayed Effects”) OR (MH “Maternal-Fetal Exchange”)) OR TI ( Exposure* OR Association* OR Relationship* OR Cohort* OR Case-Control* OR Regression* OR Odds Ratio* OR Risk Ratio* OR Linear OR Nonlinear OR Confounding OR Correlat) OR AB (Exposure OR Association* OR Relationship* OR Cohort* OR Case-Control* OR Regression* OR Odds Ratio* OR Risk Ratio* OR Linear OR Nonlinear OR Confounding OR Correlat) (1,839,797)\n\nS3 ((MH “Diabetes Mellitus, Gestational”) OR (MH “Abortion, Spontaneous”) OR (MH “Birth Weight”) OR (MH “Fetal Development”) OR (MH “Fetal Growth Retardation”) OR (MH “Fetal Macrosomia”) OR (MH “Gestational Weight Gain”) OR (MH “Pregnancy-Induced Hypertension”) OR (MH “Infant, Low Birth Weight”) OR (MH “Infant, Small for Gestational Age”) OR (MH “Infertility”) OR (MH “Pre-Eclampsia”) OR (MH “Pregnancy Complications”) OR (MH “Pregnancy Outcomes”) OR (MH “Childbirth, Premature”) OR (MH “Prenatal Diagnosis”) OR (MH “Reproductive Health”)) OR TI ( Abortion OR Miscarriage* OR Birth Weight OR Fetal Development OR Fetal Growth OR Fetal Macrosomia OR Infertil* OR Pre-Eclampsia OR Preeclampsia OR Premature Birth* OR Birth Outcome* OR Preterm Birth* OR Glucose* OR Diabet) OR AB (Abortion OR Miscarriage* OR Birth Weight OR Fetal Development OR Fetal Growth OR Fetal Macrosomia OR Infertil* OR Pre-Eclampsia OR Preeclampsia OR Premature Birth* OR Birth Outcome* OR Preterm Birth* OR Glucose* OR Diabet) (424,471)\n\nS2 ((MH “Gestational Age”) OR (MH “Infant, Newborn”) OR (MH “Parity”) OR (MH “Postnatal Period”) OR (MH “Pregnancy”) OR (MH “Pregnancy Trimester, First”) OR (MH “Pregnancy Trimester, Second”) OR (MH “Pregnancy Trimester, Third”)) OR TI ( Gestation OR Pregnan* OR Prepregnan* OR Prenat* OR Matern* OR Infant* OR Newborn* OR Postpartum OR Puerperium OR Reproductive) OR AB (Gestation* OR Pregnan* OR Prepregnan* OR Prenat* OR Matern* OR Infant* OR Newborn* OR Postpartum OR Puerperium OR Reproductive) (523,476)\n\nS1 ((MH “Carboxylic Acids”) OR (MH “Environmental Pollutants”) OR (MH “Fluorocarbons”) OR (MH “Polychlorinated Biphenyls”)) OR TI ( Polyfluoroalkyl OR Perfluoroalkyl OR Phthalate* OR Alkanesulfonic Acid* OR Caprylate* OR Carboxylic Acid* OR Decanoic Acid* OR Environmental Pollut* OR Fluorocarbon* OR Heptanoic Acid* OR Hexadecafluoro-Nonanoic Acid OR Perfluorodecanoic Acid OR Perfluorohexanesulfonic Acid OR Perfluoro-N-Heptanoic Acid OR Perfluoro-N-Nonanoic Acid OR Perfluorooctane Sulfonic Acid OR Perfluorooctanoic Acid OR Perfluoroundecanoic Acid OR Sulfonic Acid* OR Polychlorinated Biphenyl* OR Octanoic Acid* OR Perfluorononanoic Acid) OR AB (Polyfluoroalkyl OR Perfluoroalkyl OR Phthalate OR Alkanesulfonic Acid* OR Caprylate* OR Carboxylic Acid* OR Decanoic Acid* OR Environmental Pollut* OR Fluorocarbon* OR Heptanoic Acid* OR Hexadecafluoro-Nonanoic Acid OR Perfluorodecanoic Acid OR Perfluorohexanesulfonic Acid OR Perfluoro-N-Heptanoic Acid OR Perfluoro-N-Nonanoic Acid OR Perfluorooctane Sulfonic Acid OR Perfluorooctanoic Acid OR Perfluoroundecanoic Acid OR Sulfonic Acid* OR Polychlorinated Biphenyl* OR Octanoic Acid* OR Perfluorononanoic Acid) (9,896)\n\n\n\nB. Embase via Ovid SP (Excluding MEDLINE Records)\n\nDatabase: Embase <1974 to 2022 December 09>\n\n1 Alkanesulfonic Acid/ or Octanoic Acid Derivative/ or Carboxylic Acid/ or Decanoic Acid Derivative/ or Pollutant/ or Fluorocarbon/ or Heptanoic Acid Derivative/ or Perfluorodecanoic Acid/ or Perfluorohexanesulfonic Acid/ or Perfluorononanoic Acid/ or Perfluorooctanesulfonic Acid/ or Perfluorooctanoic Acid/ or Perfluoroundecanoic Acid/ or Sulfonic Acid Derivative/ or Polychlorinated Biphenyl/or (Polyfluoroalkyl or Perfluoroalkyl or Phthalate* or Alkanesulfonic Acid* or Caprylate* or Carboxylic Acid* or Decanoic Acid* or Environmental Pollut* or Fluorocarbon* or Heptanoic Acid* or Hexadecafluoro-Nonanoic Acid or Perfluorodecanoic Acid or Perfluorohexanesulfonic Acid or Perfluoro-N-Heptanoic Acid or Perfluoro-N-Nonanoic Acid or Perfluorooctane Sulfonic Acid or Perfluorooctanoic Acid or Perfluoroundecanoic Acid or Sulfonic Acid* or Polychlorinated Biphenyl* or Octanoic Acid* or Perfluorononanoic Acid).ti,ab. (143644)\n\n2 Gestational Age/ or Newborn/ or Parity/ or Puerperium/ or Pregnancy/ or First Trimester Pregnancy/ or Second Trimester Pregnancy/ or Third Trimester Pregnancy/or (Gestation or Pregnan* or Prepregnan* or Prenat* or Matern* or Infant* or Newborn* or Postpartum or Puerperium or Reproductive).ti,ab. (1802653)\n\n3 Pregnancy Diabetes Mellitus/ or Spontaneous Abortion/ or Birth Weight/ or Fetus Development/ or Intrauterine Growth Retardation/ or Macrosomia/ or Gestational Weight Gain/ or Maternal Hypertension/ or Low Birth Weight/ or “Small For Date Infant”/ or Female Infertility/ or Preeclampsia/ or Pregnancy Complication/ or Pregnancy Outcome/ or Prematurity/ or Prenatal Diagnosis/ or Reproductive Health/or (Abortion or Miscarriage* or Birth Weight or Fetal Development or Fetal Growth or Fetal Macrosomia or Infertil* or Pre-Eclampsia or Preeclampsia or Premature Birth* or Birth Outcome* or Preterm Birth* or Glucose* or Diabet).ti,ab. (2026454)\n\n4 Cohort Analysis/ or Case Control Study/ or Odds Ratio/ or Environmental Exposure/ or Maternal Exposure/ or Prenatal Exposure/ or Fetomaternal transfusion/or (Exposure* or Association* or Relationship* or Cohort* or Case-Control* or Regression* or Odds Ratio* or Risk Ratio* or Linear or Nonlinear or Confounding or Correlat).ti,ab. (8964603)\n\n5 and/1-4 (1617)\n\n6 (exp animals/ or exp invertebrate/ or animal experiment/ or animal model/ or animal tissue/ or animal cell/ or nonhuman/) and (human/ or normal human/or human cell/) (24435743)\n\n7 (exp animals/ or exp invertebrate/ or animal experiment/ or animal model/ or anim animal cell/or nonhuman/) not 6 (7039358)\n\n8 5 not 7 (1342)\n\n9 limit 8 to medline (165)\n\n10 8 not 9 (1177)\n\n11 limit 10 to embase (948)\n\n\n\nC. MEDLINE via Ovid SP\n\nDatabase: Ovid MEDLINE(R) ALL <1946 to December 09, 2022>\n\n1 Alkanesulfonic Acids/ or Caprylates/ or Carboxylic Acids/ or Decanoic Acids/ or Environmental Pollutants/ or Fluorocarbons/ or Heptanoic Acids/ or Hexadecafluoro-Nonanoic Acid/ or Perfluorodecanoic Acid/ or Perfluorohexanesulfonic Acid/ or Perfluoro-N-Heptanoic Acid/ or Perfluoro-N-Nonanoic Acid/ or Perfluorooctane Sulfonic Acid/ or Perfluorooctanoic Acid/ or Perfluoroundecanoic Acid/ or Sulfonic Acids/ or Polychlorinated Biphenyls/or (Polyfluoroalkyl or Perfluoroalkyl or Phthalate or Alkanesulfonic Acid* or Caprylate* or Carboxylic Acid* or Decanoic Acid* or Environmental Pollut* or Fluorocarbon* or Heptanoic Acid* or Hexadecafluoro-Nonanoic Acid or Perfluorodecanoic Acid or Perfluorohexanesulfonic Acid or Perfluoro-N-Heptanoic Acid or Perfluoro-N-Nonanoic Acid or Perfluorooctane Sulfonic Acid or Perfluorooctanoic Acid or Perfluoroundecanoic Acid or Sulfonic Acid* or Polychlorinated Biphenyl* or Octanoic Acid* or Perfluorononanoic Acid).ti,ab. (171796)\n\n2 Gestational Age/ or Infant, Newborn/ or Parity/ or Postpartum Period/ or Pregnancy/ or Pregnancy Trimester, First/ or Pregnancy Trimester, Second/ or Pregnancy Trimester, Third/or (Gestation or Pregnan* or Prepregnan* or Prenat* or Matern* or Infant* or Newborn* or Postpartum or Puerperium or Reproductive).ti,ab. (2098039)\n\n3 Diabetes, Gestational/ or Abortion, Spontaneous/ or Birth Weight/ or Fetal Development/ or Fetal Growth Retardation/ or Fetal Macrosomia/ or Gestational Weight Gain/ or Hypertension, Pregnancy-Induced/ or Infant, Low Birth Weight/ or Infant, Small for Gestational Age/ or Infertility, Female/ or Pre-Eclampsia/ or Pregnancy Complications/ or Pregnancy Outcome/ or Premature Birth/ or Prenatal Diagnosis/ or Reproductive Health/or (Abortion* or Miscarriage* or Birth Weight or Fetal Development or Fetal Growth or Fetal Macrosomia or Infertil* or Pre-Eclampsia or Preeclampsia or Premature Birth* or Birth Outcome* or Preterm Birth* or Glucose* or Diabet).ti,ab. (1567915)\n\n4 Cohort Studies/ or Case-Control Studies/ or Odds Ratio/ or Environmental Exposure/ or Maternal Exposure/ or Prenatal Exposure Delayed Effects/ or Maternal-Fetal Exchange/or Toxicity.fs. or (Exposure or Association* or Relationship* or Cohort* or Case-Control* or Regression* or Odds Ratio* or Risk Ratio* or Linear or Nonlinear or Confounding or Correlat).ti,ab. (7257961)\n\n5 and/1-4 (2234)\n\n6 exp Animals/not Humans.sh. (5071725)\n\n7 5 not 6 (1849)\n\n\n\nD. PubMed (Excluding MEDLINE)\n\n(Alkanesulfonic Acids [MH:NoExp] OR Caprylates [MH:NoExp] OR Carboxylic Acids [MH:NoExp] OR Decanoic Acids [MH:NoExp] OR Environmental Pollutants [MH:NoExp] OR Fluorocarbons [MH:NoExp] OR Heptanoic Acids [MH:NoExp] OR Hexadecafluoro-Nonanoic Acid [MH:NoExp] OR Perfluorodecanoic Acid [MH:NoExp] OR Perfluorohexanesulfonic Acid [MH:NoExp] OR Perfluoro-N-Heptanoic Acid [MH:NoExp] OR Perfluoro-N-Nonanoic Acid [MH:NoExp] OR Perfluorooctane Sulfonic Acid [MH:NoExp] OR Perfluorooctanoic Acid [MH:NoExp] OR Perfluoroundecanoic Acid [MH:NoExp] OR Sulfonic Acids [MH:NoExp] OR Polychlorinated Biphenyls [MH:NoExp] OR Polyfluoroalkyl [TIAB] OR Perfluoroalkyl [TIAB] OR Phthalate[TIAB] OR Alkanesulfonic Acid[TIAB] OR Caprylate[TIAB] OR Carboxylic Acid[TIAB] OR Decanoic Acid[TIAB] OR Environmental Pollut[TIAB] OR Fluorocarbon[TIAB] OR Heptanoic Acid[TIAB] OR Hexadecafluoro-Nonanoic Acid [TIAB] OR Perfluorodecanoic Acid [TIAB] OR Perfluorohexanesulfonic Acid [TIAB] OR Perfluoro-N-Heptanoic Acid [TIAB] OR Perfluoro-N-Nonanoic Acid [TIAB] OR Perfluorooctane Sulfonic Acid [TIAB] OR Perfluorooctanoic Acid [TIAB] OR Perfluoroundecanoic Acid [TIAB] OR Sulfonic Acid[TIAB] OR Polychlorinated Biphenyl[TIAB] OR Octanoic Acid[TIAB] OR Perfluorononanoic Acid[TIAB]) AND (Gestational Age [MH:NoExp] OR Infant, Newborn [MH:NoExp] OR Parity [MH:NoExp] OR Postpartum Period [MH:NoExp] OR Pregnancy [MH:NoExp] OR Pregnancy Trimester, First [MH:NoExp] OR Pregnancy Trimester, Second [MH:NoExp] OR Pregnancy Trimester, Third [MH:NoExp] OR Gestation[TIAB] OR Pregnan[TIAB] OR Prepregnan[TIAB] OR Prenat[TIAB] OR Matern[TIAB] OR Infant[TIAB] OR Newborn[TIAB] OR Postpartum [TIAB] OR Reproductive [TIAB]) AND (Diabetes, Gestational [MH:NoExp] OR Abortion, Spontaneous [MH:NoExp] OR Birth Weight [MH:NoExp] OR Fetal Development [MH:NoExp] OR Fetal Growth Retardation [MH:NoExp] OR Fetal Macrosomia [MH:NoExp] OR Gestational Weight Gain [MH:NoExp] OR Hypertension, Pregnancy-Induced [MH:NoExp] OR Infant, Low Birth Weight [MH:NoExp] OR Infant, Small for Gestational Age [MH:NoExp] OR Infertility, Female [MH:NoExp] OR Pre-Eclampsia [MH:NoExp] OR Pregnancy Complications [MH:NoExp] OR Pregnancy Outcome [MH:NoExp] OR Premature Birth [MH:NoExp] OR Prenatal Diagnosis [MH:NoExp] OR Reproductive Health [MH:NoExp] OR Abortion[TIAB] OR Miscarriage[TIAB] OR Birth Weight [TIAB] OR Fetal Development [TIAB] OR Fetal Growth [TIAB] OR Fetal Macrosomia [TIAB] OR Infertil[TIAB] OR Pre-Eclampsia [TIAB] OR Preeclampsia [TIAB] OR Premature Birth[TIAB] OR Birth Outcome[TIAB] OR Preterm Birth[TIAB] OR Glucose[TIAB] OR Diabet[TIAB]) AND (Toxicity [Subheading] OR Cohort Studies [MH:NoExp] OR Case-Control Studies [MH:NoExp] OR Odds Ratio [MH:NoExp] OR Environmental Exposure [MH:NoExp] OR Maternal Exposure [MH:NoExp] OR Prenatal Exposure Delayed Effects [MH:NoExp] OR Maternal-Fetal Exchange [MH:NoExp] OR Exposure[TIAB] OR Association[TIAB] OR Relationship[TIAB] OR Cohort[TIAB] OR Case-Control[TIAB] OR Regression[TIAB] OR Odds Ratio[TIAB] OR Risk Ratio[TIAB] OR Linear [TIAB] OR Nonlinear [TIAB] OR Confounding [TIAB] OR Correlat[TIAB]) NOT (Animals [MH] NOT Humans [MH]) NOT MEDLINE [SB] 123\n\n\n\nE. Science Citation Index Expanded (SCI-EXPANDED; 1900 – search date) and Emerging Sources Citation Index via Web of Science (ESCI; 2015 – search date) via Web of Science Core Collection\n\n- WOS.SCI: 1900 to 2022\n\n- WOS.ESCI: 2015 to 2022\n\n(Polyfluoroalkyl OR Perfluoroalkyl OR Phthalate OR Alkanesulfonic Acid* OR Caprylate* OR Carboxylic Acid* OR Decanoic Acid* OR Environmental Pollut* OR Fluorocarbon* OR Heptanoic Acid* OR Hexadecafluoro-Nonanoic Acid OR Perfluorodecanoic Acid OR Perfluorohexanesulfonic Acid OR Perfluoro-N-Heptanoic Acid OR Perfluoro-N-Nonanoic Acid OR Perfluorooctane Sulfonic Acid OR Perfluorooctanoic Acid OR Perfluoroundecanoic Acid OR Sulfonic Acid* OR Polychlorinated Biphenyl* OR Octanoic Acid* OR Perfluorononanoic Acid) AND (Gestation OR Pregnan* OR Prepregnan* OR Prenat* OR Matern* OR Infant* OR Newborn* OR Postpartum OR Reproductive) AND (Abortion* OR Miscarriage* OR Birth Weight OR Fetal Development OR Fetal Growth OR Fetal Macrosomia OR Infertil* OR Pre-Eclampsia OR Preeclampsia OR Premature Birth* OR Birth Outcome* OR Preterm Birth* OR Glucose* OR Diabet) AND (Exposure OR Association* OR Relationship* OR Cohort* OR Case-Control* OR Regression* OR Odds Ratio* OR Risk Ratio* OR Linear OR Nonlinear OR Confounding OR Correlat) (Title) OR (Polyfluoroalkyl OR Perfluoroalkyl OR Phthalate OR Alkanesulfonic Acid* OR Caprylate* OR Carboxylic Acid* OR Decanoic Acid* OR Environmental Pollut* OR Fluorocarbon* OR Heptanoic Acid* OR Hexadecafluoro-Nonanoic Acid OR Perfluorodecanoic Acid OR Perfluorohexanesulfonic Acid OR Perfluoro-N-Heptanoic Acid OR Perfluoro-N-Nonanoic Acid OR Perfluorooctane Sulfonic Acid OR Perfluorooctanoic Acid OR Perfluoroundecanoic Acid OR Sulfonic Acid* OR Polychlorinated Biphenyl* OR Octanoic Acid* OR Perfluorononanoic Acid) AND (Gestation OR Pregnan* OR Prepregnan* OR Prenat* OR Matern* OR Infant* OR Newborn* OR Postpartum OR Reproductive) AND (Abortion* OR Miscarriage* OR Birth Weight OR Fetal Development OR Fetal Growth OR Fetal Macrosomia OR Infertil* OR Pre-Eclampsia OR Preeclampsia OR Premature Birth* OR Birth Outcome* OR Preterm Birth* OR Glucose* OR Diabet) AND (Exposure OR Association* OR Relationship* OR Cohort* OR Case-Control* OR Regression* OR Odds Ratio* OR Risk Ratio* OR Linear OR Nonlinear OR Confounding OR Correlat) (Abstract) Editions: WOS.SCI,WOS.ESCI\n\nDate Run: Sun Dec 11 2022 13:53:20 GMT+0000 (Greenwich Mean Time) Results: 1878\n\nSection II – Search strategy for relevant systematic reviews (14th June 2023)\n\n\n\nA. PROSPERO\n\nSince a complex search is not possible in PROSPERO, we only searched the chemicals one by one and only reported those searches that retrieved at least one unique relevant result:\n\nFluorocarbons 2\n\nPolychlorinated Biphenyls 2\n\nPolychlorinated Biphenyl 1\n\nPolyfluoroalkyl 3\n\nDecanoic 1\n\nPFAS 1\n\n\n\nB. PubMed\n\n(Perfluoroalkyl[TI] OR PFAS[TI] OR Polyfluoroalkyl[TI] OR Endocrine Disrupting Chemical[TI] OR Persistent Organic Pollutant[TI]) AND (Diabet[TI] OR Glucose [TI] OR Hyperglyc[TI] OR Mataboli[TI] OR Insulin[TI] OR Pregnan[TI] OR Matern[TI]) AND (Systematic Review[TI] OR Meta-Analy[TI] OR Metaanaly[TI] OR Scoping Review [TI] OR PubMed [TIAB] OR MEDLINE [TIAB] OR Scopus [TIAB] OR “Web of Science”[TIAB] OR “Google Scholar”[TIAB])\n\n21 Results\n\nResults were imported to the reference management software, EndNote X9, for de-duplication. The de-duplicated search results were imported into Rayyan29 and two reviewers screened the search results independently after turning the blinding mode on. Any disagreement between the two reviewers was resolved in a meeting. We followed the same procedure for screening the full reports of the studies. For any disagreement, the two reviewers discussed and agreed on a final decision to include or exclude the report.\n\nData extraction was designed, piloted, and revised to include the following data points: study name (first author’s last name and publication year), study design, study period, country of origin, participants’ age, number of participants per group, duration of the pregnancy at the baseline of the study, time of glucose measure, name of the glucose test, diagnostic criteria for GDM, sample type for exposure measurement, time of measuring PFAS, ethnicity, setting (rural, urban), source of exposure, length of exposure, name of substances, summary statistic for PFAS and glucose concentrations per group, exposure data type, chemical analysis methods, measures of association, exposure metric (comparator), potentially relevant references for identifying more relevant studies, the lead author’s name and email address, and any relevant notes.\n\nWhen we could not find the required data in the report, we contacted the authors to request it.\n\nWe summarized the findings narratively or in tables. Because this was a scoping review, we did not run any data analysis or risk of bias appraisal for the included studies.\n\n\nResults\n\nWe identified three previously published systematic reviews that explored the GDM-PFAS association (Table 2).30–32 In the earliest systematic review on the topic, by Gao et al. (2021), data from nine studies were included, and meta-analyses of results were done separately by type of comparator and PFAS.30 Wang et al. (2022) conducted a meta-analysis of eight studies, based on the contrast of OR for the highest to lowest categories of exposure. Most recently, Yan et al. (2022) conducted a meta-analysis with data from 11 studies.32 In their meta-analysis, the original authors used a variety of comparators (e.g., odds ratio [OR] for high to low tertiles of PFAS, OR per loge increase in PFAS), and the results were combined regardless of the specific comparators used, making the meaning of the summary OR obscure. The most recent of the systematic reviews had a literature search end date of November 2021. None of the previous systematic reviews employed SWiM.33 Although our focus was not on the results of the previous systematic reviews, a summary of their results was as follows: a) no significant association was found between PFAS and GDM30; b) PFOA was significantly associated with higher risk of GDM31; and c) PFOA and PFBS increase risk of GDM.32\n\na All eight studies included in Wang et al. (2022) are in Gao et al. (2021), and all nine studies included in Gao et al. (2021) are included in Yan et al. (2022).\n\nb Meta-analysis done across results based on different types of comparators.\n\nc Wang et al. (2022) conducted a meta-analysis based on a high:low exposure category comparator.\n\nFour protocols registered in PROSPERO either explicitly addressed GDM and PFAS or might have included it in a broader definition of outcome or exposure (Table 3). Two of the protocols were old enough that it was likely the effort had been abandoned; of the more recent protocols, one did not specifically mention inclusion of pregnanct women or gestational diabetes. The remaining study described use of a high:low exposure category comparator, which is statistically inefficient because it does not include all available results from a report and has other limitations (see Discussion). None of the studies mentioned use of synthesis without meta-analysis (SWiM).33\n\n Per PubMed search 6-16-23.\n\nThe search for original data reports found 4938 records. After removing the duplicates, we screened the unique records and identified 82 possibly relevant records based on their titles and abstracts. When the full-text reports were obtained for these 82 records, we excluded 62 after documenting the reason for exclusion and included 20 reports in this review.6–11,34–47 The process of selection of reports is shown in Figure 1.\n\nTwo reports used the data from the Shanghai Birth Cohort11,45 with the possibility of duplicate and overlapping data. The source and length of exposure were not reported in any of the reports, presumably indicating that all were of populations with background exposure.\n\nCharacteristics of the reports are presented in Table 4. Based on these data, the prospective cohort (12 reports) was the most used study design followed by case-control (5). The studies were conducted between 1997 and 2021 in China (10 reports), North America (US (6) & Canada (1)), Denmark (2), and Spain (1). The 10 studies from China all had Chinese participants, the ethnicity of participants from all seven North American studies was diverse, one of the studies from Denmark included only participants of Danish ethnicity, while the other did not report participant ethnicity, and the one study from Spain had participants of primarily Spanish origin.\n\na At study baseline.\n\nb NA: Not available.\n\nc OGTT: Oral Glucose Tolerance Test.\n\nThe 20 reports included a total of 18,805 participants. Among the 15 reports that presented the number of participants with GDM, the proportion with GDM was 10% (1,655/16,513); the other five reports presented results on serum glucose only and not GDM. The number of participants across the reports ranged between 95 and 2747. The participants’ age was between 20 and 40 with the most frequent mean age reported being between 28 and 32.\n\nParticipants’ duration of pregnancy at study baseline varied between 5 and 38 weeks making it one of the most heterogenous items of data extracted.\n\nTable 5 summarizes the list of 24 PFAS (not counting isomers) for which a measure of association was reported in the included studies with results for PFOA, PFOS, PFHxS, PFNA, and PFDA being reported in almost all the studies.\n\na Frequently used alternative acronyms are in parentheses.\n\nb For PFOA and PFOS, isomer-specific CAS#s were not available at this time this manuscript was prepared (except for 6m-PFOS); we followed CDC’s example of using the same CAS# for the isomers of PFOA (sum) and PFOS (sum) (https://www.cdc.gov/nceh/dls/oatb_capacity_14.html).\n\nc Number of carbons not given for isomers.\n\nd PFBA (PFBA (C4)): Perfluorobutanoic Acid.\n\ne PFPeA (PFPeA (C5)): Perfluoropentanoic Acid.\n\nf PFHxA (PFHxA (C6)): Perfluorohexanoic Acid.\n\ng PFHpA (PFHpA (C7)): Perfluoroheptanoic Acid.\n\nh ADONA: 4,8-Dioxa-3H-Perfluorononanoic Acid.\n\ni PFOA (PFOA (C8)): Perfluorooctanoic Acid.\n\nj n-PFOA: N-Perfluorooctanoic Acid.\n\nk 6m-PFOA: Perfluoro-6-Methylpheptanoic Acid.\n\nl PFNA (PFNA (C9)): Perfluorononanoic Acid.\n\nm PFDA (PFDeA or PFDA (C10)): Perfluorodecanoic Acid.\n\nn PFUnDA (PFUnDA (C11)): Perfluoroundecanoate.\n\no PFDoA (PFDoDA or PFDoDA (C12)): Perfluorododecanoic Acid.\n\np PFTrDA (PFTriDA (C13) or PFTrDA (C13)): Perfluorotridecanoate.\n\nq PFTeDA (C14): Perflurotetradecanoate.\n\nr PFBS (PFBS (C4)): Perfluorobutanesulfonic Acid.\n\ns PFHxS (PFHxS (C6)): Perfluorohexanesulfonic Acid.\n\nt 4:2FTS: 4:2 Fluorotelomer Sulfonic Acid.\n\nu PFHpS: Perfluoroheptane Sulfonic Acid.\n\nv PFOS (PFOS (C8)): Perfluorooctanesulfonic Acid.\n\nw n-PFOS: N-Perfluorooctane Sulfonate.\n\nx 1m-PFOS: Perfluoro-1-Methylheptanesulfonate.\n\ny 3m-PFOS: Perfluoro-3-Methylheptanesulfonate.\n\nz 4m-PFOS: Perfluoro-4-Methylheptanesulfonate.\n\naa 3m+4m-PFOSc: Perfluoro-3-Methylheptanesulfonate + Perfluoro-4-Methylheptanesulfonate.\n\nbb 5m-PFOS: Perfluoro-5-Methylheptanesulfonate.\n\ncc 6m-PFOS: Perfluoro-6-Methylheptanesulfonate.\n\ndd 6:2 Cl-PFESA: 6:2 Chlorinated Polyfluorinated Ether Sulfonate.\n\nee 6:2FTS: 6:2 Fluorotelomer Sulfonic Acid.\n\nff 8:2 Cl-PFESA: 8:2 Chlorinated Polyfluorinated Ether Sulfonic Acid.\n\ngg PFDS: Perfluorodecane Sulfonate.\n\nhh PFOSA: Perfluorooctanesulfonamide.\n\nii MeFOSAA (Me-PFOSA-AcOH): Methylperfluorooctanesulfonamidoacetic Acid.\n\njj EtFOSAA (Et-PFOSA-AcOH): Ethylperfluorooctane Sulfonamidoacetic Acid.\n\nTable 6 presents the data regarding the measurement and reporting of PFAS concentration, glucose, and GDM. An oral glucose tolerance test (OGTT) was used in 16 reports as the glucose test and seven reports followed the International Association of Diabetes and Pregnancy Study Groups (IADPSG) criteria for diagnosing GDM. Among 12 reports that reported type of glucose measure, 10 reported fasting glucose (FG), six reported one hour glucose (1hG), and five reported two hour glucose (2hG), most of which reported mean ± standard deviation (nine reports). While the time for measuring glucose levels varied between 14 weeks of gestation and 1-2 days pre-delivery, measurement of PFAS was in a wider time range from 8 weeks of gestation to delivery. HPLC LC-MS/MS was the most-used chemical analysis method for PFAS. A summary statistic for PFAS concentrations was presented for 19 reports with the geometric mean being the most frequently reported (10) followed by the median (seven reports). Standard deviation was presented in only four reports with geometric means and interquartile range (IQR) for six reports with median.\n\na Adjusted for subcohort only.\n\nb Conditioned on matching factor, maternal age.\n\nTo measure the association between PFAS concentration and glucose, the reports used associations between PFAS and one or more of the glucose measures: FG, 1hG, 2hG, OGTT (average of 1hG and 2hG), Impaired Glucose Tolerance (IGT), and GDM. Adjusted odds ratio (OR) (12 reports), crude OR (eight), adjusted regression coefficient (β) relating serum glucose to PFAS (nine), and crude β (three) were the main reported association measures. When a log exposure metric (comparator) was used, it was implemented heterogeneously with per one log-unit difference in PFAS concentration presented in nine studies, per log2 (doubling) difference in four, and per log10 difference in three. Eleven of the reports examined associations with exposure data categorized as either tertiles (six reports), quartiles (four), or dichotomized (one). The majority of these were in conjunction with exposure data examined as a continuous variable, but two reports displayed results with categorized PFAS concentration only, one as tertiles and one as quartiles of exposure.\n\nWe summarized the type of data in the original reports identified by our literature review according to the comparator and outcome (Table 7). Results from reports that reported an effect measure for GDM (e.g., odds ratio) with exposure categorized into more than two categories were counted in the table as being arithmetic comparators because the results can be re-expressed that way.48 For GDM we found that 12 reports could be combined in a SWiM analysis for the two major PFAS. For reports presenting effect measures for glucose during pregnancy (same two PFAS), we found 11 results that could potentially be combined using SWiM. If results for GDM and glucose were combined in a SWiM, results for 17 could be included – assuming the participants in Wang et al. 2023a were a subset of those in Yu et al. 2021.\n\n* N of studies using total amount of PFOA or PFOS.\n\n† Includes studies with categorical results only that have more than two categories of exposure, because these can be re-expressed as ng/ml.\n\n‡ Regardless of the log of base used. For example, studies reporting difference in outcome per doubling of exposure (base log 2) are counted as well as those using natural log or base 10 log.\n\n§ Number of unique studies that could be included in a synthesis without meta-analysis. For example, if a study reported one set of results using an arithmetic comparator and another set of results using a log comparator, that study would be counted only once towards the number in the SWiM.\n\n\nDiscussion\n\nThis scoping review of the evidence and methods used in primary and secondary data on the relation of GDM with PFAS addressed the overall question whether a new systematic review was needed. Because data from several new reports were available since previous systematic reviews were conducted and because SWiM33 could make best use of all available data, an updated systematic review using SWiM would be a valuable addition to the literature.\n\nThe variety of comparators used in the original reports poses challenges to use of meta-analysis to summarize data. If the original reports include a categorical exposure scale, a meta-analysis using a high:low exposure category comparator has been presented as an option.24 The weaknesses of this approach, however, merit discussion. For PFAS, the exposure contrast corresponding to the high:low comparison is likely to vary substantially across studies. If a dose-response relation is operative, the magnitude of the meta-analytic summary would reflect the distribution of exposure in the studies, and the validity of the resulting meta-analytic statistics associated with such a summary are questionable.49 Furthermore, categorical results within-study can be re-expressed to an arithmetic effect measure, which solves the above-mentioned problem and has the further benefit of using, rather than a portion, all the available data. Another issue is that if arithmetic and logged exposure measures were interchangeable after some type of re-expression, that would facilitate meta-analysis. But such re-expression does not work reliably.50 An interesting example of the underlying problem can be found in a recent report by Padula et al. (2023).51 They analyzed individual-level data on birth weight and serum PFOA first using log (exposure) and again using arithmetic exposure. The association was inverse in both analyses, but it was statistically significant when log (exposure) was used but not when arithmetic exposure was used. SWiM is the only widely-accepted non-narrative approach to synthesizing the data from evidence streams based on different comparators.33 The three previous systematic reviews each had methodologic elements yielding results that were questionable. Specifically, a) Gao et al.30 did not provide an overall summary of results from different evidence streams, b) Wang et al.31 by using a high:low comparator, ignored part of the data and combined results in the face of varying exposure contrasts, and c) Yan et al.,32 combined results across comparators, rendering nebulous the statistics associated with the results.\n\nAnother potential improvement in a future systematic review of the GDM-PFAS association would be to integrate data from the GDM-PFAS and blood glucose-PFAS evidence streams. Among studies of blood glucose as the only outcome (no GDM analysis), four out of the five included participants with GDM. Because blood glucose is near to normally distributed, the odds ratio for GDM and the beta coefficient for blood glucose are, with re-expression, interchangeable metrics.52 Thus, data from the glucose-PFAS reports could be used to address the overall question. Even without such re-expression, SWiM could be used to combine the evidence streams.\n\nResults for five PFAS (PFOA, PFOS, PFHxS, PFNA, and PFDA) were reported in almost all the original data studies because these are the PFAS that have the highest median serum concentration in background-exposed populations. In the previous systematic reviews Gao et al. (2021) reported results for all five30; Wang et al. (2022) reported on four,31 and Yan et al. (2022) reported on these five plus three additional PFAS.32 PFAS with lower median concentrations could have been analyzed by the original authors with the comparator > LOD vs not, and such results have not, to date, been included in meta-analyses; however, they could be included in a SWiM.\n\nWhen conducting a meta-analysis of odds ratios for GDM, an assumption is that the log of the odds ratio per comparator unit (beta coefficient) does not vary by the prevalence of GDM in the underlying populations. The prevalence of GDM in the underlying populations is a function of the diagnostic criteria, the prevalence of obesity, and other study or population characteristics.53–55 Whether these characteristics modify the beta coefficient could be evaluated in a meta-regression; such regression was not done in the previous meta-analyses.\n\nTime has passed since the date of the search for relevant original data reports. Our search for relevant systematic reviews, however, was much more recent, and it is this search that is most important for our conclusions to remain valid. The number of new reports available was not as important for our conclusions as the finding that the methods employed in previous systematic reviews could be substantially improved.", "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\nDr. Hector Huang, a chemical engineer, assisted us in organizing Supplementary Table 5. Ms. Lori Crawford assisted us in compiling Table 4.\n\n\nReferences\n\nBuck RC, Franklin J, Berger U, et al.: Perfluoroalkyl and polyfluoroalkyl substances in the environment: terminology, classification, and origins. Integr. Environ. Assess. Manag. 2011; 7(4): 513–541. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nInterstate Technology Regulatory Council (ITRC): Chemistry and Naming Conventions, History and Use of PFAS, and Sources of PFAS Releases to the Environment overview – PFAS — Per- and Polyfluoroalkyl Substances 2020.Reference Source\n\nSunderland EM, Hu XC, Dassuncao C, et al.: A review of the pathways of human exposure to poly- and perfluoroalkyl substances (PFASs) and present understanding of health effects. J. Expo. Sci. Environ. Epidemiol. 2019; 29(2): 131–147. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgency for Toxic Substances and Disease Registry (ATSDR): Toxicological Profile for Perfluoroalkyls. U.S. Department of Health and Human Services; 2021.\n\nKurwadkar S, Dane J, Kanel SR, et al.: Per- and polyfluoroalkyl substances in water and wastewater: A critical review of their global occurrence and distribution. Sci. Total Environ. 2022; 809: 151003. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatilla-Santander N, Valvi D, Lopez-Espinosa MJ, et al.: Exposure to Perfluoroalkyl Substances and Metabolic Outcomes in Pregnant Women: Evidence from the Spanish INMA Birth Cohorts. Environ. Health Perspect. 2017; 125(11): 117004. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRahman ML, Zhang C, Smarr MM, et al.: Persistent organic pollutants and gestational diabetes: A multi-center prospective cohort study of healthy US women. Environ. Int. 2019; 124: 249–258. PubMed Abstract \| Publisher Full Text\n\nWang Y, Zhang L, Teng Y, et al.: Association of serum levels of perfluoroalkyl substances with gestational diabetes mellitus and postpartum blood glucose. J. Environ. Sci. (China). 2018; 69: 5–11. PubMed Abstract \| Publisher Full Text\n\nXu C, Zhang L, Zhou Q, et al.: Exposure to per- and polyfluoroalkyl substances as a risk factor for gestational diabetes mellitus through interference with glucose homeostasis. Sci. Total Environ. 2022; 838(Pt 4): 156561. PubMed Abstract \| Publisher Full Text\n\nXu H, Zhou Q, Zhang J, et al.: Exposure to elevated per- and polyfluoroalkyl substances in early pregnancy is related to increased risk of gestational diabetes mellitus: A nested case-control study in Shanghai, China. Environ. Int. 2020; 143: 105952. PubMed Abstract \| Publisher Full Text\n\nYu G, Jin M, Huang Y, et al.: Environmental exposure to perfluoroalkyl substances in early pregnancy, maternal glucose homeostasis and the risk of gestational diabetes: A prospective cohort study. Environ. Int. 2021; 156: 106621. PubMed Abstract \| Publisher Full Text\n\nYe W, Luo C, Huang J, et al.: Gestational diabetes mellitus and adverse pregnancy outcomes: systematic review and meta-analysis. BMJ. 2022; 377: e067946. Publisher Full Text\n\nNoctor E, Dunne FP: Type 2 diabetes after gestational diabetes: The influence of changing diagnostic criteria. World J. Diabetes. 2015; 6(2): 234–244. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShah NS, Wang MC, Freaney PM, et al.: Trends in Gestational Diabetes at First Live Birth by Race and Ethnicity in the US, 2011-2019. JAMA. 2021; 326(7): 660–669. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrawford L, Halperin SA, Dzierlenga MW, et al.: Systematic review and meta-analysis of epidemiologic data on vaccine response in relation to exposure to five principal perfluoroalkyl substances. Environ. Int. 2023; 172: 107734. PubMed Abstract \| Publisher Full Text\n\n3M: 3M to Exit PFAS Manufacturing by the End of 2025 3M News Center.2022 [updated December 20, 2022]. Reference Source\n\nEuropean Chemicals Agency (ECHA): Annex to the ANNEX XV RESTRICTION REPORT: PROPOSAL FOR A RESTRICTION - SUBSTANCE NAME(S): Per- and polyfluoroalkyl substances (PFASs). Helsinki, Finland: European Chemicals Agency (ECHA); 2023.\n\nPeters MDJ, Godfrey C, McInerney P, et al.: Chapter 11: Scoping Reviews.Aromataris EMZ, editor. JBI Manual for Evidence Synthesis: JBI. 2020.\n\nMoher D, Shamseer L, Clarke M, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst. Rev. 2015; 4(1): 1. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTricco AC, Lillie E, Zarin W, et al.: PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation. Ann. Intern. Med. 2018; 169(7): 467–473. PubMed Abstract \| Publisher Full Text\n\nBeller EM, Glasziou PP, Altman DG, et al.: PRISMA for Abstracts: reporting systematic reviews in journal and conference abstracts. PLoS Med. 2013; 10(4): e1001419. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRethlefsen ML, Kirtley S, Waffenschmidt S, et al.: PRISMA-S: an extension to the PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Syst. Rev. 2021; 10(1): 39. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMunn Z, Peters MDJ, Stern C, et al.: Systematic review or scoping review? Guidance for authors when choosing between a systematic or scoping review approach. BMC Med. Res. Methodol. 2018; 18(1): 143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorgan RL, Whaley P, Thayer KA, et al.: Identifying the PECO: A framework for formulating good questions to explore the association of environmental and other exposures with health outcomes. Environ. Int. 2018; 121(Pt 1): 1027–1031. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShin HM, Vieira VM, Ryan PB, et al.: Retrospective exposure estimation and predicted versus observed serum perfluorooctanoic acid concentrations for participants in the C8 Health Project. Environ. Health Perspect. 2011; 119(12): 1760–1765. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSavitz DA, Hattersley AM: Evaluating Chemical Mixtures in Epidemiological Studies to Inform Regulatory Decisions. Environ. Health Perspect. 2023; 131(4): 45001. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAali G, Shokraneh F: No limitations to language, date, publication type, and publication status in search step of systematic reviews. J. Clin. Epidemiol. 2021; 133: 165–167. PubMed Abstract \| Publisher Full Text\n\nMcGowan J, Sampson M, Salzwedel DM, et al.: PRESS Peer Review of Electronic Search Strategies: 2015 Guideline Statement. J. Clin. Epidemiol. 2016; 75: 40–46. Publisher Full Text\n\nOuzzani M, Hammady H, Fedorowicz Z, et al.: Rayyan-a web and mobile app for systematic reviews. Syst. Rev. 2016; 5(1): 210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGao X, Ni W, Zhu S, et al.: Per- and polyfluoroalkyl substances exposure during pregnancy and adverse pregnancy and birth outcomes: A systematic review and meta-analysis. Environ. Res. 2021; 201: 111632. Publisher Full Text\n\nWang J, Zhang J, Fan Y, et al.: Association between per- and polyfluoroalkyl substances and risk of gestational diabetes mellitus. Int. J. Hyg. Environ. Health. 2022; 240: 113904. PubMed Abstract \| Publisher Full Text\n\nYan D, Jiao Y, Yan H, et al.: Endocrine-disrupting chemicals and the risk of gestational diabetes mellitus: a systematic review and meta-analysis. Environ. Health. 2022; 21(1): 53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCampbell M, McKenzie JE, Sowden A, et al.: Synthesis without meta-analysis (SWiM) in systematic reviews: reporting guideline. BMJ. 2020; 368: l6890. Publisher Full Text\n\nJensen RC, Glintborg D, Timmermann CAG, et al.: Perfluoroalkyl substances and glycemic status in pregnant Danish women: The Odense Child Cohort. Environ. Int. 2018; 116: 101–107. PubMed Abstract \| Publisher Full Text\n\nLi J, Yao J, Xia W, et al.: Association between exposure to per- and polyfluoroalkyl substances and blood glucose in pregnant women. Int. J. Hyg. Environ. Health. 2020; 230: 113596. PubMed Abstract \| Publisher Full Text\n\nLiu X, Zhang L, Chen L, et al.: Structure-based investigation on the association between perfluoroalkyl acids exposure and both gestational diabetes mellitus and glucose homeostasis in pregnant women. Environ. Int. 2019; 127: 85–93. PubMed Abstract \| Publisher Full Text\n\nMehta SS, James-Todd T, Applebaum KM, et al.: Persistent organic pollutants and maternal glycemic outcomes in a diverse pregnancy cohort of overweight women. Environ. Res. 2021; 193: 110551. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPreston EV, Rifas-Shiman SL, Hivert MF, et al.: Associations of Per- and Polyfluoroalkyl Substances (PFAS) With Glucose Tolerance During Pregnancy in Project Viva. J. Clin. Endocrinol. Metab. 2020; 105(8): e2864–e2876. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRen Y, Jin L, Yang F, et al.: Concentrations of perfluoroalkyl and polyfluoroalkyl substances and blood glucose in pregnant women. Environ. Health. 2020; 19(1): 88. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShapiro GD, Dodds L, Arbuckle TE, et al.: Exposure to organophosphorus and organochlorine pesticides, perfluoroalkyl substances, and polychlorinated biphenyls in pregnancy and the association with impaired glucose tolerance and gestational diabetes mellitus: The MIREC Study. Environ. Res. 2016; 147: 71–81. Publisher Full Text\n\nStarling AP, Adgate JL, Hamman RF, et al.: Perfluoroalkyl Substances during Pregnancy and Offspring Weight and Adiposity at Birth: Examining Mediation by Maternal Fasting Glucose in the Healthy Start Study. Environ. Health Perspect. 2017; 125(6): 067016. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nValvi D, Oulhote Y, Weihe P, et al.: Gestational diabetes and offspring birth size at elevated environmental pollutant exposures. Environ. Int. 2017; 107: 205–215. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVuong AM, Braun JM, Sjodin A, et al.: Exposure to endocrine disrupting chemicals (EDCs) and cardiometabolic indices during pregnancy: The HOME Study. Environ. Int. 2021; 156: 106747. Publisher Full Text\n\nWang H, Yang J, Du H, et al.: Perfluoroalkyl substances, glucose homeostasis, and gestational diabetes mellitus in Chinese pregnant women: A repeat measurement-based prospective study. Environ. Int. 2018; 114: 12–20. Publisher Full Text\n\nWang Z, Luo J, Zhang Y, et al.: High maternal glucose exacerbates the association between prenatal per- and polyfluoroalkyl substance exposure and reduced birth weight. Sci. Total Environ. 2023; 858(Pt 3): 160130. PubMed Abstract \| Publisher Full Text\n\nZhang C, Sundaram R, Maisog J, et al.: A prospective study of prepregnancy serum concentrations of perfluorochemicals and the risk of gestational diabetes. Fertil. Steril. 2015; 103(1): 184–189. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang Y, Chen R, Gao Y, et al.: Human serum poly- and perfluoroalkyl substance concentrations and their associations with gestational diabetes mellitus. Environ. Pollut. 2023; 317: 120833. PubMed Abstract \| Publisher Full Text\n\nGreenland S, Longnecker MP: Methods for trend estimation from summarized dose-response data, with applications to meta-analysis. Am. J. Epidemiol. 1992; 135(11): 1301–1309. Publisher Full Text\n\nGreenland S: Meta-analysis.Rothman KJGS, Lash TL, editors. Modern Epidemiology. 3rd ed.Philadelphia: Wolters Kluwer; 2008; p. 681.\n\nLinakis MW, Van Landingham C, Gasparini A, et al.: Re-expressing coefficients from regression models for inclusion in a meta-analysis. bioRxiv. 2021; 2021: 466931.\n\nPadula AM, Ning X, Bakre S, et al.: Birth Outcomes in Relation to Prenatal Exposure to Per- and Polyfluoroalkyl Substances and Stress in the Environmental Influences on Child Health Outcomes (ECHO) Program. Environ. Health Perspect. 2023; 131(3): 37006. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChinn S: A simple method for converting an odds ratio to effect size for use in meta-analysis. Stat. Med. 2000; 19(22): 3127–3131. PubMed Abstract \| Publisher Full Text\n\nBehboudi-Gandevani S, Amiri M, Bidhendi Yarandi R, et al.: The impact of diagnostic criteria for gestational diabetes on its prevalence: a systematic review and meta-analysis. Diabetol. Metab. Syndr. 2019; 11: 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoyadzhieva MV, Atanasova I, Zacharieva S, et al.: Comparative analysis of current diagnostic criteria for gestational diabetes mellitus. Obstet Med. 2012; 5(2): 71–77. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTorloni MR, Betran AP, Horta BL, et al.: Prepregnancy BMI and the risk of gestational diabetes: a systematic review of the literature with meta-analysis. Obes. Rev. 2009; 10(2): 194–203. Publisher Full Text" }	[ { "id": "296883", "date": "16 Jul 2024", "name": "Brice Nouthé", "expertise": [ "Reviewer Expertise Diabetes Mellitus" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 aimed to evaluate the evidence on a potential relationship between Gestational Diabetes Mellitus (GDM) and serum per-&polyfluoroalkyl substances (PFAS). This sponsored effort (by 3M) to evaluate the risk, caused by this group of synthetic carbon-fluorine compounds ensuring slow degradation, is timely because of the important issues evolving around\n\nthe demonstrated relationship of PFAS, known to have an extensive human exposure, and diabetes mellitus the different concerns about GDM across continents despite known lifelong consequences of GDM the potential conflictual results of previous meta-analysis.\nSuggestion1: The authors used studies publicly available & sought to present the need for an updated systematic review before even looking at new source of information. We believe they do not need to expand the Introduction section because it could just be around the motivation of the study.\n\nSuggestion 2: In the Methods' section, the justification to use PECO & description the different strategies to retrieve the data could easily be included in a Supplemental Material . Also, the procedure to solve disagreement does not need to be repeated.\nSuggestion 3: The flow in the Results' section about the in-depth assessment of the 3 previous meta-analyses could be less of a narrative part but rather separated around he potential pitfalls like\nthe use of meta-analyses with different comparators ( but without meta-regression) The combination of results form different evidence streams without appropriate summary The variability of exposure contrasts also rendering the use of a high-low exposure category comparator much questionable.\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": [ { "c_id": "12550", "date": "09 Oct 2024", "name": "Farhad Shokraneh", "role": "Author Response", "response": "Suggestion 1: The authors used studies publicly available & sought to present the need for an updated systematic review before even looking at new source of information. We believe they do not need to expand the Introduction section because it could just be around the motivation of the study. Response: Thank you for spending time reviewing this scoping review and for your suggestion not to expand the introduction. Suggestion 2: In the Methods' section, the justification to use PECO & description the different strategies to retrieve the data could easily be included in a Supplemental Material. Response: Thank you. We followed your recommendations and F1000Research’s guidelines and shared the search strategies on the Open Science Framework (OSF). Comment: The procedure to solve disagreement does not need to be repeated. Response: We agree with your decision and have revised the manuscript to reflect it. Suggestion 3: The flow in the Results section about the in-depth assessment of the 3 previous meta-analyses could be less of a narrative part but rather separated around the potential pitfalls like The use of meta-analyses with different comparators (but without meta-regression) The combination of results from different evidence streams without appropriate summary The variability of exposure contrasts also rendering the use of a high-low exposure category comparator much questionable. Response: Thank you for your suggestion, based on which we changed the first section of results as follows: “In one systematic review (Yan et al., 2022), the use of meta-analysis to combine results across comparators rendered the meaning of the summary OR obscure. In another systematic review (Gao et al., 2021), results from different evidence streams were not combined using an appropriate summary. In the third systematic review (Wang et al., 2022), the focus on only high:low exposure category comparators meant: a) informative data from each included study were ignored, b) the variability of the exposure contrasts made use of this comparator questionable, and c) reports using only models with exposure as a continuous variable were ignored.”" } ] }, { "id": "324731", "date": "28 Sep 2024", "name": "Raju Kanukula", "expertise": [ "Reviewer Expertise Methodologist and pharmacist." ], "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 scoping review was conducted very well without any issues, however I have the following concerns.\n1) In the rationale, authors could have explained the causative pathway between PFAS and GDM. 2) What is the rationale behind excluding review articles on this topic, but included meta-analyses.\n\nApart from these, I have no other concerns.\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.) No", "responses": [ { "c_id": "12551", "date": "09 Oct 2024", "name": "Farhad Shokraneh", "role": "Author Response", "response": "Comment: 1) In the rationale, authors could have explained the causative pathway between PFAS and GDM. Response: Thank you for reading our review and for your comment. This scoping review examined the studies that assess the ‘Association’ from the observational studies. Considering that confounding factors such as obesity—as mentioned in the introduction—can contribute to GDM, we are unable to discuss ‘Causation’ and have yet to see research suggesting such a mechanism. Comment: What is the rationale behind excluding review articles on this topic, but included meta-analyses. Apart from these, I have no other concerns. Response: We excluded the narrative review articles with no usable data or a list of included studies. We, however, studied the systematic reviews and meta-analyses to identify more relevant studies for a possible systematic review in the future, avoid duplicate work, and discuss the suitability of conducting meta-analysis in these reviews." } ] } ]	1	https://f1000research.com/articles/12-1595
https://f1000research.com/articles/13-1182/v1	09 Oct 24	{ "type": "Research Article", "title": "Economic factors influencing the empowerment of Peruvian women", "authors": [ "Elena Jesús Alvarado Cáceres", "Enaidy Reynosa Navarro", "Lindon Vela Meléndez", "Enaidy Reynosa Navarro", "Lindon Vela Meléndez" ], "abstract": "Objective To determine whether economic factors are crucial in empowering women, guiding them towards growth and development opportunities, achieving empowerment, and contributing to two sustainable development goals of the 2030 development agenda: ending poverty and achieving gender equality.\n\nMethodology The research was foundational, with a phenomenological and hermeneutic design. The applied technique was in-depth interviews with 12 women who had started a business within the last five years in a region of Peru.\n\nResults It is evident that economic factors are decisive in business experiences and decisions, highlighting the necessity of having contingency funds to prevent operational impacts. Through entrepreneurship, women achieved economic independence, enabling them to support their families and impacting their empowerment. It concludes that to promote economic opportunity equality, addressing financing needs, encouraging economic independence, strengthening family empowerment, improving customer management, and facilitating access to government funds are essential.\n\nConclusions The narrative of the participants provides a solid foundation for designing specific policies and support programs that boost the economic empowerment of women entrepreneurs and encourage their active participation in the business sphere.", "keywords": [ "Women's Empowerment", "Financial Capacity", "Legal Framework", "Economic Independence", "Potential Customers", "Access to Financing" ], "content": "1. Introduction\n\nWomen’s empowerment has been identified as a fundamental pillar for sustainable economic growth and social development.1 In this context, economic freedom emerges as a critical factor enabling women to make economic decisions independently, thereby contributing to their personal and professional empowerment. However, in developing countries like Pakistan, women continue to face numerous disadvantages that limit their economic participation and their ability to make free decisions in the economic sphere. In this sense, relevant studies have been focusing on analyzing how economic freedom can foster women’s empowerment beyond the cultural, social, and legal barriers that, in one way or another, restrict female participation in the economy.1–4\n\nMoreover, it’s essential to highlight that the aforementioned obstacles hinder women’s full economic freedom, including limitations on women’s mobility, the decision to work, equal pay, legal barriers to marriage, working after childbirth, registering a business, property division, and regulating women’s pensions; among other limitations such as the lack of education and access to technology and its latest advancements. In this regard, access to social networks and media has also been identified as a catalyst for women’s economic empowerment, suggesting a positive correlation between women’s economic empowerment and their demographic, social, and economic characteristics.1\n\nScientific publications highlight that, in developing countries like Ethiopia, significant challenges are faced, including high population growth rates and limited opportunities for women in education and employment. These challenges underscore the importance of focusing on women’s empowerment through access to resources and agricultural inputs as key strategies to overcome economic and social barriers.1 Under this premise, social norms and restricted access to education and employment opportunities represent significant obstacles to women’s economic empowerment, particularly in rural areas. Factors such as access to and control over assets, agricultural inputs, credit, extension services, and social networks have been shown to have a positive impact on women’s economic empowerment.1 However, despite growing attention to the socioeconomic factors influencing women’s empowerment,5,6 there is a pressing need to promote sustained efforts for their empowerment over time.\n\nTo foster the economic empowerment of women entrepreneurs, it is crucial, in addition to a strong motivation to achieve ambitious goals in challenging contexts, as previously mentioned, that they have support facilitating the articulation of their objectives. Recent research underscores that support from entities, such as the government, plays a significant role in women’s economic empowerment.4 This backing can take various forms, including financial education, which is fundamental for women’s economic empowerment. This is because it enables them to make financial decisions based on solid information and manage their economic resources effectively.\n\nUltimately, female empowerment aims not only to improve women’s income and living standards but also to enhance their decision-making capacity. However, an important fact must be considered: women’s vulnerability often stems from their limited participation in decision-making processes and their restricted access to essential resources,3 which may include access to education, healthcare, employment opportunities, and involvement in decision-making processes. To address these issues, it is crucial to consider the livelihood options available to women. Policies promoting favorable conditions, such as access to relevant information and reduced interest rates, are vital to support women’s empowerment and encourage their economic independence.3\n\nIn Peru, there is a Legal Framework and Public Policies with solid foundations aimed at supporting female entrepreneurship and promoting the economic empowerment of women. Law No. 31828, the Young Entrepreneur Law, aims to establish a regulatory framework to generate employment opportunities for youth that successfully contribute to the country’s development within a social market economy7; it creates a favorable environment for young entrepreneurs, including young women, by facilitating the establishment and registration of businesses and offering tax benefits that encourage hiring.\n\nAdditionally, the National Women Entrepreneurs Strategy, established through Supreme Decree No. 012-2022-MIMP, aims to “promote and develop the economic autonomy of women in their diversity to achieve the reduction of structural gender gaps and the enjoyment of a sustainable, dignified life with full well-being”.8 This comprehensive strategy focuses efforts on creating conditions that allow women to overcome the historical and structural barriers that limit their economic empowerment.\n\nOn the other hand, Law No. 31168, which promotes the empowerment of rural and indigenous women, aims to “strengthen, through affirmative actions, the empowerment, equality of opportunities, and comprehensive development of rural and indigenous women, enhancing their economic, cultural, social autonomy, through training and productive financing”,9 constitutes a pillar in the fight for equality by establishing positive action measures and promoting access to productive and financial resources, especially aimed at women in vulnerable situations.\n\nFurthermore, Supreme Decree No. 008-2019-MIMP is another fundamental tool aimed at ensuring the exercise of women’s economic and social rights, promoting access to productive resources, and improving conditions for their formal labor insertion.10 This policy strengthens the existing legal framework, driving towards a more inclusive and equitable society.\n\nDespite this progressive legal framework and policies designed to support female entrepreneurship and economic empowerment, significant challenges persist in Peru that limit the full realization of these objectives. Women entrepreneurs still face structural obstacles, such as insufficient financial capacity, lack of knowledge of the legal framework and the norms and procedures for formulating their ventures, lack of economic independence, difficulties in attracting and retaining potential customers, as well as limitations in accessing support funds (both national and international) for entrepreneurship, among others. These barriers underline the need for effective and sustained implementation of existing laws and policies, as well as the importance of adopting additional measures to address residual inequalities and foster a truly empowering environment for women in the business sphere.\n\nThe objective of this study focused on determining whether economic factors are crucial in women’s empowerment. As specific objectives, it sought to evaluate how the economic needs of female-led ventures lead to the creation of a contingency fund, determine how the establishment of businesses has generated economic independence for women entrepreneurs, identify how women entrepreneurs have achieved family empowerment through economic success, analyze the importance of managing customers in a venture, determine the significance of formality in regulatory compliance in female-led enterprises, and assess whether women entrepreneurs have access to government funds.\n\n\n2. Methods\n\nThis research is framed within a naturalistic paradigm and follows a qualitative approach, which allows understanding to what extent economic factors are determinants in the empowerment of Peruvian women based on their perceptions and meanings. Additionally, it features a hermeneutic phenomenological design, “aimed at the description and interpretation of the fundamental structures of lived experience”11; under this design, it was possible to explore and understand the lived experiences of the participating women entrepreneurs, based on their narrative derived from their experiences, their reality, and their entrepreneurial ecosystem.\n\nThe participants included in the study were 12 entrepreneurs from the northern region of Peru who, at the time of the research, owned a medium or small business, which they had been developing for a minimum period of five years. All were female, with ages ranging from 25 to 60 years, and an average age of 35.33 years. All expressed their willingness to participate in the study in a friendly and cordial manner.\n\nThe research team, comprised of academics from two Peruvian universities, contributed extensive knowledge on economic empowerment, enriching the study with their academic and professional diversity. The applied hermeneutic phenomenological methodology allowed for the establishment of meaningful relationships with the participants, promoting a trustful environment where they freely shared their experiences. Aware of how our experiences and perspectives could influence the interpretation of the data, we adopted an “epoché” attitude, striving to understand the participants’ narratives without prejudice. This interaction between our characteristics and the study was key in shaping the approach, methodology, and interpretation of results, allowing us to identify patterns and emerging themes that enriched our findings. The adopted approach and close relationship with the participants captured the complexity of women’s economic empowerment in Peru, facilitating the transferability of the research.\n\nThe research was conducted in the northern region of Peru, an area characterized by a dynamic entrepreneurial ecosystem reflecting similar trends across the country. However, in this area, female entrepreneurship has begun to stand out significantly in recent years, challenging traditional barriers and contributing to the economic and social fabric. The choice of this region as the study site is due to its relevance in the country’s entrepreneurial landscape and the opportunity to explore the specific impact of economic factors on women’s empowerment in a context where women entrepreneurs are emerging as key actors for sustainable development. The study focuses on analyzing whether economic factors, such as access to financing and economic independence, act as catalysts for women’s empowerment, guiding them towards opportunities for growth and personal and professional development. Additionally, this research corroborates the need to better understand how female entrepreneurship can contribute to achieving key sustainable development goals, particularly ending poverty (Goal 1) and achieving gender equality (Goal 5), in the 2030 development agenda.12\n\nThe participant selection methodology for this research was centered on purposeful sampling targeting women entrepreneurs who had launched their projects within the last five years in the northern region of Peru. This approach was specifically designed to capture recent and relevant experiences that reflect both the challenges and opportunities within the realm of female entrepreneurship. The intention was twofold: to align the study with its core objectives and to deepen the understanding of how economic factors impact women’s empowerment. Twelve women participants were selected, a number deemed optimal for achieving data saturation. This decision was based on the observation that additional interviews were not yielding new themes or significant data. Continuous analysis and review of the interviews, facilitated by the use of ATLAS.ti software, allowed for the identification of recurring themes and patterns, as well as the confirmation of key categories and subcategories. These observations indicated that a comprehensive understanding of the participants’ narrated experiences had been achieved, suggesting that the sampling process had reached its saturation point and, therefore, the number of participants was sufficient for the purposes of the study.\n\nIn this study, the respect, integrity, and protection of participants’ rights were ensured. Before conducting the in-depth interviews, written informed consent was obtained from all participating entrepreneurs. This consent process not only ensured that participants were fully informed about the nature and purpose of the study but also protected their rights and confidentiality. They were fully informed about the study’s objectives, their role in it, and how their personal information would be handled and protected. Confidentiality and anonymity of the participants were guaranteed during the processing of their data and testimonies, avoiding any form of harm or discrimination.13–15 Additionally, special care was taken in the sensitive handling of topics that could evoke intense or traumatic personal experiences, providing a safe and supportive space during the interviews. It is worth noting that this study aligns with the sustainable development goals of the 2030 Agenda, specifically regarding the eradication of poverty and gender equality.12\n\nThe research project titled “ Personal, Economic, and Social Factors Influencing Women’s Empowerment,” was approved by Vice-Chancellor for Research Resolution N° 442-2022-VI-UCV.16 Subsequently, the Ethics Committee in Research of the School of Administration at Universidad César Vallejo reviewed the project under the review code 2024-1-36 and granted a favorable opinion on January 26, 2024. The research was conducted in accordance with the ethical principles outlined in the Declaration of Helsinki, ensuring informed consent from all participants and guaranteeing the confidentiality and anonymity of the collected information.\n\nAn in-depth interview was conducted, whose base code was Female Entrepreneurship, from which the study’s central category (Economic Factors) was derived, divided into five subcategories: Financial Capacity, Legal Framework, Economic Independence, Potential Customers, and Access to National and International Funds. This allowed participants to express their experiences, perceptions, and emotions openly, yet guided by a set of previously prepared questions that steered the conversation towards the study’s topics of interest. Given the wide geographic distribution of the entrepreneurs, the interviews were recorded via Zoom with an approximate duration of 60 minutes per interviewee. The applied interview was subjected to content validity by five experts in the field – as recommended in the specialized literature.17–19\n\nThe interview results were transcribed and analyzed using the content analysis technique, aiming to identify patterns, themes, and emerging categories that reflect the experiences and perceptions of women entrepreneurs. Additionally, a hermeneutic interpretation of the participants’ narratives was conducted to understand the deep meanings of the experiences narrated by the participants. For the analysis and processing of all the information, the qualitative analysis software ATLAS.ti was used, enabling coding, analysis, visualization, online collaboration, and flexibility in managing the obtained data.20\n\n\n3. Results\n\nNext, we explore qualitative categories and subcategories structured from interviews with women entrepreneurs, focusing on how these economic factors influence their experiences and business decisions. Through the narratives of these women, we examine how the need to have funds for contingencies has affected their operations, how they have achieved economic independence through entrepreneurship, how family support has impacted their empowerment, how they identify and relate to their potential customers, and what their experiences are with government entrepreneurship support programs.\n\nFigure 1 presents the Economic Factors category as a component resulting from the coding process of the central theme (Female Entrepreneurship). According to the entrepreneurs, these economic factors are linked to the Financial Capacity subcategory, necessary for managing those financial resources essential for the success of female entrepreneurship. The practitioners consider the existence of a Legal Framework with the security that is felt when an enterprise is not only successful but also formal. Likewise, they identified Economic Independence as another key related subcategory. Regarding the Potential Customers subcategory, they consider it also connected to Economic Factors. Finally, the entrepreneurs consider that the subcategory Access to national and international funds represents a need that goes beyond local borders for the growth and expansion of Female Entrepreneurship.\n\nFigure 2 highlights Financial Capacity as a critical subcategory in the context of female entrepreneurship, as perceived by the participants. From their point of view, financial capacity encompasses fundamental elements such as: having an effective fund to face contingencies; the awareness and/or situation of not having funds for contingencies, highlighting a concern for vulnerability to unforeseen events; knowledge about how to access national and international financing sources; and the importance attributed to proper fund management, reflecting a focus on responsibility and efficiency in financial resource management.\n\nIn Figure 3, according to the entrepreneurs, the Legal Framework subcategory, in addition to being an essential component for entrepreneurship, is fundamental for the formalization of the venture. Regarding accounting management, they maintained that having rigorous accounting aligned with legal norms is an essential element for achieving transparency and financial health of their enterprises. As for the “Régimen MYPE-Peru” issue, in some cases, the entrepreneurs point out the need to join this regime, while in others, they emphasize that remaining within this regime is vital for the optimal functioning and growth of their businesses within the local economy.\n\nIn Figure 4, the Economic Independence subcategory is highlighted as an element related to the challenges and goals of female entrepreneurship. According to the participants, empowerment is a factor that has allowed them to achieve economic independence, which implies a direct connection between personal strengthening and financial autonomy. Moreover, they consider economic independence as a medium and long-term goal, suggesting a perspective of planning and sustained development over time. Finally, they acknowledge that the process towards economic independence is ongoing, indicating that it is a dynamic and evolving state.\n\nIn Figure 5, the participants highlight that the lack of updated market studies and the absence of specialized studies constitute a significant limitation to fully understanding the market’s potential. Additionally, they point out that they are making efforts to gradually implement market studies that help them in the process of understanding, rescuing, and attracting new customers. They also indicate that they are in the process of implementing modern marketing systems, suggesting a transition towards modern marketing practices. They assert that the strategic and responsible use of social media is a priority for adapting to new digital marketing trends. The figure also shows that the entrepreneurs are developing strategies to recover customers, which implies a focus on customer retention and loyalty. Lastly, they identify the need for training in new technologies, thereby being able to use all the tools that allow them to reach new customers.\n\nRegarding the subcategory Access to Financing Funds, it presents two approaches: 1) Possibilities of access to national funds and 2) Access to national and international funds. Regarding national funds, the entrepreneurs recognize a lack of knowledge about support programs for women entrepreneurs and state support funds and foundations (Figure 6). They also express an interest in using financial instruments such as some ISO standards, which help improve management and thereby quality. Some participants claim to have financing granted by REACTIVA-Peru (A program of credits with governmental guarantee, designed to prevent a breakdown in the payment chain). Related to the access to international funds, there is a lack of knowledge about the procedures to apply for them (this also happens regarding the access to national funds). Despite this lack of knowledge, the value of these funds is recognized, even though they cannot use them.\n\n\n4. Discussion\n\nAccording to the narrative of the participants, Financial Capacity is fundamental for the empowerment of Peruvian women, highlighting the need for funds for contingencies, access to financing, and proper management of these resources. When contrasting these results with previous research, we find, for example, a study in Ethiopia that highlights the relevance of access to credit and ownership of resources in women’s empowerment in rural areas,1 while research in Murcia, Spain, shows gender differences in financing negotiation, suggesting the need to overcome additional barriers for women’s economic empowerment through a supportive environment.21 Moreover, the negative cultural perception towards indebtedness in Mexico highlights the importance of addressing cultural and personal barriers to financing, an aspect that is also critical in Peru where fund management and access to financing are essential, but critical.22 Similarly, studies in Mexico and Paraguay emphasize the need to improve financial capacity and access to funds as key elements for empowerment, underlining the importance of financial resources and support for entrepreneurial initiatives.11,23 Returning to Peru, other studies highlight work experience, the creation of a credit history, and governmental and non-governmental support as facilitators of access to financing; emphasizing the need for policies and programs that improve this access and promote a culture of financial management, aligned with the sustainable development goals of the 2030 agenda.24,25 These findings indicate that, despite existing challenges regarding financial capacity and access to resources, key opportunities for progress coexist through financial education, social support, and inclusive policies, underlining the importance of an integrated approach to promote women’s empowerment in Peru and enhance their economic capacity. This analysis agrees with a study conducted in the rural town of Chinchero (Cusco, Peru), where it was observed that, through entrepreneurial initiatives, businesswomen not only improved their linguistic skills (in English and Spanish) and public communication, essential for marketing their handicraft products but also generated income that significantly contributed to the success of their businesses.26\n\nRegarding the Legal Framework, participants identify as a critical component both the formalization of businesses and their alignment with legal regulations; entrepreneurs emphasize the need to adhere to the Régimen MYPE-Peru as an essential step for the development and sustainability of their ventures. This emphasis on legality and financial viability demonstrates how an adequate legal framework is vital for transparency and financial health, being crucial for the sustainability of female entrepreneurship. Research conducted in Ethiopia and Spain highlights the importance of the legal and regulatory environment in women’s economic empowerment, underscoring both the facilitations and additional barriers imposed by gender differences in financing negotiation.1,21 Similarly, studies in Mexico highlight the importance of credit programs and financial support, aligning with the need for a legal framework that promotes access to resources for entrepreneurs.22,27 These investigations converge on the urgency of policies and legal reforms that address the needs of female entrepreneurship in a more objective manner, overcoming barriers and promoting an inclusive and equitable environment. In Peru, despite having a legal framework and public policies designed to support female entrepreneurship and promote their economic empowerment,28–31 significant challenges persist that limit the full utilization of these initiatives. Therefore, the urgent need for more effective implementation and greater dissemination of these laws and strategies is crucial to overcoming the structural and cultural barriers that women entrepreneurs in the country still face. It is important to continue working on promoting a legal and social environment that not only recognizes the rights and capabilities of women but also actively facilitates their equitable participation in the economy; considering that the integration and ongoing support of women’s economic empowerment within the legal framework and public policies are fundamental to achieving a more just and equitable society.\n\nFor the participants, Economic Independence emerges as a fundamental pillar of women’s empowerment in Peru, reflecting an ongoing process of personal strengthening and financial autonomy aligned with globally observed patterns, where women’s empowerment is closely linked to economic and social factors, such as access to credit and ownership of resources.1 This focus on economic independence highlights the importance of planning and sustained development towards greater autonomy, underlining the connection between economic empowerment and financial independence, especially through the implementation of credit programs aimed at women, which have proven to be crucial for the development of micro-enterprises and female productive groups.23,27 Additionally, consulted studies emphasize gender differences in financing negotiation, which directly impacts women’s economic independence, suggesting the need for policies that promote equitable access to financial resources.22,32,33 In Peru, the need for special policies to finance ventures reflects an understanding of the challenges and opportunities to achieve economic independence,25 highlighting the importance of solid financial education and support from a conducive environment that includes family, government, private banking, and NGOs. Moreover, the interconnection between economic empowerment, financial capacity, and economic independence suggests that strengthening one contributes to the advancement of the others, highlighting a global issue that requires legal reforms and public policies focused on addressing the specific needs of female entrepreneurship.\n\nRegarding the identification and capture of Potential Customers, for the participants, it represents a significant challenge, expressing concern about the lack of updated market studies and the adoption of modern marketing strategies. In other words, most of the participants have not conducted market studies or do not have the funds to hire companies that can assist in this endeavor. Similarly, they are unaware of how to conduct such a study; therefore, the success of their ventures is usually the result of their empiricism. In this sense, the transition towards modern marketing practices, especially the strategic use of social networks and digital marketing, reflects the need to adapt to new trends to attract and retain customers, implying not only a technological change but also a shift towards a more analytical and market data-based approach. This process highlights the importance of training in new technologies to leverage all available tools to reach new customers, resonating with the importance of education and training in women’s economic empowerment.1 Moreover, the strategy of offering exclusive products and relying on good taste to attract customers emphasizes the need for market differentiation to establish a distinctive brand.22 The creation of social micro-enterprises and participation in productive groups point to a focus on specific markets, underlining the importance of precise market orientation and adaptation to customer needs.27 Adapting to market opportunities and developing skills in marketing and research are identified as crucial for business success,23 highlighting the need for additional support for some entrepreneurs in areas of limited experience and resources. This analysis suggests that success in identifying and attracting potential customers depends on the ability to adapt to market trends, product differentiation, the development of a solid brand, and the effective implementation of digital marketing strategies, in addition to emphasizing ongoing education and training in new technologies and market practices as key elements for women’s economic empowerment and business sustainability.\n\nAccess to Financing Funds is highlighted as a critical situation towards economic empowerment and business success for women, showing a key distinction between the possibilities of access to both national and international funds. The knowledge gap regarding specific support programs for women entrepreneurs and the interest in using financial instruments to improve management and quality of businesses indicate a critical need for information and accessible resources for entrepreneurs. The REACTIVA-Peru initiative, for example, underlines the existence of governmental support as it aims to “promote the financing of the replenishment of working capital funds for companies facing short-term payments and obligations with their workers and suppliers of goods and services, in order to ensure continuity in the payment chain in the national economy”34; but the general lack of knowledge about how to apply for funds highlights the importance of financial education and training, to achieve a positive impact on women’s economic empowerment.1,23 On the other hand, cultural barriers to indebtedness and challenges in accessing credit, especially in rural areas,22 along with the relevance of credit programs directed at women, underscore the need for financing mechanisms adapted to the unique circumstances of entrepreneurs.27 In summary, the strategy of financial self-sufficiency, based on personal savings and family support, highlights the vulnerability in the absence of significant governmental support,32 pointing out the need for formal financing options that support the growth and sustainability of women-led businesses. Also, the inclination towards standards, such as ISO, suggests a focus on sustainable and quality business practices, potentially increasing eligibility for funds that value high standards. Overcoming these challenges requires policies and programs that improve knowledge about available financing, offer financial education, and promote support networks to facilitate women’s economic empowerment. Finally, access to financing demands an integrated approach that includes financial education, knowledge of financing options, and the creation of a more inclusive environment for women entrepreneurs, with the collaboration of government, private sector, and NGOs to develop a business ecosystem that supports the start and sustainable growth of women’s ventures.\n\nThis study stands out for its rigorous hermeneutic phenomenological methodology, which allowed for a deep and meaningful exploration of the experiences of women entrepreneurs in Peru, revealing the complex influence of economic factors on their ventures. The research is characterized by a comprehensive approach, covering key categories and subcategories such as Financial Capacity, Legal Framework, Economic Independence, Potential Customers, and Access to Funds, providing a holistic and detailed perspective of the challenges and opportunities faced by women entrepreneurs. The careful selection of twelve participants, all women who have launched projects in the last five years, ensured the relevance and timeliness of the shared experiences, significantly enriching the study’s findings. Additionally, the sampling saturation criterion was effectively applied to determine the optimal number of participants, thus ensuring that the research was exhaustive and faithfully representative of the studied population, achieving a balance between depth of analysis and applicability of the results.\n\nThis study provides essential insights into the economic empowerment of women entrepreneurs in Peru, highlighting the need for cautious interpretation of its findings due to certain inherent limitations. Conducted in a specific region of Peru, the results offer valuable, yet contextually limited understanding, suggesting that extrapolation to other contexts or regions should be approached with caution. While the qualitative approach lends rich depth to personal narratives, the nature of this methodology implies that generalizing these findings to a broader population should be done with consideration. Additionally, although the study offers a detailed analysis focused on economic factors through twelve entrepreneurs, the future integration of non-economic variables could further enrich the understanding of female empowerment.\n\n\n5. Conclusions\n\nFinancial Capacity is a critical subcategory for women’s economic empowerment, so the ability to adequately manage financial resources, access financing, and have funds for contingencies is fundamental for the success and sustainability of the ventures led by the participants. Likewise, promoting financial education and facilitating access to various financing sources can significantly increase the capacity to make informed economic decisions and strengthen the participants’ economic independence.\n\nA solid Legal Framework is conducive and basic for the economic empowerment of female entrepreneurs as it facilitates the formalization of ventures, guarantees equitable rights, and promotes a safe business environment. This translates into access to financial and market benefits and is key for the transparency and financial health of female businesses. Therefore, it is necessary to implement and promote new inclusive policies that support gender equality and eliminate legal barriers that may limit female entrepreneurship.\n\nRegarding Economic Independence, the participants perceive it as a pillar of female empowerment, allowing them to have control over their lives and economic decisions. In this sense, through entrepreneurship, participants not only improve their financial situation but also their self-esteem and participation in society. Likewise, it is crucial to support the development of entrepreneurial skills, facilitate access to markets, and promote environments that enhance the participants’ economic independence.\n\nIdentifying and managing Potential Customers is fundamental for the growth of any business. In this sense, entrepreneurs must overcome challenges such as the lack of market studies and adapt to modern marketing strategies, especially in the digital age. Therefore, receiving training in marketing, market studies, and promoting the use of technologies to improve understanding and capture of customers can significantly boost female business success.\n\nFinally, Access to National and International Funds is viewed as a significant obstacle to the development and sustainability of ventures. Therefore, it is necessary to increase awareness, knowledge, and application to available support programs and simplifying application procedures can improve access to funds. Additionally, it is vital to create new inclusive financing programs that consider the specific needs of women, promoting equal opportunities in accessing financial resources for the development and expansion of their ventures.\n\n\nEthics and consent\n\nThe research project was approved by Vice-Chancellor for Research Resolution No. 155-2023-VI-UCV. Subsequently, the Ethics Committee in Research of the School of Administration at Universidad César Vallejo reviewed the project under the review code 2024-1-36 and granted a favorable opinion on January 26, 2024.\n\nWritten Informed consent was obtained from all participating entrepreneurs.", "appendix": "Data availability\n\nThe transcription or recording of the twelve in-depth interviews cannot be publicly shared as it compromises the identity and privacy of the participants. This study is aligned with the Sustainable Development Goals, specifically in relation to gender equality and poverty eradication, 12 and our commitment to the integrity and well-being of the participants is paramount. The interviews contain identifiable information, such as, physical characteristics, and sensitive personal details of the entrepreneurs, making de-identification impossible without violating the confidentiality guaranteed to the participants. This commitment was approved by the Ethics Committee in Research at Universidad César Vallejo (review code: 2024-1-36), 16 in accordance with the principles set forth in the Declaration of Helsinki, 13,14 ensuring the protection of identity and respect for the rights of the participants. Any request for access to the interview transcriptions or recordings must be formally submitted via email to ereynosa@ucv.edu.pe. The relevance of such requests will be evaluated by the research team in consultation with the Ethics Committee to ensure the privacy of the participants is upheld.\n\nZenodo: Economic Factors Influencing the Empowerment of Peruvian Women. https://zenodo.org/doi/10.5281/zenodo.10884402 [Version 1, 2, 3] 35\n\nThis project contains the following extended data:\n\n• Interview (English version).pdf\n\n• Instrument Validation Sheet_Expert 1. (ENGLISH VERSION).pdf\n\n• Instrument Validation Sheet_Expert 2. (ENGLISH VERSION).pdf\n\n• Instrument Validation Sheet_Expert 3. (ENGLISH VERSION).pdf\n\n• Instrument Validation Sheet_Expert 4. (ENGLISH VERSION).pdf\n\n• Instrument Validation Sheet_Expert 5. (ENGLISH VERSION).pdf\n\n• SRQR_checklist (Economic factors influencing the empowerment of Peruvian women).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\nFedasa Hordofa D, Ayele BM: Assessing the Impact of Social, Demographic, and Economic Factors on the Economic Empowerment of Rural Women in Agricultural Activitie: A Partial Proportional Odds Model Analysis in Dire Dawa Administration, Ethiopia. J Environ Dev Sustain. 2023 Mar 27 [cited 2024 Feb 28]; 1–39. Publisher Full Text\n\nDhar S: Women Empowerment-Economic Development Nexus: Bangladesh and Vietnam in Comparative Perspective. J Governance, Secur Dev. 2023 [cited 2024 Feb 28]; 3(2): 1–26. Publisher Full Text Reference Source\n\nAyisha M, Abdul Latip H: Sustainable Socio-Economic Development of Women: A Blueprint from Vulnerability to Empowerment. Int J Acad Res Econ Manag Sci. 2023 Apr 13 [cited 2024 Feb 28]; 12(2): 167–179. Publisher Full Text\n\nRohatgi S, Gera N, Dana LP: Antecedents of economic empowerment: an empirical study of working women in Delhi-NCR. Gend Manag. 2023 Jun 21 [cited 2024 Feb 28]; 38(6): 784–803. Publisher Full Text\n\nKhalid MW, Samargandi N, Shah AH, et al.: Socio-Economic Factors and Women’s Empowerment: Evidence from Punjab. Pakistan. Int Econ J. 2020; 34(1): 144–168. Publisher Full Text\n\nKaruppusamy SI: Socio-Economic Factors on Women Empowerment. Int J Sci Res Manag. 2017; 5(06): 5415–5418. Reference Source\n\nCongreso de la República: Ley del Joven Empresario. LEY No 31828 Perú.2023; 7. Reference Source\n\nMinisterio de la Mujer y Poblaciones Vulnerables: Decreto Supremo que aprueba la Estrategia Nacional Mujer Emprendedora. Decreto Supremo No 012-2022-MIMP Perú.2022; pp. 20–23. Reference Source\n\nCONGRESO DE LA REPÚBLICA: Ley que promueve el empoderamiento de las mujeres rurales e indígenas. Diario oficial, LEY No 31168 Perú.2021; pp. 5–6. Reference Source\n\nMinisterio de la Mujer y Poblaciones Vulnerables – MIMP: Política Nacional de Igualdad de Género. El Peruano, DECRETO SUPREMO N° 008-2019-MIMP Perú.2019; pp. 3–47. Reference Source\n\nFuster Guillen DE: Qualitative Research: Hermeneutical Phenomenological Method. Propósitos y Represent. 2019 Jan 1 [cited 2024 Mar 5]; 7(1): 201–229. Publisher Full Text Reference Source\n\nONU: La Agenda para el Desarrollo Sostenible. 2015. 17 Objetivos para las personas y para el planeta.Reference Source\n\nWorld Medical Association Declaration of Helsinki: Ethical Principles for Medical Research Involving Human Subjects. Clin Rev Educ. 2013 [cited 2021 May 30]; 310(20): 2191–2194. Publisher Full Text Reference Source\n\nCarlson RV, Boyd KM, Webb DJ: The revision of the Declaration of Helsinki: past, present and future. Br J Clin Pharmacol. 2004 Jun 1 [cited 2023 Sep 27]; 57(6): 695–713. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMerz JF: The Nuremberg Code and Informed Consent for Research. JAMA. 2018 Jan 2 [cited 2023 Sep 27]; 319(1): 85–86. PubMed Abstract \| Publisher Full Text Reference Source\n\nUniversidad César Vallejo: RESOLUCIÓN DE VICERRECTORADO DE INVESTIGACIÓN N°442-2022-VI-UCV. RESOLUCIÓN DE VICERRECTORADO DE INVESTIGACIÓN N°442-2022-VI-UCV, 442-2022-VI-UCV Perú.2022; 1–3.\n\nZamora-de-Ortiz MS, Serrano-Pastor FJ, Martínez-Segura MJ: Content validity of the A-SIWT (ask, see, interpret, walk, tell) teaching model by expert judgment. Form Univ. 2020; 13(3): 43–54. Publisher Full Text\n\nRodríguez Medina MA, Poblano-Ojinaga ER, Alvarado Tarango L, et al.: Validation by Expert Judment of an Evaluation Instrument for Evidence of Conceptual Learning. RIDE Rev Iberoam para la Investig y el Desarro Educ. 2021; 11(22): e080. Publisher Full Text\n\nDe la Cruz VV, Gordillo Fuentes EJ: Validation of Interviews by Judgment of Experts in the Study of Inclusive Education in the Foreign Languages Area. RIDE Rev Iberoam para la Investig y el Desarro Educ. 2020; 11(21): e110. Publisher Full Text\n\nMaciej S: Qualitative Data Analysis with ATLAS.ti. 3rd ed.Uniwersytet śląski; 2019 [cited 2024 Mar 5]; 1–223. Reference Source\n\nOrtiz García P: The discourse on entrepreneurship of women from a gender perspective. Vivat Acad Rev Comun. 2017; 140: 115–129. Publisher Full Text\n\nBriseño García O, Briseño García A, López Lira Arjona A: Female entrepreneurship: a multi-case study of critical factors in Northeastern Mexico. Innovaciones de Negocios. 2016; 13(25): 023–046. Publisher Full Text\n\nEncina Ayala LM, López Méndez G: Female Entrepreneurship: A Multi-Case Study of Factors Influencing Entrepreneurial Intention. Cienc Lat Rev Científica Multidiscip. 2021; 5(2): 1642–1659. Publisher Full Text\n\nAranibar Ramos ER, Huachani Licona DY, Zúñiga Chávez MY: Feminine Entrepreneurship in Peru: Strengths and Weaknesses to its Sustainability. Revisión Tema. 2022; 23(23): 199–223. Publisher Full Text\n\nOrihuela-Ríos NC: Female entrepreneurship: characteristics, reasons for success, limitations, involved and consequences. INNOVA Res J. 2022; 7(1): 109–122. Publisher Full Text\n\nTerry C: Tourism, education and women’s empowerment. The case of the women weavers of Chinchero (Cusco, Peru). Atlántida Rev Canar Ciencias Soc. 2021; 12: 131–157. Publisher Full Text\n\nRobinson Trapaga DG, Diaz-Carrion IA, Hernandez SC: Rural and Indigenous women empowerment through productive groups and social microbusinesses in Mexico. Retos (Ecuador). 2019; 9(17): 91–108. Publisher Full Text\n\nCONGRESO DE LA REPÚBLICA: Ley que promueve el empoderamiento de las mujeres rurales e indígenas. Diario oficial, LEY No 31168 Perú.2021; pp. 5–6.\n\nMinisterio de la Mujer y Poblaciones Vulnerables – MIMP: Política Nacional de Igualdad de Género. El Peruano, DECRETO SUPREMO N° 008-2019-MIMP Perú.2019; pp. 3–47.\n\nCongreso de la República: Ley del Joven Empresario. LEY No 31828 Perú.2023; p. 7.\n\nMinisterio de la Mujer y Poblaciones Vulnerables: Decreto Supremo que aprueba la Estrategia Nacional Mujer Emprendedora. Decreto Supremo No 012-2022-MIMP Perú.2022; pp. 20–23.\n\nOrtiz García P, OLaz Capitán Á: Competence factors in the entrepreneurship of women. Rev Esp Sociol. 2018; 27(3): 413–432. Publisher Full Text Reference Source\n\nZogning F: Financial inclusion, inclusive entrepreneurship, and alternative financing options. J Small Bus Entrep. 2023; 35(1): 8–13. Publisher Full Text\n\nDecreto Legislativo No 1455: Decreto Legislativo que crea El Programa “Reactiva Perú” para asegurar la continuidad en la cadena de pagos ante el impacto del Covid-19. Diario el peruano, Decreto Legislativo 1455.2020; pp. 2–6. Reference Source\n\nAlvarado-Cáceres EJ, Reynosa Navarro E, Vela Meléndez L: Economic Factors Influencing the Empowerment of Peruvian Women. Zenodo. 2024 [cited 2024 Mar 26]. Reference Source" }	[ { "id": "334862", "date": "08 Nov 2024", "name": "Jane Kerubo-Onsongo", "expertise": [ "Reviewer Expertise Gender equality and equity", "Women Empowerment", "Higher Education Leadership and Management", "Poverty reduction", "Leadership and Integrity", "Diplomacy and International Relations" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article reports on research findings on factors that contribute to the economic empowerment of female entrepreneurs in Northern Peru. The findings reveal that in spite of the legal framework there are challenges that face women that need attention by policy makes and researchers. The article would be strengthened if more information would be provided about the context. For example What is the population of women entrepreneurs compared to men in Northern Peru. The authors justify the selection of the region because \"female entrepreneurs in this region is has begun to stand out significantly in recent years? What has been the situation? How are they standing out? Is it that the number of business ( SMES) operated to women compared to men has increased or are they making more profits?. What is the gender inequality/inequity in Peru? How about poverty Index? Are women poorer than Men? Which targets of the SDG 1 & 5 does your study/findings contribute to? Sample What types of enterprises were the twelve female entrepreneurs selected engaged in. Is it assumed that the challenges faces by women entrepreneurs are similar regardless of the enterprise? Was there any attempt to triangulate the data with other sources like Government records on financial supports to female entrepreneurs'?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "352292", "date": "02 Jan 2025", "name": "Nicolas Sumba Nacipucha", "expertise": [ "Reviewer Expertise Behavioral Economics", "Marketing", "Business Management" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article offers an insightful exploration of the economic factors impacting the empowerment of women entrepreneurs in northern Peru, employing a hermeneutic phenomenological methodology. A notable aspect of this work is its comprehensive approach, which includes key categories such as Financial Capacity, Legal Framework, Economic Independence, Potential Customers, and Access to Funds, providing a holistic perspective on the challenges and opportunities of female entrepreneurship in this Latin American country.\nThe conclusions are clear and relevant, emphasizing the importance of financial education, legal formalization, access to inclusive financing, and training in market strategies and technology—elements that strengthen the economic autonomy and social impact of the participants.\nThe study's findings are particularly valuable for Peruvian authorities (as well as for authorities in neighboring countries such as Ecuador and Bolivia) to take action and design strategies that bolster the entrepreneurial efforts of their female citizens.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1182
https://f1000research.com/articles/13-1181/v1	09 Oct 24	{ "type": "Research Article", "title": "Uncovering etiologic genes through whole exome sequencing in pediatric epilepsy: A case series from Thailand", "authors": [ "Khanittha Khusiwilai", "Kitiwan Rojnueangnit", "Sukita Puttamanee", "Aphirak Mekmangkonthong", "Sudathip Paticheep", "Kitiwan Rojnueangnit", "Sukita Puttamanee", "Aphirak Mekmangkonthong", "Sudathip Paticheep" ], "abstract": "Introduction Developmental and epileptic encephalopathy (DEE) is characterized by seizures that are difficult to control for a long time and affect development in children who are previously normal or delayed. Therefore, children with DEE should be diagnosed promptly because certain types of the disease respond well to specific medications. In developing countries with limited universal coverage for whole exome sequencing (WES), identifying key clinical features in this patient group will help us make more accurate selections for investigations. The purpose of this study was to determine the prevalence of WES and its common clinical features in children with epileptic encephalopathy.\n\nMethods Ten volunteers aged 0-15 years were diagnosed with epilepsy with two or more symptoms of drug-resistant epilepsy, developmental delays, and abnormal nervous system/or dysmorphic features, and their electroencephalogram (EEG) showed abnormal background or specific patterns of epileptiform discharges. These were subjected to WES for the standard > 400 genes in the epilepsy panel.\n\nResults The established diagnosis was 4/10. Two known pathogenic variants, SCN2A and PCDH19. Two novel pathological variants, CHD2 and SCN1A. These are drug-resistant epilepsy, which is initially difficult to control and cannot stop antiseizure medications. Out of the 2/4 had moderate to severe intellectual disability. 3/4 had generalized epileptiform discharge activities.\n\nConclusions This study showed a similar detection rate to that of a previous WES study. All the patients had difficult-to-treat epilepsy. For those who have not found abnormalities with the same clinical symptoms, further examinations using other methods should be conducted.", "keywords": [ "Epileptic encephalopathy", "Whole exome sequencing (WES)", "Genetic testing" ], "content": "Introduction\n\nPatients with DEE represent a group of disorders that are characterized by important clinical features. The most common age range for symptoms is birth to late childhood. This group of diseases may cause severe seizures with or without fever (febrile/afebrile status epilepticus), prompting the treating physician to consider a diagnosis. Uncontrolled seizures, including status epilepticus, can occur with full anticonvulsant treatment and care for underlying conditions. Seizures could affect the brain, further beyond the identified cause, resulting in disrupted learning, slowed or regressed mental development, altered mental state, and abnormal behavior. These effects can lead to impaired intelligence and increased abnormal behavior at any age.1 An increasing number of studies have shown that developmental and epileptic encephalopathies are interrelated and have long-term pathological effects on each other. An event may occur before, during, or after a seizure. Although seizures can be controlled, brain function may still decline. There is a possibility of experiencing more seizures that may recur later in life, leading to further regression.1 This group displays specific seizure patterns such as epileptic spasms, myoclonic seizures, generalized tonic seizures, and focal clonic seizures.2–5 A physical examination of the nervous system may reveal abnormal movement, dysmorphic features, and developmental regression. Some individuals have a family history of epilepsy, or siblings with the same disease progression. Electroencephalogram (EEG) displays characteristics such as a disorganized or diffuse slowing background, focal or multifocal epileptiform discharges, and specific epileptiform discharge patterns such as burst suppression or hypsarrhythmia.6 Genetic-related epilepsy should be considered, and diagnosis is necessary to determine the cause based on clinical data.3 Diagnostic tests were available to identify single-gene disorders. On the basis of the patient’s clinical characteristics, such as SCN1A, KCNQ2, and PRRT2 abnormalities were identified. Abnormalities in more than one gene locus, including SCN1A, SCN2A, and SCN1B, are found in some epileptic syndromes, such as Dravet syndrome or Ohtahara (EIEE) syndrome, and are associated with genetic abnormalities in KCNQ2, SCN2A, STXBP1, GABRA1, and CDKL5. However, the same abnormal gene can cause clinical signs of varying severity, such as KCNQ2 in the self-limited familial neonatal-infantile seizure group and SCN1A in generalized epilepsy febrile seizure.7,8 Previous studies in various countries have revealed genetic abnormalities in one out of every four patients through deoxyribonucleic acid (DNA) sequencing testing.3 Although the remaining patients exhibited symptoms, they did not have the expected genetic abnormalities. Numerous studies have attempted to answer this question over the last ten years. There have been methods to simultaneously test many genes at the same time. This sequence is called the next sequence. Genetic testing has become easier and more efficient with the ability to test for multiple genes at once and the use of whole exome sequencing for diagnosing unknown diseases. The cause of these abnormalities was found to be as high as 30-40%.9,10 Exon testing for epilepsy panel genes can identify additional causes of epilepsy.\n\n\nMethods\n\nThis research project number MTU-EC-PE-1-141/64 was conducted by the Declaration of Helsinki and approved by a full board review of The Human Research Ethics Committee of Thammasat University (Medicine) on 13 September 2021, and written informed consent was obtained from all the patients’ guardian. We used descriptive cross-sectional statistics to measure clinically detected rates. All ten participants who presented with at least two subsequent symptoms of epilepsy were admitted to Thammasat Hospital for treatment at the Pediatric Neurology Clinic. The age of the volunteers ranged from newborns to 15 years.\n\n1. Experiment uncontrollably despite receiving adequate treatment with two or more antiseizure medications (ASMs).\n\n2. Exhibit atypical cerebral functioning, such as developmental delays or maladaptive conduct.\n\n3. A neurological assessment revealed any abnormalities and/or identified dysmorphic characteristics.\n\n4. The identified EEG characteristics included encephalopathy, disorganized background, burst suppression, hypsarrhythmia, electrodecrement, multifocal spikes and waves, and hypsarrhythmia.\n\nThe exclusion criteria for volunteers consisted of patients who had been referred for difficult-to-control epilepsy consultation due to brain injury-induced brain tumors and diseases of the nervous system caused by infectious pathogens. All recruited patients or guardians provided written informed consent. The patient’s history, age at seizure onset, clinical characteristics including seizure type, a three-generation pedigree, ASMs, comprehensive physical examination, and dysmorphic features evaluated by the geneticist (K.R.), data electroencephalogram (EEG), and neuroimaging results were recorded if feasible. Blood was collected peripherally from patients and biological parents, if accessible. Genomic DNA was isolated from leukocytes using a Puregene® blood kit. Exome sequencing was performed using the Illumina HiSeq platform (Macrogen, South Korea). All variant annotations were analyzed using a standard protocol (Burrows-Wheeler Alignment tool [BWA]).11 Then, the variants were filtered by a minor allele frequency (MAF) of >0.01 in the database for single nucleotide polymorphisms in the whole 1000 genome data (phase 3). The gene target analysis approach was used for phenotypes based on the Human Phenotype Ontology (HPO) terms12 of epilepsy (HP:0001250). The gene list is presented in the data availability. The classification used for genetic variant interpretation was based on recommendations from the American College of Medical Genetics and Genomics, and the Association for Molecular Pathology criteria for variant classification.13 In silico predictive programs, determining the novelty of variants and determining the supposed evidence of pathogenicity of identified variants were performed using Franklin, Clinvar,gnomAD, and our Thai database Sanger sequencing was performed to confirm the presence of pathogenic and likely pathogenic variants in the patients and their parents. The polymerase chain reaction was used 10 mMol of dNTP-Mix (GeneON®, lot number 101.183) volume 0.5 microliter (uL), 10xTaq buffer (Thermo Scientific®, lot number 00892578) volume 2.5 uL, 5 uM/uL of forward and reverse primer (Macrogen®) volume 1.5 uL per each (sequence of forward and reverse in Supplementary tablexxx), 25 mM MgCl2 (Thermo Scientific, lot number 00892580) volume 1.5 uL, Taq DNA Polymerase recombination (Thermo Scientific, lot number 2667134) volume 0.2 uL, DNA (50 ng/uL) volume 3 uL, and water upto 25 uL per reaction.\n\nThe copy number variants (deletions and duplications) test was additionally performed in patients with severe and uncontrolled epilepsy with negative sequencing results, using the next-generation technique (PacBio sequencing).\n\n\nResults\n\nParticipating in this research are ten volunteers who meet the inclusion criteria. These patients included seven males and three females. Upon enrollment, their ages ranged from 10 months to 10 years and 9 months with a median age of 70 months. Every individual is referred to a pediatric neurology clinic on account of their primary ailments, which consist of seizures that are uncontrollable and have developmental delays. The age of seizure onset ranged from 3 months to 10 years and 9 months, with a median of 11 months. We report the clinical symptoms and main findings of each patient and summarize their clinical characteristics in Table 1.\n\nClinical features, forms of seizures, and preliminary significant neuroinvestigations.\n\nA 10-month-old boy’s preterm and perinatal period are comparatively typical unless the baby is delivered at 35 weeks of gestation, and there are no major health complications. Neither epilepsy nor developmental delay affected any family member. Uncontrollable seizures and global developmental delay led to a referral to our hospital. Upon awakening, there were many clusters in both arms and during staring. A hypsarrhythmic pattern and burst suppression were observed on the electroencephalogram (EEG). The first ASMs prescribed were prednisolone, vigabatrin, and phenobarbs; while his seizures decreased somewhat, they still occurred on occasion. Due to his positive HLA-B1502 status, phenytoin and carbamazepine could not be administered to him. During this period, his plasma amino acid levels and brain magnetic resonance imaging (MRI) findings remained normal.\n\nA 2-year and 10-month-old female child, the only child born at full term and in the family, had no history of epilepsy or developmental delay. At 3 months of age, she presented with left arm dystonia and focal tonic posture while awake. Her video EEG revealed multifocal epileptiform discharges, a diffuse slowing background, and electroclinical seizures accompanying her clinical symptoms. As a result, her physician began treating her epilepsy with phenobarb. There were no lesions in the basal ganglia or any other regions of the brain on MRI.\n\nAn almost 4–year–old-male, experienced a seizure at 2 years of age. His seizure type was a blank space, followed by a generalized tonic seizure. Slowing background and multifocal epileptiform activity were detected on EEG. Following a seizure, his overall development regressed, with language development being particularly compromised. By augmenting the patient’s prior phenobarb dosage with topiramate, his seizures significantly improved.\n\nA 5-year and 9-month-old male was diagnosed with delayed development and epilepsy at 10 months of age. The patient had a history of recurrent pneumonia. Over that period, we assumed that his seizures were caused by hypoxia. However, the patient slightly improved after supportive treatment and controlled seizures. He presented with new-onset multiple episodes of atonic seizures upon awakening. His EEG evolved from diffuse slowing to burst suppression, paroxysmal fast activities, and bifrontal slowing. Computed Tomography of the brain was unremarkable.\n\nA 3-year-old male child had delayed development, abnormal movement, and myoclonic seizure when he was going asleep at 8 months of age. The patient did not have any unusual coloration or systemic involvement. He exhibited hypsarrhythmia and multifocal epileptiform discharges on the EEG. Prednisolone and vigabatrin did not stop his seizures. Brain magnetic resonance imaging showed no abnormalities. He showed slight improvement with numerous ASMs. However, the patient experienced intermittent seizures that sometimes occurred in clusters.\n\nA 10-year-old girl with low birth weight was born at 35 weeks of gestation. She presented with intellectual disabilities and began to experience seizures. She also had aggressive conduct and behavioral problems. Her seizure type was a generalized tonic-clonic seizure that was initially difficult to control with valproic acid and topiramate. Generalized epileptiform discharge with photoparoxysmal activity was observed on EEG.\n\nAn almost 7-year-old male, who has seizure onset at 6 months of age. He had multiple episodes of a cluster of brief generalized tonic seizures that occurred during febrile illness. Electroencephalography (EEG) showed mild diffuse slowing background. At the time of enrollment, the seizures were partially controlled by multiple ASMs. He also had cognitive and learning problems.\n\nA 9-year-old male had wide anterior teeth and had been diagnosed with global developmental delay (GDD) and epilepsy since the age of 5 years. Initially, his seizures were difficult to control, and EEG showed burst suppression and a slowing background. Later on, his cognition did not worsen but did not improve despite stopping the seizures.\n\nA girl who was 7 years and 9 months old with normal intellectual ability came in because she had multiple febrile seizures since the age of 1 year. After she turned 5 years old, she still had fevers that caused short generalized tonic seizures, while valproic acid was being lowered. Adding Levetiracetam to her medication stopped her seizures. However, after two years of seizure remission, she always had a seizure when she had fever in the first six months of stopping ASM.\n\nA boy aged 7 years and 3 months was diagnosed with epilepsy, delayed development, especially in language, and aggressive behavior. His mother’s younger sister has intellectual disabilities. The results of the metabolic lab, thyroid function test, and CGG copy numbers were all normal. The brain on MRI was also normal. A generalized tonic-clonic seizure is present, and it is controlled by topiramate. Multifocal epileptiform activity was observed on the EEG\n\nWe conducted Whole Exome Sequencing (WES) on all patients, followed by Sanger sequencing, to confirm the presence of pathogenic and likely pathogenic variants in our patients and their parents, if available. We identified four pathogenic variants: SCN2A (Patient no. 1) (Figure 1a), CHD2 (Patient no. 6) (Figure 1b), SCN1A (Patient no. 7) (Figure 1c), and PCHD19 (Patient no. 9) (Figure 1d). Sadly, undetected pathologic variants were observed in patients no. 2, no. 3, no. 4, no. 5, no. 8, and no. 10. Sanger sequencing results are shown in Figure 1. However, due to epileptic spasms, global developmental delay (GDD), and abnormal EEG in Patient no. 5, we also performed copy number variant (deletions and duplications) testing using the next-generation technique (PacBio sequencing). Unfortunately, the patient’s results were inconclusive, and this case was classified as a variant of uncertain significance.\n\na: SCN2A (Patient no. 1). b: CHD2 (Patient no. 6). c: SCN1A (Patient no. 7). d: PCHD19 (Patient no. 9).\n\n\nDiscussion\n\nDevelopmental and epileptic encephalopathy is a clinical condition that involves epilepsy and developmental issues. This is the most common reason for consultations in pediatric neurology clinics. The symptoms include uncontrolled seizures, specific seizure types such as epileptic spasm or myoclonic seizure with concomitant developmental delay or regression, intellectual disabilities (ID), autistic features, aggressive mood, behavioral problems, abnormal movement or gait, and dysmorphic features. However, these symptoms are indicative of many diseases and syndromes. In developing countries, resources are limited, and it may not be possible to investigate all possible diseases simultaneously. Our study aimed to find a way to accurately diagnose and provide specific treatments for patients with DEE. Each participant underwent EEG, brain MRI, or CT, as well as basic metabolic, electrolyte, or thyroid function tests based on their symptoms and signs. However, these investigations yielded no significant findings. A small number of volunteers may not be representative samples for the statistical evaluation of the clinical characteristics of this group of diseases. However, we were able to identify pathological variants in 4 of 10 cases. These patients share the same clinical symptoms as those of delayed development, which may not be normal in the age range before a seizure occurs. If uncontrolled seizures occur, learning abilities are affected. Internally, seizures may be somewhat controlled, but their development may not be the same. SCN1A and PCHD19 variants have a similar clinical spectrum that is linked to both febrile seizures and epilepsy. The onset of febrile seizures occurred during infancy in both groups; however, SCN1A tended to occur earlier. Seizure duration may be prolonged in SCN1A, while PCHD19 usually has shorter durations and occurs in clusters of brief durations. However, the incidence of febrile status epilepticus did not differ between the two conditions.\n\nSCN1A can occur in both males and females, whereas PCHD19 related to epilepsy is mostly found in female patients and rarely in male patients with somatic mosaicism. Approximately one-third of PCHD19 patients may have a normal intelligence quotient (IQ), and those affected may range from mild to severe intellectual disability. In contrast, cognition is more severely affected in SCN1A, and there is a rapid worsening of either cognition or motor skills.14–16 Both our patients had clinical spectrums identical to those in previous studies.\n\nSodium channel blockers may cause seizures in some patients with SCN1A. This may be more effective for certain SCN2A variants. Based on a previous study conducted on SCN2A variant subtypes,17 our patient with de novo SCN2A presented with epileptic spasms that began at the age of 10 months and did not respond to vigabatrin and/or prednisolone treatment. According to the categorization of previous studies, our patient falls under the infantile epileptic encephalopathy onset category, with an onset period of > 3 months. This group is associated with de novo loss-of-function (LOF) missense, protein-truncating, and splice site variants or missense variants with mixed gain-of-function (GOF) and LOF characteristics.17,18 This might be due to the poor response to sodium channel blockers. However, another study found that in 50% of SCN2A patients in this age group, seizure onset was improved by oxcarbazepine.19 Our patient seemed to improve slightly after receiving sodium channel blockers (lamotrigine and topiramate). In terms of prognosis, most de novo SCN2A cases exhibit developmental delays.18 Patients with seizure onset after 11 months of age may be the furthest non-missense variation group and lead to LOF, which exhibits delayed development or autism, and then has epilepsy in late infancy or early childhood.20 Patients with de novo SCN2A variants usually have poor clinical outcomes and lack specific anti-seizure medications.\n\nSome patients may exhibit delayed development and behavioral issues for a long time before they experience seizures. They may not receive a specific diagnosis until they experience seizures in late childhood. Patient no. 6 was born prematurely at 35 weeks, and her family was made aware of the potential developmental delays associated with this condition. Her seizures began at 10 years of age and were accompanied by aggressive behavior. She experienced generalized tonic seizures and brief absence seizures that were difficult to control. After three months of treatment with valproic acid and topiramate, her behavior returned to baseline, and she stopped experiencing seizures. Interestingly, her interictal EEG showed fewer generalized epileptiform activities, but there were still some photo-paroxysmal activities. In a previous study, CHD2 variants were found to be associated with neurodevelopmental disorders. This disorder should be considered in patients with intellectual disability and/or autism spectrum disorders who have drop attacks, myoclonus, atonic-myoclonic-absence seizure, rapid onset of multiple seizure types associated with generalized spike-wave on EEG, and clinical photosensitivity.21,22 Further studies to better understand genotype and phenotype are necessary for prognosis, specific medication, and genetic counseling. All patients were informed of the gene results by a medical geneticist (Table 2). They followed up and re-evaluated their seizures and other medical problems at the pediatric neurology clinic. Our team provides developmental pediatric consultation, all aspects of physical medicine, and rehabilitation care by physicians and physical therapists.\n\nGene results.\n\n https://gnomad.broadinstitute.org/.\n\n** https://trex.nbt.or.th/home.\n\n\nConclusion\n\nAccording to this study, the detection rate of pathologic variants was similar to that in the previous WES study, standing at 4 out of 10 (40%). All patients in this study had difficult-to-treat epilepsy and required two or more anti-seizure medications. The most common type of seizure observed was generalized seizures. In this type of epilepsy, specific patterns, such as epileptic spasms, atypical absences, and mixed-type seizures, should be considered. Furthermore, EEG patterns such as hypsarrhythmia, burst suppression, generalized epileptiform, and photosensitivity epilepsy should be evaluated. However, neuroimaging findings initially appeared unremarkable in this study. Family history remains an important gathering, and a normal family history does not exclude the possibility of developmental and epileptic encephalopathy. Those who exhibited the same clinical symptoms, but had not been diagnosed with any abnormalities. Consequently, the low detection rate of WES for pathogenic variations is due to its inability to detect non-coding areas, minor deletions or duplications, and repeat expansions.23 Thus, further examinations using other methods should be considered.\n\nWritten informed consent was obtained from all patients’ guardians for this research project (MTU-EC-PE-1-141/64), which was conducted in accordance with the Declaration of Helsinki and approved by a full board review of The Human Research Ethics Committee of Thammasat University (Medicine) on September 13, 2021\n\n\nAuthor contributions\n\nKK designed the conceptualization, project administration, and funding acquisition; wrote the original draft; and reviewed and edited the manuscript. SP. prepares and performs genetic testing under supervision of KR. KR. interpreted the genetic tests, and reviewed and edited the manuscript. All authors contributed to and approved the manuscript.\n\n\nData availability\n\nFigshare: Genome data, epilepsy gene panel, primer for each pathogenic likely pathogenic variant, and Sanger results for Uncovering Etiologic Genes through Whole Exome Sequencing in Pediatric Epilepsy: A Case Series from Thailand. https://doi.org/10.6084/m9.figshare.25930408.v1\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nAccession numbers\n\nAdditional data is available in the Clinvar database, which can be accessed through the following link: https://www.ncbi.nlm.nih.gov/clinvar/.\n\nThe relevant accession numbers are detailed as follows:\n\nClinVar: patient no.1 SCV004848932 NM_001040142.2(SCN2A):c.719C>T (p.Ala240Val); Accession number; VCV000449164.4 http://identifiers.org/clinvar:449164\n\nClinVar: patient no. 6 SCV004848930 NM_001271.4(CHD2):c.1719+1G>A; Accession number; VCV003076079.1 http://identifiers.org/clinvar:3076079\n\nClinVar: patient no. 7 SCV004848931 NM_001165963.4(SCN1A):c.955C>T (p.Gln319Ter); Accession number; VCV003076079.1 http://identifiers.org/clinvar:3076080\n\nClinVar: patient no. 9 SCV004848933 NM_001184880.2(PCDH19):c.1019A>G (p.Asn340Ser); Accession number; VCV000206364.34 http://identifiers.org/clinvar:206364", "appendix": "Acknowledgments\n\nWe would like to thank the Faculty of Medicine, Thammasat University for the research funding and extend our appreciation to the patients and their families and research support staff who participated in the research. We have utilized AI for English language editing to describe our work and have made it comprehensible to everyone.\n\n\nReferences\n\nSpecchio N, Curatolo P: Developmental and epileptic encephalopathies: what we do and do not know. Brain 2021; 144(1): 32–43. PubMed Abstract \| Publisher Full Text\n\nKamien BA, Cardamone M, Lawson JA, et al.: A genetic diagnostic approach to infantile epileptic encephalopathies. J. Clin. Neurosci. 2012; 19(7): 934–941. Publisher Full Text\n\nSymonds JD, Zuberi SM, Stewart K, et al.: Incidence and phenotypes of childhood-onset genetic epilepsies: a prospective population-based national cohort. Brain. 2019; 142(8): 2303–2318. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGul Mert G, Herguner MO, Incecik F, et al.: Risk factors affecting prognosis in infantile spasm. Int. J. Neurosci. 2017; 127(11): 1012–1018. PubMed Abstract \| Publisher Full Text\n\nGursoy S, Ercal D: Diagnostic Approach to Genetic Causes of Early-Onset Epileptic Encephalopathy. J. Child Neurol. 2016; 31(4): 523–532. Publisher Full Text\n\nMastrangelo M, Celato A, Leuzzi V: A diagnostic algorithm for the evaluation of early onset genetic-metabolic epileptic encephalopathies. Eur. J. Paediatr. Neurol. 2012; 16(2): 179–191. PubMed Abstract \| Publisher Full Text\n\nRusso A, Gobbi G: A reflection on the role of genetics in the concept of “epileptic encephalopathy”, as emerged from the most recent ILEA classification of epilepsy. Ital. J. Pediatr. 2020; 46(1): 2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShbarou R, Mikati MA: The Expanding Clinical Spectrum of Genetic Pediatric Epileptic Encephalopathies. Semin. Pediatr. Neurol. 2016; 23(2): 134–142. Publisher Full Text\n\nLazaridis KN, Schahl KA, Cousin MA, et al.: Outcome of Whole Exome Sequencing for Diagnostic Odyssey Cases of an Individualized Medicine Clinic: The Mayo Clinic Experience. Mayo Clin. Proc. 2016; 91(3): 297–307. PubMed Abstract \| Publisher Full Text\n\nBenson KA, White M, Allen NM, et al.: A comparison of genomic diagnostics in adults and children with epilepsy and comorbid intellectual disability. Eur. J. Hum. Genet. 2020; 28(8): 1066–1077. Publisher Full Text\n\nLi H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25(14): 1754–1760. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKohler S, Doelken SC, Mungall CJ, et al.: The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014; 42(Database issue): D966–D974. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRichards S, Aziz N, Bale S, et al.: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 2015; 17(5): 405–424. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRagona F, Granata T, Dalla Bernardina B, et al.: Cognitive development in Dravet syndrome: a retrospective, multicenter study of 26 patients. Epilepsia. 2011; 52(2): 386–392. PubMed Abstract \| Publisher Full Text\n\nDepienne C, LeGuern E: PCDH19-related infantile epileptic encephalopathy: an unusual X-linked inheritance disorder. Hum. Mutat. 2012; 33(4): 627–634. PubMed Abstract \| Publisher Full Text\n\nTrivisano M, Pietrafusa N, Ciommo V, et al.: PCDH19-related epilepsy and Dravet Syndrome: Face-off between two early-onset epilepsies with fever sensitivity. Epilepsy Res. 2016; 125: 32–36. PubMed Abstract \| Publisher Full Text\n\nReynolds C, King MD, Gorman KM: The phenotypic spectrum of SCN2A-related epilepsy. Eur. J. Paediatr. Neurol. 2020; 24: 117–122. PubMed Abstract \| Publisher Full Text\n\nWolff M, Johannesen KM, Hedrich UBS, et al.: Genetic and phenotypic heterogeneity suggest therapeutic implications in SCN2A-related disorders. Brain. 2017; 140(5): 1316–1336. PubMed Abstract \| Publisher Full Text\n\nZeng Q, Yang Y, Duan J, et al.: SCN2A-Related Epilepsy: The Phenotypic Spectrum, Treatment and Prognosis. Front. Mol. Neurosci. 2022; 15: 809951. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLauxmann S, Verbeek NE, Liu Y, et al.: Relationship of electrophysiological dysfunction and clinical severity in SCN2A-related epilepsies. Hum. Mutat. 2018; 39(12): 1942–1956. PubMed Abstract \| Publisher Full Text\n\nCarvill GL, Mefford HC: CHD2-Related Neurodevelopmental Disorders.Adam MP, Feldman J, Mirzaa GM, et al., editors. GeneReviews® Seattle (WA): University of Washington, Seattle; 2015 Dec 10 [Updated 2021 Jan 21]; 1993–2024. Bookshelf. Reference Source\n\nBernardo P, Galletta D, Iasevoli F, et al.: CHD2 mutations: Only epilepsy? Description of cognitive and behavioral profile in a case with a new mutation. Seizure 2017; 51: 186–189. PubMed Abstract \| Publisher Full Text\n\nSadat R, Emrick L: Genetic Testing and Counseling and Child Neurology. Neurol. Clin. 2021; 39(3): 705–717. Publisher Full Text" }	[ { "id": "334762", "date": "12 Nov 2024", "name": "Vorasith Siripornpanich", "expertise": [ "Reviewer Expertise Neuroscience", "Spectral analysis of EEG", "Event-related potential", "Pathogenesis of CNS diseases", "Cognitive functions" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 and well-written manuscript, I can understand the key information and things which authors want to present, however, few correction may improve the quality of this manuscript.\n1. Provide more information on the DEE including the epidemiology profile (such as prevalence), the criteria for diagnosis and epileptic syndromes belong to this group, as well as overall prognosis.\n2. Provide the information about knowing the causative gene in epileptic patients can lead to better treatment option (such as selection of appropriate antiepileptic drug) and disease prognosis. This is an important issue to show the benefit of your work, not only to know, but also can help in patient's care.\n3. Emphasize the benefits of whole exome sequencing, compare to other genetic testing. Why do you select this technique for your work.\n4. In patient 8, apart from wide anterior teeth, please describe other dysmorphic features for him (if any), if no other dysmorphism, please also mention.\n5. Please revise the conclusion, there is too much information in this section, please emphasize only the key information of your work which will lead to apply this knowledge in caring of epileptic patient as well as provide more information on the further study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "12895", "date": "11 Dec 2024", "name": "KHANITTHA KHUSIWILAI", "role": "Author Response", "response": "I sincerely appreciate all of your valuable suggestions. Thank you for your insights. We are a little behind schedule while we wait for additional reviewers to provide their insights, but we are still hopeful. In the meantime, we have addressed your question. Our co-author, Kittiwan, an expert in genetics, suggested that KBG syndrome might be involved in patient no. 8 based on observed anomalies, including widely spaced and enormous anterior teeth. Whole-exome sequencing (WES) offers significant advantages for diagnosing and managing epileptic encephalopathy. As noted in our paper, WES can identify pathogenic variants in many patients, leading to precise genetic diagnoses that facilitate personalized treatment. Additionally, secondary gain helps differentiate diseases with similar clinical features. We will incorporate the proposed in the revised version simultaneously, after being guided by the valuable insights from you and the other reviewers." }, { "c_id": "13031", "date": "28 Dec 2024", "name": "KHANITTHA KHUSIWILAI", "role": "Author Response", "response": "We would like to respond to question three as follows: The advantage of whole exome sequencing (WES) compared to single-gene testing is its ability to analyze multiple genes simultaneously. This is beneficial because clinical symptoms of epilepsy may not specifically indicate a single gene. Therefore, next-generation sequencing (NGS) techniques are more appropriate for diagnosing diseases caused by multiple genes and/or several exons per gene. WES hole Exome Sequencing (WES) Within the different NGS platforms, WES is more cost-effective in the context of Thailand. This is because it will provide a comprehensive analysis by sequencing all the protein-coding regions (exons), which can be conducted even with a limited number of patients without the need to design a gene panel, which may not be cost-effective when there are only a few cases. Additionally, gene panels need to be updated when new disease-causing genes are discovered. Although exons make up only about 1-2% of the total genome, they contain the majority of disease-causing mutations. On the other hand, whole genome sequencing (WGS) offers greater coverage compared with WES. However, it generates an enormous amount of genetic data for analysis, which makes it more expensive and time-consuming to process and interpret such vast amounts of information. We now have more guidance from the second reviewer. We will take care of the issue right away and correct it in the next version." } ] }, { "id": "344647", "date": "19 Dec 2024", "name": "Tun Jao", "expertise": [ "Reviewer Expertise Clinical neurology", "adult epilepsy", "consciousness", "brain networks" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 involved 10 subjects aged 0-15 years with drug-resistant epilepsy and developmental delays despite anti-seizure medications. Whole exome sequencing (WES) was performed with peripheral blood samples, yielding positive results in 4 subjects (SCN2A, PCDH19, CHD2, SCN1A). The 40% detection rate aligns with existing literature, though the sample size is small. Despite being on multiple medications, genomic findings did not seem to change treatment strategies. The study concludes that genomic tests should be considered for patients with significant symptoms but no clear brain imaging abnormalities.\n(1) Is the work clearly and accurately presented and does it cite the current literature? Partly. The entire article is written in a narrative style; some sentences need clarification for the audience to better understand. Here are some examples (non-exhaustive list):\nAbstract/ Introduction: “The purpose of this study was to determine the prevalence of WES”, it should be “The purpose of this study was to determine the prevalence of genetic variants of ... using WES”. Methods: “Experiment uncontrollably” should be “Experience uncontrollable seizures”. Methods: “(sequence of forward and reverse in Supplementary table xxx)”, xxx should be specified.\n\n(2) Is the study design appropriate and is the work technically sound? Partly. This study offers genetic information about a small patient population. It provides an initial understanding of the clinical situation in the specified medical institution.\n(3) Are sufficient details of methods and analysis provided to allow replication by others? Yes. The authors list the genetic test panels and brands.\n(4) If applicable, is the statistical analysis and its interpretation appropriate? Not applicable. This study involves a single group and employs descriptive analysis.\n(5) Are all the source data underlying the results available to ensure full reproducibility? Yes. The authors provide sources from databases.\n(6) Are the conclusions drawn adequately supported by the results? Partly. The authors recommended WES for patients with significant symptoms but no clear brain structure abnormalities. The article would benefit from discussing a clinical management flowchart and linking genetic variants to treatment options.\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": [ { "c_id": "13030", "date": "30 Dec 2024", "name": "KHANITTHA KHUSIWILAI", "role": "Author Response", "response": "Your kind and helpful advice regarding clinical application and language is greatly appreciated. We will promptly address the problem and fix it in the updated version." } ] }, { "id": "344651", "date": "27 Dec 2024", "name": "Yagoub Adam", "expertise": [ "Reviewer Expertise Bioinformatics", "Computational Biology", "System Biology", "GWAS", "post GWAS analysis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors aimed to investigate the genetic basis of epilepsy by performing whole exome sequencing on ten volunteers diagnosed with the condition. Although the sample size is small, they reported interesting findings that warrant validation in a larger study. The manuscript is well-written, using scientific language that is easy to understand regarding the methods and results. However, as noted in the comments above, a few additional details should be included to engage a broader audience.\nPlease extend the introduction to include additional details regarding the genetic basis of epilepsy. The authors mentioned several genes that are targeted for sequencing to aid in diagnosis, including SCN1A, KCNQ2, PRRT2, SCN2A, STXBP1, GABRA1, and CDKL5. I recommend that the authors present these genes in a table with additional information for each gene. This table should cover aspects such as the Online Mendelian Inheritance in Man (OMIM) terms related to epilepsy, gene annotations, the functions of the coded proteins, common mutation types associated with epilepsy, and any recommended treatments, if applicable. Additionally, the authors should provide the current of epilepsy status, including the available genetic diagnosis, in Thailand. The authors state that \"all variant annotations were analyzed using a standard protocol (Burrows-Wheeler Alignment tool [BWA]).\" However, it is essential to clarify that BWA is a mapping tool typically used within a variant calling pipeline. Therefore, the authors should provide further details about the variant calling pipeline used in this study. Moreover, the authors should elaborate on the approach regarding copy number variants in this study. Lastly, it is crucial to specify whether all 10 volunteers belong to the same ethnic group. If they represent multiple ethnic groups, the authors should discuss how ethnic diversity may impact variant calling.\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": "13100", "date": "10 Jan 2025", "name": "KHANITTHA KHUSIWILAI", "role": "Author Response", "response": "We appreciate your feedback, which has improved the interesting features and the usefulness of our work for our readers. We will release a new and revised version in the near future." } ] } ]	1	https://f1000research.com/articles/13-1181
https://f1000research.com/articles/13-920/v1	13 Aug 24	{ "type": "Research Article", "title": "Epigallocatechin-3-gallate (EGCG) reduced expression of Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) and Transforming Growth Factor-β1 (TGF-β1) in visceral pleural tissue cultures of patients with empyema", "authors": [ "Muhammad Riendra", "Nur Indrawaty Lipoeto", "Rauza Sukma Rita", "Masrul Basyar", "Nur Indrawaty Lipoeto", "Rauza Sukma Rita", "Masrul Basyar" ], "abstract": "Abstract*\nBackground Increased expression of signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) and Transforming Growth Factor-β1 (TGF-β1) has been thought to influence the fibrosis process in many tissues. However, increased expression of these two factors has never been assessed in pleural fibrosis. Pleural fibrosis is a disease that usually results from various infectious processes, such as empyema. Fibrosis formation is recently known to be prevented by Epigallocatechin-3-gallate (EGCG), which is the most potent active substance found in Gambir (Uncaria gambir Roxb) leaves. Thus, further research is needed to determine the potential of EGCG to inhibit the process of pleural fibrosis caused by empyema.\n\nMethods An in vitro experimental study with post test-only controlled group was conducted on the pleural tissue of all patients who underwent decortication surgery due to empyema at Dr. M. Djamil Hospital, Padang, Indonesia between March 1st and April 30, 2024. Case samples were obtained by consecutive sampling, and three patients who met the inclusion criteria were obtained. Pleural tissue in each patient was then divided into several groups based on the treatment, namely the control group, 50 μg EGCG administration group, and 100 μg EGCG administration group. We used to determine SCUBE3 and TGF-β1 genes expression. Data were tested using ANOVA and Least Significant Difference (LSD) tests.\n\nResults There were significant differences in the SCUBE3 and TGF-β1 genes expression of 50 μg and 100 μg EGCG administration groups and the control groups in the 2 × 2 cm sample preparation (p=0.002) (p=0.014, respectively). Significant differences in TGF-β1 expression were also found between the groups treated with EGCG 50 μg and 100 μg and the control group in the 1 × 1 cm preparation (p=0.019).\n\nConclusion EGCG can potentially decrease SCUBE3 and TGF-β1 expression in patients with pleural empyema.", "keywords": [ "Key words : Empyema", "Pleural Tissue", "Epigallocatechin-3-gallate", "Transforming Growth Factor-β", "SCUBE3" ], "content": "Introduction\n\nEmpyema is a medical condition characterized by accumulation of pus in the body cavity, particularly within the pleural space surrounding the lungs. The incidence of empyema in the United States is approximately 32,000 cases/year (Bostock et al., 2018). The incidence of empyema continues to grow. According to a retrospective study conducted by Antonio Bobbio and colleagues in 2020, the number of patients with pleural empyema who were treated at the French National Hospital from 2013 to 2017 tended to increase. Bobbio found that the average incidence of empyema in 2013 was approximately 7.15 cases in 100,000 population and increased to 7.75 cases in 100,000 population in 2017 (Bobbio et al., 2021).\n\nThere is no clear data on the prevalence of empyema in Indonesia. However, based on the theory that empyema is a complication that accompanies pneumonia, it can be said that the development of pneumonia in Indonesia can be used as a benchmark to estimate the possible development of empyema. The prevalence of pneumonia based on the diagnosis of health workers in Indonesia according to Riskesdas 2018 increased from the previous year, which was 2.0%. Based on 2018 Riskesdas data, the prevalence of pneumonia in West Sumatra Province in 2018 was 1.7%, which increased from 1.4% in 2007. The percentage was calculated based on the number of cases per total population in the same age range (Kemenkes RI, 2018).\n\nInflammation caused by infection in the pleural space triggers a cascade of immune responses including the release of inflammatory cytokines and growth factors. These immune responses can stimulate the activation and proliferation of fibroblasts, which are responsible for producing collagen and other components of the extracellular matrix (Feller-Kopman and Light, 2018).\n\nStudies have shown that Transforming Growth Factor-β1 (TGF-β1) is a key role in the development of fibrosis in various organs, including the pleura. This factor can bind to type II beta receptors (TβR-II) to activate the smad2 and smad3 pathways that play a role in the Mesothelial Mesenchymal Transition (MMT) process. This process converts pleural mesothelial cells into mesenchymal cells that further develop into fibroblast cells. If TGF-B continues to increase, the fibroblasts will turn into myofibroblasts, which are highly contractile cells that play a major role in the production of collagen and other extracellular matrix components, leading to excessive production of collagen and subsequent pleural fibrosis in empyema (Cui and Liu, 2022).\n\nActivation of smad2 and smad3 pathways influenced by Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3). SCUBE3 is an endogenous ligand for the TGF-β1 receptor and is also involved in the regulation of MMT. Additionally, SCUBE3 modulates the activity of BMP-3, further contributing to the development of pleural fibrosis (Tu et al., 2014).\n\nEpigallocatechin-3-gallate (EGCG) is a potent antioxidant and anti-inflammatory compound found in green tea, especially in the gambier leaves (Uncaria gambir Roxb). The plant is commonly found and cultivated in West Sumatera. (Sampurno et al., 2007). EGGC has anti-inflammatory properties that can inhibit the formation of pro-inflammatory cytokines and profibrotic factors in inflammatory tissues (Panji et al., 2021).\n\nHowever, the direct effect of EGCG on the expression of SCUBE3 and TGF-β1 in the context of empyema-induced pleural fibrosis has not been previously reported. This study aimed to examine the effect of EGCG on the expression of SCUBE3 and TGF-β1 in patients with fibrotic pleural empyema.\n\n\nMethods\n\nThis in vitro experimental study with a posttest-only controlled group design was conducted at Dr. M. Djamil Hospital, Padang, Indonesia between March 1st and April 30, 2024. The inclusion criteria in this study were patients who underwent pleural fibrosis decortication surgery due to empyema and were willing to participate in the study by filling out an informed consent sheet. Exclusion criteria in this study were pleural fibrosis patients accompanied by pleural effusion and patients with a history of pleural fibrosis other than due to empyema. Case samples were obtained by consecutive sampling and pleural tissue in each patient was divided into two large groups based on the incubation time, namely, 24 h and 72 h. Each group consisted of samples with 1 × 1 cm and 2 × 2 cm preparations that were administered three treatments, namely the control group, the group with 50 μg EGCG administration, and the group with 100 μg EGCG administration.\n\nTissue culture, EGCG treatment, and examination of SCUBE3 and TGF-β genes expression were carried out at the Biomedical Laboratory of the Faculty of Medicine, University of Andalas (UNAND). Data analysis was performed to determine whether there was a difference in the mean SCUBE3 and TGF-β1 gene expression between groups.\n\nSCUBE3 and TGF-β1 cDNA were synthesized using a synthesis kit (Thermo Fisher Scientific, Vilnius, Lithuania). After cDNA synthesis was completed, RT-PCR was performed using gene primers in accordance with the design and temperature optimization using an Applied Biosystems Veriti 96 PCR Thermalcycler machine (PCR gradient) and Thermalcycler PCR PRD Flex PCR System. The primary outcomes were changes in SCUBE3 and TGF-β1 gene expression. The secondary outcome was the prevention of the development of fibrosis in the pleural tissue.\n\nThe data normality test uses the Shapiro Wilk test to determine the normality of the data. If the data were normally distributed, then proceed with the Levene test to test the homogeneity of the data. If the data were normally distributed and homogeneous, it was continued with the ANOVA test. This test was conducted to assess whether there was a difference in the mean expression of SCUBE3 and TGF-β1 between all groups. A multiple comparison test or Least Significant Difference (LSD) was conducted after the ANOVA test to compare the expression of SCUBE3 and TGF-β1 in one group and another. If the data were not normally distributed and not homogeneous, Kruskal Wallis and Mann Whitney tests were performed.\n\n\nResults\n\nAfter monitoring all patients who underwent decortication surgery for two months, four patients met the inclusion criteria. Of the four samples, three samples were found to have viable pleural tissue for study.\n\nThe results of the Saphiro-Wilk–Wilk normality test in each group indicated that the data were normally distributed. The Levane homogeneity test was then performed, and the results demonstrated that the data were homogenous. Analysis of variance (ANOVA) and least significant difference (LSD) tests were run as the data were normally distributed and homogenous.\n\nThe results of the ANOVA test showed that there were no significant differences in all groups of 1×1 cm and 2×2 cm preparations (p=0.113) (p=0.678), respectively (Figures 1, 2). As for differences between groups, LSD analysis showed that there was a significant difference between the control with 0 hours incubation and the control with 24 hours incubation in the 1×1 cm preparations (p=0.025) (Figure 1).\n\nNotes: Significance values in all groups based on ANOVA test (p=0.113); “a” sign indicate significant differences between groups based on LSD comparison test (p<0.05), a=0.025.\n\nNotes: Significance values in all groups based on ANOVA test (p=0.678).\n\nIn samples incubated for 72 hours, the ANOVA test showed that there was no significant difference in the 1×1 cm preparation group (p=0.443) (Figure 3). A significant relationship was observed in the 2×2 cm preparation group (p=0.002) (Figure 4). LSD test showed a significant difference between the control with 0 hour incubation and the groups administered EGCG 50 μg and 100 μg in the 2×2 cm preparation (p=0.002) (p=0.001) respectively (Figure 4). Significant differences were also found between the control with 72 hours incubation and the groups administered EGCG 50 μg and 100 μg in 2×2 preparations (p=0.041) (p=0.008) respectively (Figure 4).\n\nNotes: Significance values in all groups based on ANOVA test (p=0.443).\n\nNotes: Significance in all groups based on ANOVA test (p=0.002); different “a,b,c”,…. indicate significant differences between groups based on LSD comparison test (p<0.05), SD: Standard Deviation, a=0.002, b=0.001, c=0.041, d=0.008.\n\nThe ANOVA test showed a significant relationship in the 1×1 cm preparation group (p=0.019) (Figure 5) and there was no significant relationship in the 2×2 preparation group (p=0.375) (Figure 6) LSD test showed significant differences between the control with 0 hours incubation and the control with 24 hours incubation (p=0.003) (Figure 5). Significant differences were also observed between the control group with 24 hours incubation and the group administered EGCG 50 μg and 100 μg in 1×1 cm preparation (p=0.016), (p=0.035) respectively (Figure 5).\n\nNotes: Significant values in all groups based on ANOVA test (p=0.019); different a,b,c,…. indicate significant differences between groups based on LSD comparison test (p < 0.05), SD: Standard Deviation, a=0.003, b=0.016, c=0.035.\n\nNotes: Significance values in all groups based on ANOVA test (p=0.375).\n\nThe ANOVA test showed there was no significant relationship in the group 1×1 cm preparation (p=0.65) (Figure 7). A significant relationship was observed in the 2×2 cm preparation group (p=0.014) (Figure 8). LSD test showed significant differences between the control with 0 hours incubation and the groups administered EGCG 50 μg and 100 μg in 2×2 preparations (p=0.005) respectively (Figure 8).\n\nNotes: Significance values in all groups based on ANOVA test (p=0.65).\n\nNotes: Significant values in all groups based on ANOVA test (p=0.014); different a,b,c,…. indicate significant differences between groups based on LSD comparison test (p<0.05), SD: Standard Deviation, a,b = 0.005.\n\n\nDiscussion\n\nSeveral studies have shown that SCUBE3 is associated with the development of several human cancers. Several studies have found an association between SCUBE3 and early stage lung cancer (Chou et al., 2013), osteosarcoma (Liang et al., 2015), liver cancer (Xu et al., 2022), breast cancer (Shen et al., 2024), and the tooth development phase (Huo et al., 2021). Based on these studies, it is possible that SCUBE3 expression can also increase in other types of diseases, such as inflammatory diseases caused by empyema infection.\n\nTo the best of our knowledge, research on SCUBE3 expression in patients with empyema has not been conducted. Several studies have shown that empyema indirectly affects SCUBE3 expression. This began with a study conducted by Fiorelli in 2016, who found that pleural fluid levels of MMP-1, MMP-8, and MMP-9 were higher in patients with empyema parapneumonic effusions. MMP-2 levels were higher in patients with effusion but without empyema (Fiorelli et al., 2016).\n\nRegarding its relationship with SCUBE3, research conducted by Qin in 2021 showed that MMP-2 and MMP-9 are proteins known to show the highest correlation with SCUBE3. This research supports the finding that empyema patients with increased levels of MMP-2 and MMP-9 also show an increase in the expression of SCUBE3 (Huo et al., 2021). It is also possible that MMP-1 and MMP-8 which are also widely secreted in empyema patients can also be related to SCUBE3, this can be material for future research. The findings of this study, which revealed an increase in SCUBE3 expression in pleural samples of empyema patients after 24 hours of incubation, may be supported by the findings of the aforementioned studies.\n\nRegarding the effect of EGCG on SCUBE3, no studies have directly analyzed the relationship between the two. However, several studies have discussed the effect of EGCG on MMPs, a protein that is correlated with SCUBE3 (Huo et al., 2021). Research conducted by Garbisa et al. showed that EGCG can suppress the gelatinolytic activity of MMP2 and MMP9 (Garbisa et al., 2001). An explanation of this process was explained in Maeda-Yamamoto’s study which found that EGCG inhibited phosphorylation of extracellular signal-regulated kinase 1/2 (ERK) and suppression of p38 activity which is required for the upregulation of MMP9 (Maeda-Yamamoto et al., 1999).\n\nThese findings suggest that the suppression of ERK phosphorylation by EGCG is involved in the decrease in MMP2 and MMP9 mRNA expression. Similar results were obtained by Cheng-hung and colleagues, who found that EGCG also reduced ERK phosphorylation and the levels of AP-1 and Sp1, leading to the downregulation of MMP2 and MMP9 (Chou et al., 2013).\n\nThe decreased expression of MMP2 and MMP9, which are proteins that correlate with SCUBE3, suggests that the decreased expression of MMP2 and MMP9 can also reduce the expression of SCUBE3. This supports the results obtained in this study, where researchers found that samples given EGCG at a concentration of 50 μg or 100 μg had a lower SCUBE3 expression than the control sample. This study has limitations because it did not assess the expression of MMP2 and MMP9; therefore, this can be used as a suggestion for future research.\n\nThe increase in TGF-β1 expression in pleural control samples from empyema patients in this study is in line with the findings of several previous studies. Research conducted by Scott et al. in 2003 on rabbit-induced empyema found that there was an increase in TGF-β1 concentration in the pleural fluid of mice (Sasse et al., 2003). One year later this research was supported by Craig and friends who found that intrapleural injection of anti-TGF-β1 in the pleura of mice induced by empyema was known to inhibit the development of empyema and significantly reduce the process of rabbit pleural fibrosis (Kunz et al., 2004).\n\nThe opposite result was found by Samanta and colleagues in 2018, who observed an increase in TGF-β1 levels in mice with induced pleural empyema. The study found no significant difference in TGF-β1 concentration between the experimental and control groups. However, they found a significant decrease in TGF-β1 levels between 12 and 24 h after bacterial inoculation (da Silva et al., 2018).\n\nDifferences in research results may be due to differences in sample types and research objects. Research conducted by Scott and Craig examined the concentration of TGF-β1 in rabbit pleural fluid and Samanta examined the concentration in mouse pleural fluid. Meanwhile, this study used human pleural tissue to observe the presence of TGF-β1 expression. The difference in sample types between pleural tissue in both humans and experimental animals may have affected the results obtained, although there are studies that show that there are highly homologous TGF-β1 amino acid sequences among mammalian species (Terrell et al., 1993).\n\nWe speculate that the increased expression of TGF-β1 in pleural tissue in this study occurred because of inflammation caused by empyema infection. This is based on the finding of TGF-β1 in mesothelial cells (Gerwin et al., 1987) alveolar macrophages (Assoian et al., 1987), lymphocytes, fibroblasts (Awad et al., 1998) and inflammatory cells in the stimulated pleural fluid. All these cell types are present in the visceral pleura and in some inflammatory exudates during early fibrotic formation in empyema (Martin et al., 2000). Previous studies that examined the relationship between TGF-β1 and pleural disease also suggested that the elevated TGF-β1 in pleural fluid is produced by inflammatory cells (Lee and Lane, 2001).\n\nTo the best of our knowledge, no study has discussed the effect of EGCG on TGF-β1 in the pleural tissue. Research on this topic is often focused on lung fibrosis and cancer. For example, research conducted by Sriram and colleagues on lung fibrosis in bleomycin-induced mice showed that EGCG can inhibit fibroblast activation and collagen accumulation by inhibiting TGF-β1 expression. Based on these results, EGCG is considered to be an effective therapy for lung fibrosis. In an in vitro study, Sriram and colleagues also revealed that EGCG was able to reverse TGF-β1 induced proliferation and activation of fibroblasts (Sriram et al., 2015).\n\nThe same study was conducted by Tsai et al. in a rat lung fibrosis model. Tsai showed that EGCG decreased TGF-β1 expression, MMP-2, and MMP-9 levels, and also had anti-fibrotic effects. This study also found that EGCG reduced mortality; improved lung histological changes; reduced serum levels of TGF-β1, IL-6, IL-10, and TNFα; and reduced collagen deposition and fibroblast proliferation (Tsai et al., 2019).\n\nAlthough the two studies were only on lung fibrosis, they support the results of this study, which showed that there was a decrease in TGF-β1 expression in the pleura of patients given EGCG as much as 50 μg and 100 μg EGCG in the first 72 hours of incubation. A possible mechanism to explain the inhibitory effect of EGCG on TGF-β1 activation is the suppression of various TGF-β1 activators such as inflammatory cytokines, MMPs, macrophages, and other inflammatory cells (Sriram et al., 2009). The authors also assume that such a mechanism is also involved in the reduction of TGF-β1 expression in pleural tissue.\n\n\nConclusion\n\nIn Summary, our research indicated that EGCG has the potential to lower SCUBE3 and TGF-β1 expression in patients with pleural empyema. This discovery might have applications in EGCG treatment to prevent pleural fibrosis in patients with empyema in the future.\n\nThe research was approved by the Universitas Andalas Ethical Clearance Committee (Protocol number: DP.04.03/D.XVI.XI/26/2024), and the gatekeeper’s consent letters were provided by Dr. M. Djamil of the Teaching Hospital on January 9, 2024 and is valid until January 2025. This research has been declared to be ethically appropriate in accordance to 7 (seven) WHO 2011 Standards, 1) Social values, 2) Scientific Values, 3) Equitable Assessment and Benefits, 4) Risks, 5) Persuasion/Exploitation, 6) Confidentiality and Privacy, and 7) Informed Consent, referring to the 2016 CIOMS Guidelines. This is as indicated by the fulfilment of the indicators of each standard. All the participants provided written informed consent.", "appendix": "Data availability\n\nZenodo: [Bar Charts of the Analysis of SCUBE3 and TGF-B Gene Expression]. https://doi.org/10.5281/zenodo.12716059 (Riendra et al., 2024a).\n\nThis project contains the following underlying data:\n\n• Mean SCUBE3 Gene Expression in 1×1 cm Preparation of Pleural Tissue with 24 Hours Incubation Period\n\n• Mean SCUBE3 Gene Expression in 2×2 cm Preparation of Pleural Tissue with 24 Hours Incubation Period\n\n• Mean SCUBE3 Gene Expression in 1×1 cm Preparation of Pleural Tissue with 72 Hours Incubation Period\n\n• Mean SCUBE3 Gene Expression in 2×2 cm Preparation of Pleural Tissue with 72 Hours Incubation Period\n\n• Mean TGF-β1 Gene Expression in 1×1 cm Preparation of Pleural Tissue with 24 Hours Incubation Period\n\n• Mean TGF-β1 Gene Expression in 2×2 cm Preparation of Pleural Tissue with 24 Hours Incubation Period\n\n• Mean TGF-β1 Gene Expression in 1×1 cm Preparation of Pleural Tissue with 72 Hours Incubation Period\n\n• Mean TGF-β1 Gene Expression in 2×2 cm Preparation of Pleural Tissue with 72 Hours Incubation Period\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: [Raw Data of Polymerase Chain Reaction (RT-PCR) results of SCUBE3 and TGF-B expression], https://doi.org/10.5281/zenodo.12250382 (Riendra et al., 2024b).\n\nThis project contains the following underlying data:\n\n• Raw data of the SCUBE3 gene expression\n\n• Raw data of the TGF-β1 gene expression\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank the family and colleagues of Dr. M. Djamil Hospital Padang, who provided support until this study could be carried out. The authors would also like to thank the team of analysts from the Biomedical Laboratory of Andalas University who assisted with the completion of this study.\n\n\nReferences\n\nAssoian RK, Fleurdelys BE, Stevenson HC, et al.: Expression and secretion of type beta transforming growth factor by activated human macrophages. Proc. Natl. Acad. Sci. USA. 1987; 84 (17): 6020–6024. United States. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAwad MR, El-Gamel A, Hasleton P, et al.: Genotypic variation in the transforming growth factor-beta1 gene: association with transforming growth factor-beta1 production, fibrotic lung disease, and graft fibrosis after lung transplantation. Transplantation. 1998; 66(8): 1014–1020. United States. Publisher Full Text\n\nBobbio A, Bouam S, Frenkiel J, et al.: Epidemiology and prognostic factors of pleural empyema, Thorax. BMJ. 2021; 76(11): 1117–1123. Publishing Group Ltd. Publisher Full Text\n\nBostock IC, Sheikh F, Millington TM, et al.: Contemporary outcomes of surgical management of complex thoracic infections. J. Thorac. Dis. 2018; 10(9): 5421–5427. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChou C-H, Cheng Y-F, Siow TY, et al.: SCUBE3 regulation of early lung cancer angiogenesis and metastatic progression. Clin. Exp. Metastasis. 2013; 30(6): 741–752. Netherlands. PubMed Abstract \| Publisher Full Text\n\nCui H, Liu G: DOCK-t(w) o Pleural Fibrosis. Am. J. Respir. Cell Mol. Biol. 2022; 66(2): 117–119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeller-Kopman D, Light R: Pleural Disease. N. Engl. J. Med. 2018; 378(8): 740–751. United States. Publisher Full Text\n\nFiorelli A, Ricci S, Feola A, et al.: Matrix metalloproteinase-9 and tissue inhibitor of metalloproteinase-1 in diagnosis of pleural effusion of malignant origin. Interact. Cardiovasc. Thorac. Surg. 2016; 22(4): 411–418. Oxford Academic. PubMed Abstract \| Publisher Full Text\n\nGarbisa S, Sartor L, Biggin S, et al.: Tumor gelatinases and invasion inhibited by the green tea flavanol epigallocatechin-3-gallate. Cancer. 2001; 91(4): 822–832. United States. PubMed Abstract \| Publisher Full Text\n\nGerwin BI, Lechner JF, Reddel RR, et al.: Comparison of production of transforming growth factor-beta and platelet-derived growth factor by normal human mesothelial cells and mesothelioma cell lines. Cancer Res. 1987; 47(23): 6180–6184. United States. PubMed Abstract \| Publisher Full Text\n\nHuo Q, He X, Li Z, et al.: SCUBE3 serves as an independent poor prognostic factor in breast cancer. Cancer Cell Int. 2021; 21(1): 268. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKemenkes RI: PROFIL KESEHATAN INDONESIA TAHUN 2020.2018.\n\nKunz CR, Jadus MR, Kukes GD, et al.: Intrapleural injection of transforming growth factor-beta antibody inhibits pleural fibrosis in empyema. Chest. 2004; 126(5): 1636–1644. United States. PubMed Abstract \| Publisher Full Text\n\nLee YC, Lane KB: The many faces of transforming growth factor-beta in pleural diseases. Curr. Opin. Pulm. Med. 2001; 7(4): 173–179. United States. PubMed Abstract \| Publisher Full Text\n\nLiang W, Yang C, Peng J, et al.: The Expression of HSPD1, SCUBE3, CXCL14 and Its Relations with the Prognosis in Osteosarcoma. Cell Biochem. Biophys. 2015; 73(3): 763–768. PubMed Abstract \| Publisher Full Text\n\nMaeda-Yamamoto M, Kawahara H, Tahara N, et al.: Effects of tea polyphenols on the invasion and matrix metalloproteinases activities of human fibrosarcoma HT1080 cells. J. Agric. Food Chem. 1999; 47(6): 2350–2354. United States. PubMed Abstract \| Publisher Full Text\n\nMartin M, Lefaix J, Delanian S: TGF-beta1 and radiation fibrosis: a master switch and a specific therapeutic target? Int. J. Radiat. Oncol. Biol. Phys. 2000; 47(2): 277–290. United States. PubMed Abstract \| Publisher Full Text\n\nPanji M, Behmard V, Zare Z, et al.: Suppressing effects of green tea extract and Epigallocatechin-3-gallate (EGCG) on TGF-β- induced Epithelial-to-mesenchymal transition via ROS/Smad signaling in human cervical cancer cells. Gene. 2021; 794: 145774. Publisher Full Text\n\nSampurno KR, Niniek SA, Evie L, et al.: Acuan sediaan herbal. Jakarta: BPOM RI; 2007.\n\nSasse SA, Jadus MR, Kukes GD: Pleural fluid transforming growth factor-beta1 correlates with pleural fibrosis in experimental empyema. Am. J. Respir. Crit. Care Med. 2003; 168(6): 700–705. PubMed Abstract \| Publisher Full Text\n\nShen J, Ma X, Wei Z, et al.: β-catenin/TCF4-induced SCUBE3 upregulation promotes ovarian cancer development via HIF-1 signaling pathway. Mol. Cell. Endocrinol. 2024; 582: 112127. Publisher Full Text\n\nda Silva SS , Peterson GE, Amantéa SL, et al.: Transforming growth factor beta1 (TGF-ß1) levels in a rat model of induced pleural empyema. Acta Cir. Bras. 2018; 33(2): 156–162. PubMed Abstract \| Publisher Full Text\n\nSriram N, Kalayarasan S, Manikandan R, et al.: Epigallocatechin gallate attenuates fibroblast proliferation and excessive collagen production by effectively intervening TGF-β1 signalling. Clin. Exp. Pharmacol. Physiol. 2015; 42(8): 849–859. Australia. PubMed Abstract \| Publisher Full Text\n\nSriram N, Kalayarasan S, Sudhandiran G: Epigallocatechin-3-gallate augments antioxidant activities and inhibits inflammation during bleomycin-induced experimental pulmonary fibrosis through Nrf2-Keap1 signaling. Pulm. Pharmacol. Ther. 2009; 22(3): 221–236. England. PubMed Abstract \| Publisher Full Text\n\nRiendra M, Lipoeto NI, Rita RS, et al.: Bar Chart of the Analysis of the Mean Number of SCUBE3 and TGF-B Expressing Cells in the Treatment Group. Zenodo. 2024a. Publisher Full Text\n\nRiendra M, Lipoeto NI, Rita RS, et al.: Raw Data of Polymerase Chain Reaction (qPCR) results of SCUBE3 and TGF-B expression. [Data set]. Zenodo. 2024b. Publisher Full Text\n\nTerrell TG, Working PK, Chow CP, et al.: Pathology of recombinant human transforming growth factor-beta 1 in rats and rabbits. Int. Rev. Exp. Pathol. 1993; 34: B43–B67. United States. Publisher Full Text\n\nTsai M-J, Chang W-A, Liao S-H, et al.: The Effects of Epigallocatechin Gallate (EGCG) on Pulmonary Fibroblasts of Idiopathic Pulmonary Fibrosis (IPF)-A Next-Generation Sequencing and Bioinformatic Approach. Int. J. Mol. Sci. 2019; 20(8). Switzerland. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTu C-F, Tsao K-C, Lee S-J, et al.: SCUBE3 (signal peptide-CUB-EGF domain-containing protein 3) modulates fibroblast growth factor signaling during fast muscle development. J. Biol. Chem. 2014; 289(27): 18928–18942. United States. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXu P, Luo A, Xiong C, et al.: SCUBE3 downregulation modulates hepatocellular carcinoma by inhibiting CCNE1 via TGFβ/PI3K/AKT/GSK3β pathway. Cancer Cell Int. 2022; 22(1): 1. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "316474", "date": "14 Sep 2024", "name": "Amal Ali El-Koa", "expertise": [ "Reviewer Expertise pulmonology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe review of the original paper entitled “Epigallocatechin-3-gallate (EGCG) reduced expression of Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) and Transforming Growth Factor-β1 (TGF-β1) in visceral pleural tissue cultures of patients with empyema”\nComments: Methods:\nThe sample size is too small.\nComment: Can you mention how the method of sample size calculation?\n\nPreparations used were 1x1cm and 2x2 cm\nComment: Can you mention the explanation of using 2 different preparations?\n\nResults and discussion:\n\nSome results need to be explained as there is some conflict:\n\nRegarding SCURBE3 expression in 1x1 cm preparations (figures 1 and 3)\n\nSignificance between control 0hr and 24 hr, while no significance between controls in 0hr and 72 hrs…..is there any explanation?\n\nRegarding TGF-ß 1 expression in\n\nA significant relationship in the 1×1 cm preparation groups with 24-hour incubation (figure 5) and there was no significant relationship in the 1×1 preparation group with 72-hour incubation (figure 7), while in the 2x2 cm preparation group the reverse occurred in Figure 6 and 8. Can you explain why this occurred?\n\nAdd the limitations of your study.\n\nThe spelling and grammar should be revised.\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?\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": "12518", "date": "09 Oct 2024", "name": "Muhammad Riendra", "role": "Author Response", "response": "Dear Mr. Amal Ali El-Koa Thank you for your willingness to be a reviewer on our research titled “Epigallocatechin-3-gallate (EGCG) reduced expression of Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) and Transforming Growth Factor-β1 (TGF-β1) in visceral pleural tissue cultures of patients with empyema” We appreciate the time and effort that you have dedicated to providing your valuable feedback on our manuscript. We are grateful to the reviewers for their insightful comments on my paper. We have been able to incorporate changes to reflect most of the suggestions provided by the reviewers. We have highlighted the changes within the manuscript. Here is a point-by-point response to the reviewers’ comments and concerns. Comment 1: Can you mention how the method of sample size calculation? Response: In this study, we did not use a sample calculation formula because this research is in vitro experimental study with primary tissue culture from patients. Because resource is human, we calculate sample size using human sample size, in this investigation, we acquired only three patients who met the inclusion criteria. Therefore, we have added the explanation in the methodology section. Comment 2: Can you mention the explanation of using 2 different preparations? Response: There were research indicates that the best preparations size for culturing human pleural mesothelial cells and pleural fibroblasts is 8.5 mm. Therefore, for easier measurement, we standardized it to 1x1 cm. Meanwhile, for the 2x2 cm preparation, we were trying to expand the size to see if a larger size can still serve as a reference for making tissue preparations. Numerous studies indicate that bigger specimen sizes are susceptible to necrosis; however, our findings reveal that tissue samples measuring 2x2 cm did not exhibit necrosis. We suggest that utilizing a 2x2 cm preparation could encourage novel approaches in the examination of pleural tissue collection methodologies. Comment 3: Significance between control 0hr and 24 hr, while no significance between controls in 0hr and 72 hrs…..is there any explanation? Response: You have raised an important point here. In this study, we found a significant difference between the 0-hour incubation control and the 24-hour incubation. However, there was no difference between the 0-hour incubation control sample and the 72-hour incubation. This is possible because increasing of SCUBE3 expression is greater in the control with 24 hours incubation than 72 hour incubation. We have not found literature that specifically discusses the changes of SCUBE3 expression at certain times in pleural tissue culture. But, some study found that gene expression in tissue culture can change over time. Research has demonstrated that gene expression is dynamic and can vary significantly depending on various factors, including the duration of culture, cellular environment, and specific treatments applied. Studies have shown that gene expression profiles can change at different time points during cell culture. For instance, one study observed significant transcriptional changes in cells treated with a carcinogen over time, with specific genes showing increased or decreased expression at various intervals from one hour to eight days post-treatment. (Ohmori et al., 2022) Another study highlighted that the transcriptional profiles of human adipose-derived stem cells differ significantly between freshly isolated cells and those expanded in culture (passage 0 vs. passage 1). This indicates that the process of culturing cells can lead to substantial alterations in gene expression profiles.(Januszyk et al., 2015). Comment 4: A significant relationship in the 1×1 cm preparation groups with 24-hour incubation (figure 5) and there was no significant relationship in the 1×1 preparation group with 72-hour incubation (figure 7), while in the 2x2 cm preparation group the reverse occurred in Figure 6 and 8. Can you explain why this occurred? Response: We found that the 1x1 cm control sample incubated for 24 hours had a higher expression of the TGF-β1 gene compared to the 1x1 cm control sample incubated for 72 hours. This resulted a significant difference between the 0-hour incubation control and the 24-hour incubation control. Researchers suspect that the reason for the significant increase in TGF-β1 expression after 24 hours of incubation is the same as that occurring in SCUBE3 expression. This leads to a new finding where the control samples of tissue culture incubated for 24 hours exhibit greater gene expression than those incubated for 72 hours. This study also found that there is a significant difference in TGF-β1 expression in the 2x2 cm samples incubated for 0 hours compared to the samples treated with 50 µg and 100 µg of EGCG incubated for 72 hours. The reason for this result is that EGCG is capable of reducing TGF-β1 expression by suppressing various TGF-β1 activators such as inflammatory cytokines, MMPs, macrophages, and other inflammatory cells (Sriram et al., 2009). In addition to the factor of EGCG administration, the reduction in TGF-β1 expression in the samples incubated for 72 hours was also lower than in those incubated for 24 hours. The reason for this has been explained previously. Thus, this is what causes the significant difference in the samples treated with 50 µg and 100 µg of EGCG incubated for 72 hours compared to those incubated for 24 hours. Therefore, we have added the details in the discussion section. Comment 5: Add the limitations of your study. Response: Thank you for your reminder to complete this study. We have add some limitations to this study. We will restate the phrase here : “ This study did not explore the presence of other profibrotic factors that could potentially influence the occurrence of pleural fibrosis such as matrixmetalloproteinase-1,2,8, and 9 (MMP-1, MMP-2, MMP-8, and MMP-9). The researchers only studied the effects of EGCG on pleural tissue, it is preferable to perform a comparative trial of the effect of EGCG on the potential fibrosis in pulmonary tissue due to empiema.” In addition to the above comments, all spelling and grammatical errors pointed out by the reviewers have been corrected. We look forward to hearing from you in due time regarding our submission and to respond to any further questions and comments you may have. Sincerely, Muhammad Riendra" } ] } ]	1	https://f1000research.com/articles/13-920
https://f1000research.com/articles/13-1179/v1	09 Oct 24	{ "type": "Research Article", "title": "Mega corruptions in mega projects: Debating the dynamics of dam construction in Ethiopia", "authors": [ "Awol Ali Mohammed" ], "abstract": "Background This study critically examines the dynamics of corruption within Ethiopia’s dam construction projects, focusing on the Grand Ethiopian Renaissance Dam (GERD the Gilgel Gibe series, and Genale Dawa. The research highlights how weak management practices, insufficient oversight, and centralized decision-making, resulting in contribute to inflated costs, project delays, and compromised construction quality. A comprehensive understanding of these issues is crucial for addressing the challenges that impede Ethiopia’s infrastructure development.\n\nMethods A qualitative research approach was employed, integrating both primary and secondary data sources. The study utilized four theoretical frameworks—Principal-Agent Theory, Rent-Seeking Theory, Institutional Theory, and Neo-Patrimonialism—to analyze the structural and behavioral factors enabling corruption in Ethiopia’s dam construction projects.\n\nResults The study found that corruption is largely driven by weak management practices, insufficient oversight, and centralized decision-making. These factors contribute to inflated project costs, significant delays, and compromised construction quality. The lack of transparency and inadequate monitoring exacerbate these issues, leading to inefficient resource use and undermining the projects’ intended benefits. Economic impacts include increased public debt and strained financial resources. Socially, corruption erodes public trust and adversely affects the communities involved. The findings also highlight how information asymmetry and misaligned incentives contribute to corruption, with weak governance structures and informal networks further exacerbating the problem. These issues lead to cost overruns, increased debt, and diminished public confidence, which negatively impacts development outcomes.\n\nConclusions While corruption in Ethiopia’s dam construction projects poses significant challenges, it is not insurmountable. Strengthening legal and regulatory frameworks, enhancing institutional capacity, promoting community participation, and leveraging international cooperation are crucial for mitigating these risks. Recommendations include implementing e-procurement systems, establishing independent oversight bodies, and promoting transparency to ensure these mega projects achieve their intended economic and social benefits.", "keywords": [ "Dam-construction", "Corruption", "Ethiopia", "GERD", "Gilgel-Gibe", "Genale-Dawa" ], "content": "1. Background and context\n\nThe construction of large-scale dams has played a pivotal role in shaping the developmental landscape of many countries. Globally, these mega projects have been instrumental in generating hydroelectric power, ensuring water supply, and providing irrigation for agriculture, among other benefits. In Africa, where economic development and energy security are pressing concerns, dams are seen as crucial infrastructural investments. However, while these projects promise substantial socio-economic benefits, they often come with significant challenges, particularly in the realms of governance and financial management (IWMI, 2023).\n\nMega projects, by their very nature, involve enormous financial resources and complex multi-stakeholder engagements, making them susceptible to mismanagement and corruption. Corruption in dam construction manifests in various forms, from inflated contracts and kickbacks to embezzlement of funds. The consequences of such corruption are far-reaching, leading to cost overruns, delays, and substandard project outcomes. Moreover, the socio-economic implications extend beyond the immediate financial losses, affecting the long-term sustainability and effectiveness of these projects (Mwangi, 2019a, b).\n\nThe Three Gorges Dam in China, one of the largest hydroelectric projects in the world, has been a focal point of global attention for its engineering feats and socio-environmental impacts. However, the project has also been criticized for its lack of transparency, forced relocations, and environmental degradation, highlighting the complexities of managing such large-scale projects (Liu et al., 2016; Wang, 2018). Similarly, the Itaipú Dam, straddling the border between Brazil and Paraguay, is a testament to the potential benefits of hydroelectric power. However, the project has faced allegations of corruption, particularly in the awarding of contracts and the distribution of benefits between the two countries (Aitken & Harrison, 2013). Similarly, The Aswan High Dam in Egypt, a project that transformed the Nile River’s flow and the nation’s agricultural capacity, also experienced significant challenges. These included the displacement of thousands of people and environmental issues, compounded by financial mismanagement and corruption during its construction (Collins, 2002).\n\nThe common thread across these global examples is the susceptibility of large-scale projects to corruption and management inefficiencies. These issues are often exacerbated by the lack of transparency, weak regulatory frameworks, and the complex interactions between multiple stakeholders, including governments, private contractors, and international financiers.\n\nIn Africa, the Akosombo Dam in Ghana, built in the 1960s, was one of the continent’s earliest large-scale hydroelectric projects. While it has been pivotal in providing electricity and supporting industrial growth, the project was plagued by significant cost overruns and socio-economic challenges, including the displacement of communities and environmental degradation (Hart, 1980; Tsikata, 2006). Moreover, he Merowe Dam in Sudan, completed in 2009, is another example where the intended benefits of the project were overshadowed by controversies related to forced evictions, inadequate compensation for displaced populations, and corruption in project management (Verhoeven, 2011). Furthermore, the Kariba Dam, on the border between Zambia and Zimbabwe, is one of the largest man-made lakes in the world. The project has faced its share of financial and management issues, including corruption in the maintenance and upgrade processes, which have raised concerns about the dam’s long-term viability and safety (Scudder, 2010).\n\nIn the African context, the intersection of corruption and management inefficiency is particularly acute. Weak governance structures, limited capacity for oversight, and the influence of political elites often result in projects that are over-budget, delayed, and fail to meet their intended objectives. This, in turn, exacerbates the economic costs, both in terms of direct financial losses and the opportunity costs of delayed or compromised development (Ameyaw & Chan, 2015).\n\nThe political and economic implications of these projects are profound. Corruption and mismanagement not only undermine the potential benefits of dam construction but also erode public trust in governmental and international institutions. The diversion of resources due to corruption affects the overall economic development of the countries involved, leading to increased debt burdens and stunted growth.\n\nThe construction of mega projects, particularly large-scale dams, has become a focal point of economic development and political discourse in many developing nations. Ethiopia’s Grand Ethiopian Renaissance Dam (GERD) epitomizes this phenomenon, representing both a beacon of hope for national development and a source of significant controversy. With the potential to generate over 5,000 megawatts of electricity, the GERD aims to address the acute energy shortages faced by a nation where approximately 54% of the population lacks access to electricity (World Bank, 2021). However, the project has been marred by allegations of corruption, mismanagement, and geopolitical tensions, particularly with downstream nations like Egypt and Sudan, who view the dam as a threat to their water security (Elhance, 2020).\n\nThe literature surrounding mega projects, especially in the context of developing countries, highlights a dual narrative. On one hand, such projects are often lauded for their potential to stimulate economic growth, create jobs, and improve infrastructure. For instance, the GERD is expected to significantly boost Ethiopia’s energy capacity, thereby facilitating industrialization and improving living standards (Alemayehu, 2019). The Ethiopian government has positioned the dam as a cornerstone of its national development strategy, aiming to transform the country into a middle-income economy by 2025 (Federal Democratic Republic of Ethiopia, 2016). On the other hand, scholars have documented the adverse effects associated with these projects, including environmental degradation, displacement of communities, and the entrenchment of corruption within governmental structures.\n\nEthiopia’s ambitious dam construction projects, including the Grand Ethiopian Renaissance Dam (GERD) and the Gilgel Gibe series, are emblematic of the broader trends observed in mega projects across the African continent. While these projects are central to Ethiopia’s development goals, they have been marred by allegations of corruption, financial mismanagement, and political controversies. Understanding the dynamics at play in Ethiopia is crucial for grasping the broader implications of corruption in mega projects, particularly in the context of developing nations.\n\nEthiopia’s landscape of dam construction is dominated by several key projects, each of which has played a role in the nation’s quest for energy security and economic development. The GERD, the largest of these projects, is designed to be a cornerstone of Ethiopia’s energy infrastructure, with the potential to generate 6,450 MW of electricity. However, the project has faced significant delays and cost overruns, with allegations of mismanagement and corruption being central to its challenges (Teshome, 2020).\n\nThe Gilgel Gibe series, including Gilgel Gibe I, II, and III, represents a significant portion of Ethiopia’s hydroelectric capacity. These projects, while successful in increasing the nation’s power generation, have also been marred by issues related to project management, environmental concerns, and financial mismanagement. The Genale Dawa series, although smaller in scale, has similarly faced challenges related to cost overruns and allegations of corruption (Gebre, 2017).\n\nThe management of Ethiopia’s dam projects has been characterized by inefficiencies at various stages, from planning and procurement to construction and operation. These inefficiencies are often compounded by a lack of transparency and accountability, which creates opportunities for corruption. Allegations of corrupt practices, including the misappropriation of funds and bribery in the awarding of contracts, have been reported in connection with several of Ethiopia’s major dam projects (Mulatu, 2021).\n\nThe economic impacts of these issues are substantial. Cost overruns have led to increased national debt and diverted resources away from other critical development needs. Furthermore, delays in project completion have resulted in lost opportunities for economic growth and development, as the anticipated benefits of these projects have been postponed. The financial strain on the Ethiopian economy is further exacerbated by the need to service loans and manage the increased costs associated with these projects (Tesfaye & Gebregziabher, 2018).\n\nDespite the extensive research on dam construction and corruption, there are significant gaps in the literature, particularly concerning the specific dynamics of these issues in the Ethiopian context. Previous studies have often focused on the technical aspects of dam construction or the environmental and social impacts, with limited attention given to the governance and economic implications of corruption. This study seeks to address this gap by providing a comprehensive analysis of how management inefficiencies and corruption interact and affect the outcomes of dam projects in Ethiopia (Muller, 2018). While some studies have addressed the economic impacts of the GERD, few have systematically analyzed the corruption dynamics that have emerged throughout its construction. This oversight is critical, as corruption can undermine project efficacy, lead to financial losses, and exacerbate social inequalities (Transparency International, 2022).\n\nEffective governance is crucial for ensuring that mega projects are managed efficiently and that the risks of corruption are minimized. Transparency, in this context, refers to the openness and accountability of the processes involved in project management, from procurement to execution. The relationship between governance, transparency, and development is particularly pertinent in the context of dam construction, where the stakes are high, both in terms of financial investment and socio-economic outcomes (Kaufmann, 2016).\n\nThe political economy of mega projects, including dam construction, is a complex interplay of political interests, economic incentives, and social impacts. In many cases, mega projects are initiated and driven by political agendas, which can lead to the prioritization of short-term gains over long-term sustainability. This dynamic often results in compromised project management practices and opens the door for corrupt activities. Understanding the political economy of these projects is essential for analyzing the underlying causes of corruption and inefficiency, as well as for developing strategies to mitigate these risks (Flyvbjerg, 2009).\n\nThis study aims to explore the dynamics of dam construction in Ethiopia, focusing on the Grand Ethiopian Renaissance Dam (GERD), the Gilgel Gibe series and Genale Dawa series. Employing a qualitative research approach, the study integrates Principal-Agent Theory, Rent-Seeking Theory, Institutional Theory, and Neo-Patrimonialism to analyze the structural and behavioral factors that enable corruption. It also examines how management inefficiencies contribute to corruption and its subsequent economic impacts. The key research questions guiding this inquiry include: How do management practices in Ethiopia’s dam construction projects facilitate corruption? What are the economic consequences of corruption in these projects? How can governance and transparency be improved to mitigate these risks?\n\nThis study’s significance lies in its potential to contribute new insights to the academic community and inform policy-making processes. By exploring the Ethiopian case within the broader context of global and African experiences, this research will offer a nuanced understanding of the challenges and opportunities associated with dam construction. The findings of this study will be valuable for academics, policymakers, and practitioners involved in the planning, management, and oversight of mega projects, particularly in developing countries. The study’s recommendations will provide a basis for improving governance and transparency in future projects, thereby mitigating the risks of corruption and enhancing the socio-economic benefits of dam construction (Ayee, 2016).\n\nThe implications of this study extend beyond Ethiopia, offering lessons and insights that are applicable to other developing countries facing similar challenges. The research will highlight the importance of strong governance frameworks, transparent processes, and effective management practices in ensuring the success of mega projects. By addressing the root causes of corruption and inefficiency, this study will contribute to the broader goal of sustainable development, where mega projects can achieve their intended benefits without being undermined by corruption and mismanagement (World Bank, 2019).\n\n\n2. Theoretical framework\n\nCorruption in mega projects, particularly in dam construction, is a multifaceted phenomenon that can be examined through various theoretical lenses. Understanding the theoretical underpinnings of corruption helps illuminate the structural and behavioral factors that contribute to corrupt practices in such projects. This section explores four key theories—Principal-Agent Theory, Rent-Seeking Theory, Institutional Theory, and Neo-Patrimonialism—and contextualizes them within the case of dam construction in Ethiopia. These theories provide a comprehensive framework for analyzing how corruption emerges, how it is sustained, and its broader implications for economic development and governance.\n\nPrincipal-Agent Theory provides a foundational understanding of corruption as a consequence of information asymmetry and misaligned incentives between principals (those who delegate authority) and agents (those who exercise authority on behalf of the principals). In this context, principals could be government authorities, donors, or international financial institutions, while agents are the contractors, project managers, and government officials responsible for executing dam construction projects (Eisenhardt, 1989).\n\nIn Ethiopia’s dam construction projects, the Principal-Agent relationship is often characterized by a lack of transparency and accountability, which allows agents to exploit their positions for personal gain. For instance, procurement processes are frequently manipulated, with contracts awarded based on favoritism or bribery rather than merit. This misalignment of incentives is exacerbated by weak monitoring mechanisms, which fail to detect or deter corrupt practices effectively. The agents, motivated by the potential for personal enrichment, may engage in activities that inflate project costs, delay completion, and compromise the quality of construction, all of which have significant economic and social consequences (Rose-Ackerman & Palifka, 2016).\n\nThe Principal-Agent Theory also highlights the importance of institutional checks and balances to mitigate corruption. In the Ethiopian context, the absence of robust auditing processes and the lack of an independent judiciary or anti-corruption body to hold agents accountable perpetuate corrupt practices. Moreover, the complexity of dam construction projects, involving multiple stakeholders and layers of bureaucracy, further complicates oversight and creates additional opportunities for corruption (Eisenhardt, 1989; Banfield, 1975).\n\nRecent studies have underscored the need for stronger governance frameworks to align the interests of principals and agents more closely. Implementing transparent bidding processes, enhancing the capacity of oversight institutions, and fostering a culture of accountability are critical steps toward mitigating corruption in mega projects (Transparency International, 2022). These measures can reduce the opportunities for agents to engage in corrupt behavior, ensuring that the principal’s objectives are more effectively achieved.\n\nRent-Seeking Theory offers a critical perspective on how individuals and organizations attempt to gain economic rents—unearned income derived from manipulating the economic or political environment—through non-productive activities. This theory suggests that corruption arises when actors use their influence to secure benefits, such as government contracts or favorable regulatory conditions, without contributing to productive economic activities (Krueger, 1974).\n\nIn the Ethiopian dam construction context, rent-seeking behavior is pervasive. The large-scale nature of these projects, combined with their strategic importance to national development, creates significant rent-seeking opportunities. Government officials and politically connected contractors often exploit their positions to extract rents through corrupt practices such as bid rigging, price inflation, and kickbacks. These activities lead to the misallocation of resources, where contracts are awarded not to the most qualified bidders but to those willing to engage in corrupt exchanges (Tanzi & Davoodi, 1997).\n\nThe impact of rent-seeking on Ethiopia’s economy is profound. Not only does it result in inflated project costs and substandard construction, but it also diverts resources away from other critical areas of development, such as education and healthcare. Moreover, rent-seeking behavior entrenches inequalities, as those with access to power and influence benefit disproportionately at the expense of the broader population (Khan, 2006).\n\nThe theory also explains why anti-corruption efforts in Ethiopia often face significant resistance. Rent-seeking behavior is deeply embedded in the political and economic fabric of the country, with powerful elites benefiting from the status quo. Efforts to reform the system and reduce corruption threaten these entrenched interests, leading to a lack of political will and effective enforcement (Khan, 2006; Rose-Ackerman & Palifka, 2016). Addressing rent-seeking requires not only technical solutions, such as improving procurement processes and increasing transparency but also a broader commitment to altering the underlying power structures that sustain corrupt practices.\n\nInstitutional Theory provides a broader framework for understanding how the institutional environment shapes behavior, including corruption. It posits that institutions—defined as the formal and informal rules, norms, and practices that guide behavior—play a crucial role in determining the prevalence and nature of corruption (North, 1990).\n\nIn the Ethiopian context, Institutional Theory is particularly relevant given the weak governance structures and the blurred lines between formal regulations and informal practices. The formal institutions governing dam construction projects, such as procurement laws and anti-corruption regulations, are often undermined by informal networks and patronage systems that operate behind the scenes. These informal institutions enable corrupt practices by creating a parallel system of rules that prioritize personal relationships and loyalty over legal and ethical standards (Helmke & Levitsky, 2004).\n\nThe theory also emphasizes the role of social norms in perpetuating corruption. In environments where corruption is normalized or viewed as a necessary means of navigating the system, individuals are more likely to engage in or tolerate corrupt practices. In Ethiopia, the prevalence of corruption in dam construction projects can be partly attributed to the societal acceptance of such practices, particularly in contexts where public sector salaries are low, and opportunities for legitimate economic advancement are limited (March & Olsen, 2008).\n\nAddressing corruption from an institutional perspective requires more than just strengthening formal laws and regulations; it also necessitates changing the underlying social norms and values that sustain corrupt practices. Efforts to reform Ethiopia’s dam construction sector must therefore include initiatives to promote ethical behavior, enhance public awareness of the costs of corruption, and build a culture of integrity across all levels of society (Ostrom, 2005; Johnston, 2014).\n\nNeo-Patrimonialism is a concept that describes a system of governance where formal state structures coexist with, and are often undermined by, informal patron-client networks. In such systems, public officials use their official positions to pursue personal interests, blurring the lines between public and private resources. Corruption in neo-patrimonial systems is systemic, pervasive, and deeply embedded in the political culture (Bratton & van de Walle, 1997).\n\nEthiopia’s dam construction projects are heavily influenced by neo-patrimonial dynamics. The awarding of contracts, the allocation of resources, and the overall management of these projects are often driven by personal relationships, loyalty to political elites, and the need to maintain patronage networks. This system creates a cycle of corruption, where officials prioritize the interests of their patrons over the public good, leading to inefficiencies, inflated costs, and compromised project quality (Chabal & Daloz, 1999).\n\nNeo-Patrimonialism also explains the resilience of corruption in Ethiopia’s dam construction sector. Because the system relies on personal loyalty and the distribution of patronage to maintain political stability, efforts to combat corruption are often undermined by the very actors who benefit from the status quo. Anti-corruption initiatives that threaten to disrupt these networks are likely to face significant resistance, both from within the government and from external stakeholders who benefit from the existing system (Bratton & van de Walle, 1997; Erdmann & Engel, 2007).\n\nAddressing corruption in a neo-patrimonial context requires a multifaceted approach that goes beyond technical fixes. It necessitates a fundamental restructuring of the political and economic systems that sustain patronage networks, as well as efforts to build a more inclusive and accountable governance framework. This includes strengthening civil society, promoting political pluralism, and creating mechanisms for greater public participation and oversight in the management of mega projects (Van de Walle, 2001; Hough, 2013).\n\nApplying these theories to the case of Ethiopia’s dam construction projects provides a comprehensive understanding of the mechanisms and drivers of corruption in this context. The Principal-Agent Theory highlights the misalignment of incentives and the lack of oversight that allows corruption to flourish. Rent-Seeking Theory explains how individuals and groups exploit their access to resources for personal gain, leading to inefficiencies and increased project costs. Institutional Theory underscores the role of weak governance structures and social norms in facilitating corruption, while Neo-Patrimonialism contextualizes the personalized and informal nature of power relations in Ethiopia that perpetuate corrupt practices.\n\nThese theoretical insights are crucial for developing strategies to combat corruption in Ethiopia’s dam construction projects. Building robust institutional frameworks, improving transparency and accountability, and fostering a culture of integrity are essential steps in addressing the root causes of corruption. Additionally, understanding the role of informal networks and patronage in perpetuating corruption can help policymakers design interventions that target these specific dynamics.\n\n\n3. Methods\n\nA qualitative research approach was employed to explore the complex dynamics of corruption, mismanagement, and their broader socio-economic impacts within the context of dam construction in Ethiopia. This approach was chosen due to its suitability for examining the underlying processes, behaviors, and experiences of stakeholders involved in these mega projects. By using qualitative methods, the research was able to capture the nuanced perspectives and contextual factors that influence dam construction outcomes, which are often overlooked by quantitative approaches (Denzin & Lincoln, 2018).\n\nThe research adopted a case study design, focusing specifically on Ethiopia’s Grand Ethiopian Renaissance Dam (GERD) and other significant dam projects such as the Gilgel Gibe and Genale Dawa dams. This design was selected because it allowed for an in-depth exploration of the phenomenon within its real-life context, where the boundaries between the phenomenon and the context were not clearly defined (Yin, 2018). The case study approach provided a comprehensive analysis of the dynamics of dam construction and corruption, offering detailed insights that could inform both academic and policy discussions.\n\nThe study utilized both primary and secondary data sources to ensure a robust analysis. Primary data was collected through in-depth interviews and key informant interviews with individuals who had direct involvement in or knowledge of the dam construction projects. A qualitative research approach was employed, utilizing both primary and secondary data sources. Data collection involved conducting interviews using a structured interview guide. Participants were provided with written consent forms outlining the study’s purpose and their role. Those who agreed to participate were invited to a 60-minute interview, which could be conducted via Zoom, Skype, telephone, or in person, depending on their preference and convenience. With participants’ consent, the interviews were audio-recorded to ensure accurate transcription of their responses. The recordings were securely stored and accessible only to the research. (Interview Guide). This included obtain credible and reliable information, the researcher engaged government officials, project managers, engineers, consultants, construction companies, financial institutions, academics, civil society organizations, opposition political party members, and legal experts (see Table 1). These interviews provided rich, firsthand accounts that were critical for understanding the intricate relationships between governance, project management, and corruption (Patton, 2015).\n\nSecondary data was gathered from a range of existing literature, including academic articles, government reports and project documents. These sources provided essential background information, contextual insights, and additional perspectives that complemented and triangulated the primary data. The inclusion of secondary data was vital for situating the research within the broader political, economic, and social context of dam construction in Ethiopia (Bryman, 2016).\n\nData collection was conducted using in-depth interviews and key informant interviews. In-depth interviews were carried out with a purposively selected sample of stakeholders who were directly involved in the GERD and other dam projects. These interviews facilitated a deep exploration of participants’ experiences and perspectives, allowing the researcher to uncover the complexities and subtleties of the issues under investigation (Rubin & Rubin, 2011).\n\nKey informant interviews were conducted with experts and professionals who possessed specialized knowledge about dam construction and corruption in Ethiopia. These interviews were instrumental in providing critical insights into the technical, managerial, and governance aspects of the projects, as well as the broader socio-political implications (Marshall, 1996). This study did not use any third-party materials or proprietary assessment tools. All data collection and analysis were conducted using original instruments developed specifically for this research.\n\nAs shown in Table 1, the study involved a sample size of 36 participants, selected using purposive sampling. This sample size was sufficient to achieve data saturation, where no new information or themes emerged from additional interviews, ensuring that the data collected was comprehensive and reflective of the various stakeholder perspectives (Guest, Bunce, & Johnson, 2006).\n\nThe purposive sampling technique was chosen for its ability to identify and select participants who were most likely to provide rich, relevant, and diverse data. This non-probability sampling method was appropriate for the qualitative nature of the research, as it allowed the researcher to focus on individuals with direct experience or specialized knowledge relevant to the research questions (Creswell & Poth, 2018).\n\nThe data collected was analyzed using thematic analysis, which involved identifying, analyzing, and reporting patterns (themes) within the data. Thematic analysis was chosen for its flexibility and rigor, allowing the researcher to generate detailed accounts of the data that were grounded in participants’ experiences and perspectives (Braun & Clarke, 2006).\n\nThe analysis process began with familiarization, where the researcher thoroughly reviewed the interview transcripts to gain an in-depth understanding of the data. This was followed by the coding phase, where initial codes were generated based on recurring ideas, concepts, and patterns within the data. These codes were then grouped into broader themes that reflected the key issues related to dam construction, corruption, and project management. The themes were reviewed and refined to ensure they accurately represented the data and addressed the research questions. Finally, the analysis was written up, linking the identified themes to the research questions and the broader literature.\n\nThe research adhered to stringent ethical standards to protect participants and maintain the integrity of the research process. Written consent was obtained from all participants, who were fully informed about the nature, purpose, and potential risks of the study before agreeing to participate. The study obtained informed consent from all participants prior to their involvement. In this case, written consent was secured to ensure that participants were fully aware of the study’s objectives, procedures, and their rights, including the right to withdraw at any time. The ethical approval committee reviewed and approved this consent procedure. If any participants had been unable to provide written consent, verbal consent would have been considered, provided that the ethical approval committee deemed it appropriate under specific circumstances. However, in this study, all consent was obtained in written form, and there were no waivers granted by the ethical approval committee. This ensured that participants were aware of their rights, including the right to withdraw from the study at any time without consequences (Orb, Eisenhauer, & Wynaden, 2001).\n\nConfidentiality and anonymity were strictly maintained throughout the research process. Identifying information was removed from transcripts, and data was securely stored to prevent unauthorized access. This approach was essential for protecting the privacy of participants and ensuring the ethical conduct of the research (Wiles, 2012). The study received ethical approval from the relevant ethics committee. The approval was granted on 20/11/2023 number for this study is GaDS-102/23. The approval process involved a thorough review of the research protocol to ensure compliance with ethical standards, including considerations for participant consent, data confidentiality, and the overall integrity of the research process. This approval confirms that the study adhered to all necessary ethical guidelines and regulations., ensuring compliance with all ethical guidelines and regulations (Resnik, 2018). Additionally, all efforts were made to minimize potential harm to participants, including psychological distress or social repercussions, by conducting the research in a manner that respected the dignity and rights of all participants.\n\n\n4. Result and discussion\n\nThe phenomenon of corruption in large-scale infrastructure projects is a multifaceted issue, deeply rooted in management practices, governance structures, and socio-political dynamics. Ethiopia’s dam construction projects, notably the Grand Ethiopian Renaissance Dam (GERD) and others like Gilgel Gibe and Genale Dawa, offer a compelling case study in understanding how specific management practices can create environments conducive to corruption.\n\nAccording Sovacool and Walter (2017), the potential link between hydropower projects and corruption focusing on whether countries with significant hydropower activity exhibit higher levels of corruption compared to non-hydro countries. Studies show that hydropower countries tend to have lower scores on the control of corruption index than their non-hydro counterparts. However, these differences are not statistically significant. In comparison, hydropower countries show slightly higher corruption control scores than OPEC and lower-income nations.\n\nAccording to studies, corruption is a widespread issue affecting all types of infrastructure projects, not just hydropower. According to Haas (2008), corruption in the hydropower sector results in annual losses of $5 to $6 billion. This figure is relatively small when compared to broader global corruption, with Plummer (2008) estimating that corruption could account for 10% to 30% of infrastructure project budgets (Sovacool & Walter, 2017). Given that global infrastructure spending totals around $2.7 trillion annually, corruption in these projects could range from $270 billion to $810 billion. The World Bank (2013) also estimates that global bribery alone constitutes a $1 trillion industry each year (Ibid). Consequently, while there are trends suggesting a possible link between hydropower and increased corruption, the evidence does not robustly support this hypothesis, and the scale of corruption in hydropower projects is minor relative to the global context.\n\nTable 2 shows the Corruption Index (CPI Score) related to mega project constructions in Ethiopia. Corruption Index (CPI Score) typically range from 0 (highly corrupt) to 100 (very clean). This column should reflect the corruption perception score related to the specific projects. If CPI scores are not available for specific projects, you might need to use general CPI scores for the country or regional reports.\n\nThe World Bank (WB) report titled “Diagnosing Corruption in Ethiopia” identifies corruption in Ethiopia’s construction sector as being just as pervasive and detrimental as it is in the land, education, and telecommunications sectors (World Bank, 2013). The report highlights several typical indicators of corruption within the construction sector, such as substandard construction quality, inflated costs per unit, and project delays. These issues are often rooted in ambiguous or inequitable contractual agreements, inadequate enforcement of professional standards, significant salary disparities between the public and private sectors, the extensive discretionary power of government officials, a lack of transparency, and widespread perceptions of hidden obstacles to market entry (World Bank, 2013).\n\nEthiopia’s construction sector can be categorized into four main areas: roads, water supply and irrigation, power, and various public works, including the construction of educational institutions, healthcare facilities, and marketplaces. The annual expenditure on road construction alone is estimated at US$1.2 billion (World Bank, 2013). Unlike many other African nations, Ethiopia’s government retains significant control over the construction sector, which remains largely unprivatized in comparison (World Bank, 2013).\n\nCorruption in Ethiopia’s construction industry is fueled by a variety of interconnected issues. These include deficiencies in accountability—specifically, the lack of transparency due to unclear performance standards—limitations in capacity, such as inadequate material and human resources and failure to follow proper procedures, and issues with trust, which affect the market’s confidence and influence businesses’ willingness to invest in improving their capabilities. In Ethiopia, the absence of capacity enables corruption, the lack of accountability facilitates it, and the deficit in trust allows it to thrive (World Bank, 2013).\n\nThe WB report outlines six key dimensions where corruption is particularly prevalent in Ethiopia’s construction sector:\n\n• Policymaking and regulatory processes: Corruption in this area significantly impacts sector governance. Policies and regulations may either foster or conceal corrupt practices, and if left unaddressed, they can perpetuate corruption by individuals or groups. The Ethiopian government exerts considerable control over the prices of construction materials, access to financing, equipment, professional and company registrations, and maintains high-level bilateral infrastructure agreements with China. This dominance, coupled with inadequate competition, insufficient quality control, lax enforcement of professional standards, and a general absence of transparency, intensifies the problem of corruption. Concerns have been raised regarding potential links between the predominant role of Chinese contractors and the close ties between the Ethiopian and Chinese governments (World Bank, 2013).\n\n• Planning and budgeting: Corruption in this dimension arises when planning and budgeting processes deviate from rational and objective criteria for prioritizing resource allocation. In Ethiopia, the planning and budgeting process is marked by a lack of distinction between policymaking, budget allocation, and implementation functions, coupled with top-down planning driven by government decrees.\n\n• This leads to issues such as the adoption of inappropriately high construction standards, neglect of existing facilities, conflicts of interest, and aiding politically-aligned construction companies (World Bank, 2013).\n\n• Management and performance monitoring: Management weaknesses can lead to corruption through lack of basic controls, inadequate data management and reporting systems, and incompetent management. In Ethiopia, issues such as low remuneration of managers, poor performance by shortlisted companies, difficulty obtaining public information, and weak enforcement of professional standards contribute to corruption (World Bank, 2013).\n\n• Tendering and procurement: Corruption in the T&P process includes sale of inside bidding information, collusion between contractors, and bribery. In Ethiopia, corruption is evident through a lack of transparency, shortlisting of poor-performing companies, exclusion of capable companies, and distortions in the bidding process (World Bank, 2013).\n\n• Operations phase: Contractors who have engaged in bribery frequently seek to recover their expenditures through fraudulent practices during the construction phase. These practices include using substandard materials, falsifying quantities, submitting inflated claims, and hiding defects. In Ethiopia, it is common for contracts to exceed the budget, with significant delays and issues with construction quality being prevalent (World Bank, 2013).\n\n• Payment and settlement of certificates: Corruption in this area involves fabrication of justifications for withholding payments, bribery, blackmail of witnesses, and excess billing. In Ethiopia, facilitation payments are often required to expedite settlement, and contractors may curtail progress due to cash flow problems from late payments (World Bank, 2013).\n\nConsistent with the above assertion, interview results confirmed that:\n\n\"Many of our procurement processes lack stringent oversight mechanisms, which has created ample opportunities for corrupt practices to thrive. The existing regulatory frameworks are often insufficiently enforced, leading to a culture where corrupt behavior is not only possible but often goes unchecked. For instance, the lack of detailed auditing and transparent reporting requirements has made it difficult to track the flow of funds and ensure accountability\"(Interview, Senior Official, Ministry of Water, Irrigation, and Energy, Addis Ababa, 2024).\n\nAccording to Key informants, collusion among bidders and bribery during the tendering process are common practices that distort fair competition. The lack of a truly competitive bidding environment, often due to prearranged agreements or manipulation of bid requirements, results in inflated project costs and compromised quality. For instance, we’ve seen instances where bid requirements are tailored to favor certain companies, which undermine the integrity of the procurement process (KII, representative from a major construction company, 2024).\n\nOn the other hand, conflicts of interest and opaque processes in the selection of consultants are major enablers of corruption. We have observed that favoritism in awarding consultancy contracts often stems from personal connections or financial incentives. This lack of transparency in the selection process undermines the credibility of consultancy work and can lead to biased recommendations and compromised project outcomes\" (KII, Project Consultant, 2024).\n\nIn the Ethiopian construction sector, the government holds a central position as both the leading client and the exclusive authority responsible for policy-making and regulation. This situation effectively turns the government into EthioConstruction Corruption, Inc. Despite the WB report’s cautious language, it is clear that corruption in the Ethiopian construction sector spans policy making, budgetary processes, project selection, tender specifications, procurement outcomes, contract negotiations, and payments (World Bank, 2013).\n\nIn June 2013, the Ethiopian Roads Authority signed a contract with two Chinese companies to improve the 133 km Kombolcha-Bati-Mille road to an asphalt-concrete standard. The agreement allocated 2.8 billion Br. to the Chinese firms for this project (Ethiopian Roads Authority, 2013). Questions arise about why Ethiopian companies are not securing such contracts and whether Ethiopia is getting value for money from these foreign contractors (Ethiopian Roads Authority, 2013). There several factors enabling corruption in Ethiopia’s dam construction projects:\n\n4.1.1 Weak institutional frameworks and oversight mechanisms\n\nOne of the most significant factors enabling corruption in Ethiopia’s dam construction projects is the weakness of institutional frameworks and oversight mechanisms. The absence of stringent regulatory controls and the lack of transparency in procurement processes have allowed corrupt practices to thrive. For example, the GERD project has been criticized for its opaque tendering processes, where contracts were often awarded without competitive bidding, leading to inflated costs and substandard work (Transparency International, 2021). The lack of independent auditing and monitoring further exacerbates the situation, as it limits accountability and allows corrupt activities to go unchecked. This is related to Principal-Agent Theory in that the Principal-Agent relationship is often characterized by a lack of transparency and accountability, which allows agents to exploit their positions for personal gain. For instance, procurement processes are frequently manipulated, with contracts awarded based on favoritism or bribery rather than merit.\n\nConsistently, interview results confirmed as follow:\n\n\"From our experience, poorly defined roles and responsibilities within project teams, coupled with inadequate internal controls, have significantly contributed to corruption. For example, ambiguous job descriptions and overlapping responsibilities can lead to inefficiencies and a lack of clear accountability, making it easier for unethical practices to occur. Additionally, the absence of regular internal audits and oversight mechanisms has allowed corrupt behaviors to persist” (KII, Project Expert, Addis Ababa, 2024).\n\nCorruption is facilitated by the absence of standardized procedures and rigorous quality checks. In several cases, project specifications have been altered to benefit particular contractors, often leading to subpar construction quality. This lack of adherence to consistent standards not only undermines project integrity but also opens avenues for bribery and kickbacks. For example, changes in material specifications to cheaper alternatives have frequently been linked to corrupt agreements\" (Interview, Engineer Involved in the Project, 2024).\n\nThis scenario is not unique to Ethiopia; similar patterns have been observed in other African countries. In Nigeria, the management of the Ajaokuta Steel Plant, which was intended to be a cornerstone of the country’s industrialization, was marred by corruption and mismanagement, resulting in the project’s failure despite massive investments (Smith, 2010). The parallels between Ethiopia and Nigeria highlight the critical role of robust institutional frameworks in mitigating corruption in large-scale projects.\n\n4.1.2 Centralization of decision-making\n\nThe centralization of decision-making power in the hands of a few individuals or entities is another management practice that fosters corruption. In Ethiopia, the decision-making process for dam construction projects has often been concentrated within the upper echelons of government, with limited input from other stakeholders, including local communities and civil society organizations. This centralization creates opportunities for rent-seeking behavior, where officials can exploit their positions for personal gain.\n\nResearch has shown that centralization of power in project management often leads to a lack of checks and balances, increasing the risk of corrupt practices (Rose-Ackerman & Palifka, 2016). In the case of the GERD, the Ethiopian government’s tight control over the project’s planning and execution stages has been linked to allegations of embezzlement and misallocation of funds, further burdening the country’s economy (Alemayehu & Lakew, 2020).\n\nIn line with the above, interview results confirmed as follows:\n\nThe centralization of mega project management in the hands of a select few often leads to corruption. We need robust mechanisms to ensure that every dollar spent on these projects is accounted for and serves the public good. The lack of transparency in mega projects like the GERD is a serious concern. Centralized control over mega projects often results in corruption and inefficiency. Decentralized oversight and greater community involvement are necessary to ensure that these projects are managed effectively and equitably. The systemic issues that allow corruption to thrive in mega projects need to be addressed (Interview, Opposition Political Party, 2024).\n\n4.1.3 Inefficient project management practices\n\nInefficient project management practices, characterized by poor planning, lack of coordination, and inadequate risk management, have also contributed to the prevalence of corruption in Ethiopia’s dam construction projects. These inefficiencies often lead to cost overruns and delays, which create fertile ground for corrupt activities. Contractors and government officials may collude to manipulate project timelines and budgets, inflating costs to siphon off funds (Flyvbjerg, 2017).\n\nFor instance, the Gilgel Gibe III dam project, initially projected to cost $1.8 billion, ultimately ballooned to over $2 billion due to delays and mismanagement (International Rivers, 2014). Such cost escalations are often symptomatic of underlying corrupt practices, where stakeholders benefit from prolonged project timelines and increased budgets.\n\nMoreover, geopolitical and economic pressures have also played a role in perpetuating corruption within Ethiopia’s dam construction projects. The urgent need to complete these projects to meet domestic energy demands and assert regional influence has led to compromises in governance and management standards. The rush to deliver these mega projects often results in the bypassing of standard procedures, creating opportunities for corrupt practices (Mwangi, 2019a, b). In the context of the GERD, Ethiopia’s ambition to become a regional power in hydroelectricity has led to expedited project timelines and the overlooking of governance protocols. This haste has not only strained the country’s financial resources but has also opened doors for corrupt practices, as oversight mechanisms are weakened in the pursuit of rapid project completion (Elhance, 2020).\n\nThe phenomenon of corruption in Ethiopia’s dam construction projects, such as the Grand Ethiopian Renaissance Dam (GERD) and other projects like Gilgel Gibe and Genale Dawa, can be understood through a multi-theoretical framework. By analyzing the findings through the lenses of Principal-Agent Theory, Rent-Seeking Theory, Institutional Theory, and Neo-Patrimonialism, a nuanced understanding of the complex dynamics enabling corruption is achieved. Each theory not only offers unique insights but also intersects with the others to form a comprehensive explanation of corruption.\n\nOn the other hand, Principal-Agent Theory and Institutional Theory are closely linked in their explanation of corruption, particularly through the concept of information asymmetry and the weaknesses in institutional frameworks. In the context of Ethiopia’s dam projects, the absence of stringent regulatory controls and the lack of transparency in procurement processes (Institutional Theory) exacerbate the principal-agent problem. The weak institutional environment allows agents (contractors, project managers) to exploit their positions for personal gain without sufficient oversight from the principals (government authorities). This dynamic is evident in the opaque tendering processes of the GERD project, where contracts were often awarded without competitive bidding, leading to inflated costs and substandard work (Transparency International, 2021). The failure of institutions to enforce accountability mechanisms directly contributes to the agency problem, where agents operate with greater autonomy and less accountability, fostering an environment ripe for corruption.\n\nSimilarly, Rent-Seeking Theory and Neo-Patrimonialism converge in their explanation of how power and resources are manipulated for personal gain in Ethiopia’s dam construction projects. The centralization of decision-making in the hands of a few government officials creates opportunities for rent-seeking behavior, where these officials exploit their positions to extract economic rents through corrupt means. This centralization is a hallmark of neo-patrimonial systems, where formal state institutions are overshadowed by informal practices, such as patronage and clientelism (Rose-Ackerman & Palifka, 2016). The tight control over the GERD project by the Ethiopian government illustrates this dynamic, where the concentration of power has led to allegations of embezzlement and misallocation of funds (Alemayehu & Lakew, 2020). In this context, rent-seeking and neo-patrimonial practices reinforce each other, with the centralization of power facilitating the extraction of rents through corrupt practices, further entrenching the neo-patrimonial structure.\n\nMoreover, the intersection of Principal-Agent Theory and Neo-Patrimonialism is particularly evident in the way corruption manifests in Ethiopia’s dam construction projects. In a neo-patrimonial context, the principal-agent relationship is characterized by personal loyalties and patronage rather than formal institutional arrangements. This leads to a scenario where agents are less accountable to the principals and more to the patrons who secure their positions. For instance, the manipulation of procurement processes in the GERD project can be seen as a consequence of neo-patrimonial dynamics, where agents act in the interests of their patrons rather than adhering to formal rules and regulations (Smith, 2010). The personalization of authority in neo-patrimonial systems exacerbates the agency problem, as agents operate with greater discretion, often prioritizing personal or factional interests over the public good.\n\nFurthermore, Institutional Theory and Rent-Seeking Theory intersect in explaining how weak institutional frameworks create opportunities for rent-seeking behavior. The absence of robust regulatory controls and oversight mechanisms in Ethiopia’s dam construction projects allows rent-seeking activities to flourish, as there are few checks and balances to prevent the exploitation of power for personal gain (Flyvbjerg, 2017). For example, the inefficient project management practices in the Gilgel Gibe III dam project, where delays and cost overruns were prevalent, can be attributed to weak institutional oversight that failed to curb rent-seeking behavior (International Rivers, 2014). In this way, institutional weaknesses directly contribute to the emergence of rent-seeking activities, as stakeholders exploit these gaps to extract rents at the expense of project efficiency and integrity.\n\nComing to the synthesis, the interrelations between Principal-Agent Theory, Rent-Seeking Theory, Institutional Theory, and Neo-Patrimonialism provide a comprehensive framework for understanding corruption in Ethiopia’s dam construction projects. These theories do not operate in isolation; rather, they intersect and reinforce each other, creating a complex web of factors that enable corrupt practices. Weak institutional frameworks and oversight mechanisms exacerbate the principal-agent problem, while centralized decision-making power fosters rent-seeking behavior, all within a neo-patrimonial context that prioritizes personal loyalties over formal governance structures. Understanding these interconnections is crucial for developing effective strategies to combat corruption in large-scale infrastructure projects, not only in Ethiopia but also in similar contexts globally.\n\nCorruption in Ethiopia’s dam construction projects has had far-reaching economic and social consequences, undermining both the potential benefits of these infrastructural developments and the broader developmental goals of the country. The pervasive nature of corruption in these projects manifests through various channels, including mismanagement of funds, embezzlement, and the inflation of project costs, all of which contribute to substantial economic and social costs.\n\n4.2.1 Economic impacts\n\nCorruption in dam construction projects has significant economic repercussions, particularly in the form of cost overruns. These overruns often stem from the deliberate inflation of project budgets by officials and contractors seeking personal gain (Alemayehu, 2019). For example, the Gilgel Gibe III dam, initially projected to cost $1.4 billion, ended up exceeding $1.8 billion, with corruption playing a role in this discrepancy (International Rivers, 2014). These inflated costs strain the national budget, forcing the government to allocate additional resources that could have been used for other critical areas, such as healthcare, education, and rural development.\n\nMoreover, these increased costs contribute to a rise in public debt. Ethiopia, like many developing countries, relies heavily on loans to finance large-scale infrastructure projects, including dams. When corruption leads to cost overruns, the government is often compelled to seek additional financing under unfavorable terms, exacerbating the country’s debt burden and limiting fiscal space for other essential investments (World Bank, 2020).\n\nCorruption also affects the broader economy by reducing the efficiency of public spending. Delays and inefficiencies in project completion hinder economic growth, as seen with the Grand Ethiopian Renaissance Dam (GERD). The delayed operationalization of GERD, partly due to corruption, has postponed expected benefits like electricity generation and export, crucial for Ethiopia’s economic development (Gebre, 2021).\n\nIn addition to increasing national debt, corruption in mega construction projects contributes to inflationary pressures. Rising project costs are often passed on to consumers and the government, leading to higher prices for goods and services. This trend diminishes purchasing power, undermines economic stability, and raises the cost of living (World Bank, 2020). Corruption also deters investment, both domestic and foreign. High corruption levels are perceived as significant risks by investors, leading to reduced foreign direct investment (FDI) and slower economic growth. The inflated costs and associated risks of projects like the GERD discourage investment in other sectors, hampering broader economic development (Reda, 2018).\n\nInfrastructure quality is another area adversely affected by corruption. Financial mismanagement and project delays, such as those in the Addis Ababa Light Rail Transit project, often lead to compromised infrastructure. Substandard construction and maintenance not only impede economic development but also reduce the efficiency of transportation and trade, further impacting the country’s overall economic performance (Tsegaye, 2018).\n\nCorruption also exacerbates social and economic inequalities. When funds intended for public welfare and development projects are misappropriated, poverty and income inequality are aggravated. For instance, the mismanagement of funds in sugar and fertilizer factories has negatively affected agricultural productivity and food security, disproportionately impacting poorer segments of the population (National Audit Office, 2021).\n\nGenerally, corruption in mega construction projects has profound economic impacts, influencing national debt, inflation, investment climate, infrastructure quality, and social equity. Addressing these issues requires comprehensive anti-corruption measures to promote sustainable economic development. Table 3 summarizes the impact of corruption on construction costs for selected projects in Ethiopia:\n\nConsistent with the above assertions, primary data sources complement that corruption has led to substantial cost overruns and delays in dam construction projects, severely impacting economic efficiency. Inflated costs due to corrupt practices, such as bribery and kickbacks, divert funds away from their intended development purposes. Furthermore, the resulting delays hinder the timely realization of project benefits, thereby affecting the overall economic growth and development objectives of the country,” acknowledged a senior government official (Interview, Government Officials, Addis Ababa 2024).\n\nSimilarly, interview results confirmed that corruption has had a detrimental impact on project quality and cost-effectiveness. For example, cost overruns due to substandard construction and the use of inferior materials have resulted in higher long-term maintenance costs and reduced project durability. These issues ultimately affect the economic returns and operational efficiency of the projects,” reported a project manager (Interview, Project Managers, Addis Ababa 2024). In addition, the data asserted that compromises in construction quality, often driven by corrupt practices, have led to increased maintenance and repair costs. Additionally, operational inefficiencies resulting from substandard construction have negatively impacted the economic returns of these projects. For instance, infrastructure that fails to meet performance standards requires costly rectifications and compromises the expected economic benefits (Interview, Engineer, Addis Ababa, 2024).\n\nConsistently with the above assertions, primary data sources further confirmed that corruption increases project costs and reduces the overall value for money. Mismanagement and fraudulent practices often lead to a mismatch between project outcomes and initial objectives. This inefficiency results in a poor return on investment and can undermine the broader economic benefits of the project,” noted a consultant. Moreover, corrupt practices create an uneven playing field, resulting in inefficient resource allocation and inflated project costs. The use of substandard materials and practices due to corruption often leads to additional costs for repairs and maintenance, further exacerbating economic inefficiencies,” said a representative from a construction firm.\n\nCorruption distorts financial planning and risk assessments, leading to poor investment decisions and economic losses. Misappropriation of funds and inflated project costs compromise the financial stability of both public and private stakeholders, affecting the overall economic viability of the projects,” stated a financial institution representative. The broader economic implications of corruption include diminished investor confidence and increased borrowing costs. Perceived risks associated with corrupt practices can deter investment and lead to higher financial costs for development projects, thereby undermining economic stability and growth,” explained an academic (Interview, Academician, Hawasaa, 2024).\n\n4.2.2 Social impacts\n\nThe social consequences of corruption in dam construction are equally severe. Corruption erodes public trust in government institutions and undermines the social contract between the state and its citizens. In Ethiopia, communities affected by dam construction projects have often been marginalized and neglected due to the misappropriation of funds meant for compensation and resettlement. For instance, the communities displaced by the construction of the Gilgel Gibe III dam reported inadequate compensation and poor resettlement conditions, which have led to social unrest and conflicts (International Rivers, 2014).\n\nThe misallocation of funds intended for community development has also undermined the potential benefits of these projects. Rather than improving the livelihoods of affected populations, corruption has left many communities worse off. The promised development projects, such as schools, health clinics, and infrastructure improvements, often fail to materialize, leaving affected communities to bear the brunt of the negative consequences of dam construction without reaping any of the intended benefits.\n\nPractical examples of corruption in Ethiopia’s dam construction projects are numerous. The Gilgel Gibe II and III dams serve as stark examples of how corruption can lead to economic and social degradation. Reports have highlighted how contracts were awarded without proper bidding processes, leading to inflated costs and substandard construction work (Alemayehu, 2019). These practices not only increased the financial burden on the state but also resulted in technical failures, such as the collapse of a tunnel in the Gilgel Gibe II dam shortly after its completion, which required costly repairs and delayed the project’s benefits.\n\nAnother case is the Grand Ethiopian Renaissance Dam (GERD), which has faced numerous challenges, including allegations of corruption related to the procurement process and the management of funds. These challenges have contributed to delays in the project’s completion, which has had significant economic repercussions for the country, including the delayed realization of expected revenue from electricity exports and increased costs due to the prolonged construction period (Gebre, 2021).\n\nCorruption in large infrastructure projects, such as dam construction, poses significant challenges to economic development, governance, and social equity. Ethiopia, with its ambitious dam projects like the Grand Ethiopian Renaissance Dam (GERD) and the Gilgel Gibe series, has faced notable instances of corruption that have undermined the economic and social benefits these projects were intended to deliver. To mitigate the risks of corruption in such projects, a comprehensive set of strategies is required, encompassing legal, institutional, and community-based approaches.\n\n4.3.1 Strengthening legal and regulatory frameworks\n\nA robust legal and regulatory framework is essential for combating corruption in dam construction projects. Ethiopia can strengthen its anti-corruption laws by enhancing the powers and independence of anti-corruption agencies such as the Federal Ethics and Anti-Corruption Commission (FEACC). Ensuring that these agencies have the autonomy to investigate and prosecute corruption cases without political interference is critical. For example, the introduction of the Anti-Corruption Proclamation No. 881/2015 in Ethiopia was a step towards empowering the FEACC, but its effectiveness has been hampered by limited enforcement capacity and political pressures (Yehualashet, 2017).\n\nAdditionally, enforcing transparency in procurement processes is vital. The adoption of e-procurement systems can reduce the opportunities for corruption by minimizing direct human intervention and increasing transparency. For instance, countries like Kenya have successfully implemented e-procurement in their public sectors, resulting in reduced incidences of corruption (Mwangi, 2019). Ethiopia could adopt similar systems to ensure that all stages of the procurement process for dam construction projects are transparent and accessible to the public.\n\n4.3.2 Institutional reforms and capacity building\n\nInstitutional reforms are necessary to create an environment where corruption is less likely to thrive. This includes improving the governance structures of institutions involved in dam projects, such as the Ethiopian Electric Power Corporation (EEPCo) and the Ministry of Water, Irrigation, and Energy. Strengthening the capacity of these institutions to manage and oversee large-scale projects effectively is crucial. For example, providing training on anti-corruption measures, project management, and financial oversight can enhance the ability of these institutions to detect and prevent corrupt practices.\n\nMoreover, the establishment of independent oversight bodies can play a significant role in monitoring the implementation of dam projects. These bodies should include representatives from civil society, academia, and the private sector to ensure diverse perspectives and impartial oversight. For example, the Ethiopian Construction Project Management Institute (ECPMI) could be expanded to include anti-corruption monitoring in its mandate, providing regular audits and assessments of ongoing projects.\n\n4.3.3 Promoting community participation and transparency\n\nCommunity involvement in dam projects is another effective strategy for mitigating corruption. When local communities are engaged in the planning, implementation, and monitoring of projects, there is a greater likelihood of accountability and transparency. In Ethiopia, the displacement of communities for dam construction, such as in the case of the Gilgel Gibe III dam, has often led to social unrest due to inadequate consultation and compensation (International Rivers, 2014). Implementing a more inclusive approach, where affected communities are actively involved in decision-making processes, can help ensure that their interests are represented and that corruption is minimized.\n\nAdditionally, promoting transparency through public disclosure of project information is critical. Ensuring that contracts, financial reports, and project progress updates are publicly accessible allows for greater scrutiny by the media, civil society, and the general public. For example, the Public Procurement and Property Administration Agency (PPPAA) in Ethiopia could mandate the publication of all procurement-related documents for public infrastructure projects, fostering a culture of transparency and accountability (Transparency International, 2019).\n\n4.3.4 International cooperation and best practices\n\nInternational cooperation can provide valuable support in mitigating corruption risks. By partnering with international organizations such as the World Bank, the African Development Bank, and Transparency International, Ethiopia can benefit from technical assistance, funding, and best practices in anti-corruption measures. These organizations often have stringent anti-corruption policies that require compliance as a condition for funding, which can help enforce accountability.\n\nAdopting best practices from other countries can also be beneficial. For example, Brazil’s success in reducing corruption in its infrastructure projects through the use of transparency portals and citizen participation initiatives could serve as a model for Ethiopia (Speck, 2011). These practices include real-time monitoring of project expenditures, public access to detailed project data, and the use of technology to enhance oversight.\n\n4.3.5 Strengthening judicial processes and enforcement\n\nEffective judicial processes and enforcement mechanisms are essential to deter corruption in dam projects. Ensuring that corruption cases are prosecuted swiftly and that penalties are severe enough to act as a deterrent is crucial. In Ethiopia, the judiciary has faced challenges in handling corruption cases due to limited resources, lack of expertise, and political influence (Yehualashet, 2017). Enhancing the capacity of the judiciary through specialized training in financial crimes, increasing resources, and ensuring its independence from political interference are critical steps in strengthening the enforcement of anti-corruption laws.\n\nMoreover, establishing special anti-corruption courts or tribunals that focus exclusively on corruption cases can improve the efficiency and effectiveness of the judicial process. These courts can expedite the handling of corruption cases and ensure that they are dealt with by judges who have expertise in this area (Kim, 2019).\n\nAddressing corruption in Ethiopia requires massive involvement of civil society watchdogs and rigorous independent audits. Successful countries in controlling construction sector corruption have implemented rigorous compliance audits, made comprehensive contract information available online, and allowed civil society to observe the tendering process (World Bank, 2013). Ethiopia’s freedom of information law (Proclamation No. 590/2008) is criticized for its extensive exemptions and limitations on disclosure, which perpetuate corruption by keeping information about government activities, financial institutions, and public institutions secret (Proclamation No. 590/2008). Corruption thrives in darkness. The people of Ethiopia need robust transparency measures to combat corruption and ensure that public funds are used effectively. To track corruption, one must follow the money—it often leads straight to the top.\n\nConsistent with the above assertions, interview results confirmed that mitigating corruption in dam construction projects requires several key strategies:\n\nStrengthening oversight mechanisms, implementing stricter anti-corruption regulations, and enhancing transparency in procurement processes are crucial. Establishing robust auditing procedures, improving procurement practices, and ensuring stricter compliance with anti-corruption laws were identified as essential measures.\n\nThe importance of clear internal controls, improved staff training on ethical practices, and fostering a culture of accountability within project teams was also emphasized. Regular internal audits and transparent reporting mechanisms were highlighted as necessary for effectively addressing corruption. Standardized procedures and regular quality checks are vital in preventing manipulation and ensuring adherence to project specifications. Enhanced reporting mechanisms for unethical practices and promoting a culture of integrity were noted as critical steps to mitigate corruption risks.\n\nEnsuring a transparent and competitive selection process for consultancy contracts, addressing conflicts of interest, and enforcing ethical standards were seen as essential for maintaining integrity. Strict guidelines and consistent monitoring of compliance were recommended to uphold ethical practices. Transparent bidding processes, strict anti-corruption policies, and independent audits were identified as important measures to enhance accountability. Ensuring fair competition and monitoring contractor performance were seen as vital in preventing corrupt practices.\n\nImproving financial oversight, enhancing auditing procedures, and collaborating with stakeholders to ensure effective financial management were emphasized. Robust financial controls and monitoring mechanisms were deemed necessary to detect and prevent misappropriation of funds. The implementation of robust governance frameworks, the promotion of public involvement in oversight, and the enhancement of institutional capacity were recommended. Strengthening legal and regulatory frameworks and fostering a culture of transparency and accountability were considered essential strategies.\n\nIncreasing transparency, fostering public participation in oversight, and strengthening whistleblower protections were highlighted as key strategies to combat corruption. Encouraging community involvement and improving access to information were seen as crucial for enhancing accountability and reducing corruption risks. Supporting investigative reporting and media oversight were recognized as effective means to expose and challenge corrupt practices. Legal protections for journalists and encouragement of independent reporting were recommended for the effective exposure of corruption. Comprehensive legal reforms, including closing loopholes, strengthening anti-corruption laws, and ensuring effective enforcement, were seen as necessary to mitigate corruption risks. Robust and enforceable legal frameworks were emphasized as essential to effectively address and prevent corruption in dam construction projects.\n\nThe implementation of these strategies in practice can be observed in various international contexts. For instance, the successful prosecution of corruption cases in South Korea’s Four Major Rivers Restoration Project, where several government officials and contractors were held accountable, demonstrates the effectiveness of strong legal and institutional frameworks (Choi, 2014). Similarly, the use of e-procurement systems in India’s infrastructure projects has significantly reduced opportunities for corruption, as evidenced by the successful implementation of the e-Government Procurement (e-GP) system in the state of Andhra Pradesh (Kumar & Srinivas, 2018).\n\n\nConclusion\n\nThis study critically examines the dynamics of corruption within Ethiopia’s dam construction projects, with a particular focus on the Grand Ethiopian Renaissance Dam (GERD), Gilgel Gibe series and Genale Dawa series. The findings reveal that corruption in these large-scale infrastructure projects is deeply intertwined with systemic weaknesses in management practices, oversight mechanisms, and decision-making processes. The application of theoretical frameworks—Principal-Agent Theory, Rent-Seeking Theory, Institutional Theory, and Neo-Patrimonialism—provides a comprehensive understanding of the structural and behavioral factors that enable corruption to thrive in this context.\n\nWeak institutional frameworks and oversight mechanisms have allowed corrupt practices to flourish, particularly in the procurement processes of projects like the GERD, the Gilgel Gibe series and Genale Dawa series. The lack of transparency and independent auditing has led to inflated costs and substandard work, ultimately straining Ethiopia’s economy and undermining the potential benefits of these projects. Principal-Agent Theory elucidates how information asymmetry and misaligned incentives between government authorities, donors, and project managers contribute to corruption. The lack of transparency and ineffective monitoring mechanisms has allowed agents to prioritize personal gain over public interest, leading to inflated costs, project delays, and compromised construction quality. Rent-Seeking Theory further explicates the economic consequences of corruption, wherein individuals and organizations engage in non-productive activities to extract unearned income, misallocating resources, and entrenching economic disparities.\n\nThe centralization of decision-making exacerbates the situation by concentrating power within a small group of individuals, reducing accountability, and increasing the risk of rent-seeking behavior. Inefficiencies in project management, characterized by poor planning, lack of coordination, and inadequate risk management, have also contributed to cost overruns and delays. These inefficiencies not only increase the financial burden on the state but also create opportunities for corrupt practices. Institutional Theory offers insights into how Ethiopia’s weak governance structures and the coexistence of formal regulations with informal patronage systems perpetuate corrupt practices. The normalization of corruption within societal norms complicates efforts to implement effective reforms. Neo-Patrimonialism highlights the systemic nature of corruption, where formal state structures are undermined by informal networks that prioritize personal loyalty and the distribution of patronage over public accountability and project integrity.\n\nThe economic consequences of corruption in Ethiopia’s dam construction projects are profound, including cost overruns, increased public debt, and hindered economic growth. These financial strains divert resources from other critical areas, such as healthcare and education, perpetuating a cycle of borrowing that stifles broader developmental goals. Socially, corruption erodes public trust, marginalizes affected communities, and exacerbates social unrest, particularly in cases where resettlement and compensation are inadequately managed.\n\nHowever, the findings also suggest that corruption in large-scale infrastructure projects is not an insurmountable challenge. By strengthening legal and regulatory frameworks, enhancing institutional capacity, promoting community participation, and leveraging international cooperation, Ethiopia can mitigate the risks of corruption and enhance the effectiveness of its dam construction projects. Implementing strategies such as e-procurement systems, independent oversight bodies, and robust judicial processes can create a more transparent and accountable environment, ultimately ensuring that these mega projects fulfill their intended economic and social benefits.\n\nTherefore, while the challenges posed by corruption in Ethiopia’s dam construction projects are significant, they are not insurmountable. Through a comprehensive approach that combines legal, institutional, and community-based strategies, Ethiopia can address these challenges and unlock the full potential of its infrastructure investments. This requires a concerted effort from all stakeholders, including the government, civil society, and the international community, to create a more transparent, accountable, and corruption-resistant environment for the management of large-scale projects.\n\n\nEthics and consent\n\nThe research adhered to stringent ethical standards to protect participants and maintain the integrity of the research process. Written consent was obtained from all participants, who were fully informed about the nature, purpose, and potential risks of the study before agreeing to participate. In this study, informed consent was obtained from all participants. Written consent was secured to ensure that participants fully understood the study’s purpose, procedures, and their rights, including the right to withdraw at any time without consequence. The study adhered to all ethical guidelines as approved by the ethical review committee, and no waiver of consent was granted. If verbal consent had been used, it would have been clearly documented along with the reasons for this approach, and such a procedure would have been explicitly approved by the ethics committee. However, in this study, written consent was used to maintain rigorous ethical standards. This ensured that participants were aware of their rights, including the right to withdraw from the study at any time without consequences (Orb, Eisenhauer, & Wynaden, 2001).\n\nConfidentiality and anonymity were strictly maintained throughout the research process. Identifying information was removed from transcripts, and data was securely stored to prevent unauthorized access. This approach was essential for protecting the privacy of participants and ensuring the ethical conduct of the research (Wiles, 2012). This study received full ethical approval from the Institutional Review Board (IRB) of Hawassa University College of Law and Governance, which comprises five members. The approval was granted on 20/11/2023 with number GaDS-101/2023. All procedures involving human participants were conducted in strict adherence to the Declaration of Helsinki to ensure the ethical integrity of the research.", "appendix": "Data availability statement\n\nAll data supporting the findings of this study are included within the manuscript. No additional or supplementary data are available.\n\nThe data that underpin the findings of this study are fully included within the manuscript. No additional or supplementary datasets are available.\n\nRestrictions on data: Access to the data is subject to the following restrictions:\n\n• The data are proprietary and confidential, collected under agreements that restrict sharing beyond the immediate research team.\n\n• All personal and sensitive information has been anonymized to ensure privacy and comply with data protection regulations.\n\nInstitutional Review Board (IRB) or equivalent recommendations: The Institutional Review Board (IRB) or equivalent ethical review body provided approval for the study and did not impose specific conditions or restrictions regarding data sharing. The research adhered to all applicable ethical guidelines.\n\nAccess conditions: Requests for access to the data should be directed to the corresponding author. Access may be granted under the following conditions:\n\n• The requester must provide a valid rationale for the data request.\n\n• The requester must agree to adhere to all confidentiality and data protection protocols.\n\nZenodo: Extended Data, Doi: https://zenodo.org/uploads/13843108 (Mohammed, 2024).\n\nThis project contains the following extended data:\n\n• Extended Data.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\nAitken R, Harrison P: The many lives of corruption: The reform of power and postcolonial relations in Africa. Afr. Stud. Rev. 2013; 56(2): 139–160.\n\nAlemayehu G: Economic Challenges and Corruption in Ethiopia’s Infrastructure Projects. Addis Ababa: Ethiopian Economic Policy Research Institute; 2019.\n\nAlemayehu G, Lakew D: The Political Economy of Mega Projects: The Case of the Grand Ethiopian Renaissance Dam. J. Afr. Econ. 2020; 29(4): 453–475.\n\nAmeyaw EE, Chan APC: Risk allocation in public-private partnership projects in developing countries: Empirical comparison between Ghana and Hong Kong. J. Facil. Manag. 2015; 13(2): 169–180.\n\nAyee JRA: Public sector governance and accountability in Ghana: Challenges and prospects. Afr. Stud. 2016; 75(2): 159–177.\n\nBanfield EC: Corruption as a Feature of Governmental Organization. J. Law Econ. 1975; 18(3): 587–605. Publisher Full Text\n\nBratton M, van de Walle N : Democratic Experiments in Africa: Regime Transitions in Comparative Perspective. Cambridge University Press; 1997.\n\nBraun V, Clarke V: Using thematic analysis in psychology. Qual. Res. Psychol. 2006; 3(2): 77–101. Publisher Full Text\n\nBryman A: Social Research Methods. Oxford University Press; 5th ed2016.\n\nChabal P, Daloz J-P: Africa Works: Disorder as Political Instrument. James Currey; 1999.\n\nChoi J: Corruption and Anti-Corruption in South Korea’s Four Major Rivers Restoration Project. Seoul: Korea University Press; 2014.\n\nCollins RO: The Nile. Yale University Press; 2002.\n\nCreswell JW, Poth CN: Qualitative Inquiry and Research Design: Choosing among Five Approaches. 4th ed.SAGE Publications; 2018.\n\nDenzin NK, Lincoln YS, editors: The SAGE Handbook of Qualitative Research. 5th ed.SAGE Publications; 2018.\n\nEisenhardt KM: Agency Theory: An Assessment and Review. Acad. Manag. Rev. 1989; 14(1): 57–74. Publisher Full Text\n\nElhance AP: Hydropolitics in the 3rd World: Conflict and Cooperation in International River Basins. United States Institute of Peace Press; 2020.\n\nErdmann G, Engel U: Neopatrimonialism Reconsidered: Critical Reflections on an Unfashionable Concept. Commonwealth & Comparative Politics. 2007; 45(1): 95–119. Publisher Full Text\n\nEthiopian Roads Authority: Kombolcha-Bati-Mille Road Upgrade Agreement.2013. Ethiopian Roads Authority website\n\nFederal Democratic Republic of Ethiopia: Ethiopia’s Growth and Transformation Plan II (GTP II) 2015/16-2019/20. Addis Ababa: National Planning Commission; 2016.\n\nFlyvbjerg B: Megaprojects and Risk: An Anatomy of Ambition. Cambridge University Press; 2009.\n\nFlyvbjerg B: The Oxford Handbook of Megaproject Management. Oxford University Press; 2017.\n\nGebre A: The Grand Ethiopian Renaissance Dam and Its Implications for Ethiopia’s Development. Addis Ababa: Addis Ababa University Press; 2021.\n\nGebre T: Environmental and socio-economic impacts of dams on rural communities: The case of Gilgel Gibe III Dam, Ethiopia. Int. J. Water Resour. Dev. 2017; 33(2): 238–251.\n\nGuest G, Bunce A, Johnson L: How many interviews are enough? An experiment with data saturation and variability. Field Methods. 2006; 18(1): 59–82. Publisher Full Text\n\nHaas M: The challenges of water governance in the global context: Lessons from the local level.Water Policy.2008; 10(2): 179–190. Publisher Full Text\n\nHart JD: The Akosombo Dam: Construction and political challenges in Ghana. J. Mod. Afr. Stud. 1980; 18(1): 145–159.\n\nHelmke G, Levitsky S: Informal Institutions and Comparative Politics: A Research Agenda. Perspect. Polit. 2004; 2(4): 725–740. Publisher Full Text\n\nHough D: Rethinking Neo-Patrimonialism: The Relationship between the State, Patronage, and Corruption. Afr. Stud. Rev. 2013; 56(2): 59–76.\n\nInternational Rivers: The Gilgel Gibe Affair: An Assessment of Corruption and Environmental Impact. International Rivers Reports.2014.\n\nInternational Water Management Institute (IWMI): Sharing the benefits of large dams in West Africa.2023. Publisher Full Text Reference Source\n\nJohnston M: Corruption and the Governance Agenda.Heywood PM, editor. The Politics of Corruption. Routledge; 2014.\n\nKaufmann D: Transparency and accountability: Imperatives for development. Glob. Gov. 2016; 22(3): 369–386.\n\nKhan MH: Governance and growth: The role of institutions in economic development.World Bank Policy Research Working Paper.2006. Publisher Full Text\n\nKim S: Anti-Corruption Measures in Infrastructure Projects: Lessons from South Korea. Asian Development Bank Working Papers.2019.\n\nKrueger AO: The Political Economy of the Rent-Seeking Society. Am. Econ. Rev. 1974; 64(3): 291–303.\n\nKumar S, Srinivas V: E-Government Procurement in India: Successes and Challenges. Journal of Public Procurement. 2018; 18(2): 124–145.\n\nLiu J, Wang W, Hwang BG: Mitigating bribery risk in construction projects: An exploratory study. J. Constr. Eng. Manag. 2016; 142(6): 04016010.\n\nMarch JG, Olsen JP: The Logic of Appropriateness. Understanding Institutions: The Science and Philosophy of Living Together. University of Chicago Press; 2008.\n\nMarshall MN: Sampling for qualitative research. Fam. Pract. 1996; 13(6): 522–526. Publisher Full Text\n\nMohammed AA: Extended Data. [Data set]. Zenodo. 2024. Publisher Full Text\n\nMulatu G: Corruption in Ethiopia: Historical overview and contemporary issues. Ethiop. J. Soc. Sci. 2021; 6(2): 101–117.\n\nMuller M: Water resource management and development: The role of dams in Africa’s economic development. Water Policy. 2018; 20(2): 240–257.\n\nMwangi O: Infrastructure Development and Corruption in Africa: A Study of Mega Projects. J. Afr. Dev. Stud. 2019a; 15(2): 97–113.\n\nMwangi O: Infrastructure Development and Corruption in Africa: A Study of Mega Projects. J. Afr. Dev. Stud. 2019a; 15(2):97–113.\n\nMwangi W: E-Procurement and its Impact on Corruption: The Case of Kenya’s Public Sector. Nairobi: University of Nairobi Press; 2019b.\n\nNational Audit Office: Annual Report on Project Management and Financial Mismanagement. Addis Ababa: 2021.\n\nNorth DC: Institutions, Institutional Change, and Economic Performance. Cambridge University Press; 1990.\n\nOrb A, Eisenhauer L, Wynaden D: Ethics in qualitative research. J. Nurs. Scholarsh. 2001; 33(1): 93–96. Publisher Full Text\n\nOstrom E: Understanding Institutional Diversity. Princeton University Press; 2005.\n\nPatton MQ: Qualitative Research & Evaluation Methods: Integrating Theory and Practice. 4th ed.SAGE Publications; 2015.\n\nPlummer J: Infrastructure, growth, and poverty reduction in Africa. Public Policy for the Private Sector Note.World Bank Group.2008. Publisher Full Text\n\nProclamation No. 590/2008: A Proclamation to Provide for Freedom of the Mass Media and Access to Information. Federal Democratic Republic of Ethiopia; 2008.\n\nReda A: The political dimensions of anti-corruption measures in Ethiopia. Addis Ababa University Press; 2018.\n\nResnik DB: The Ethics of Research with Human Subjects: Protecting People, Advancing Science, Promoting Trust. Springer; 2018.\n\nRose-Ackerman S, Palifka BJ: Corruption and Government: Causes, Consequences, and Reform. 2nd ed.Cambridge University Press; 2016.\n\nRubin HJ, Rubin IS: Qualitative Interviewing: The Art of Hearing Data. 3rd ed.SAGE Publications; 2011.\n\nScudder T: The Future of Large Dams: Dealing with Social, Environmental, Institutional and Political Costs. Earthscan; 2010.\n\nSmith D: Nigeria’s Ajaokuta Steel Project: Corruption, Mismanagement, and Failure. J. Mod. Afr. Stud. 2010; 48(3): 437–458.\n\nSovacool BK, Walter G: Major hydropower states, sustainable development, and energy security: Insights from a preliminary cross-comparative assessment.2017. Publisher Full Text\n\nSpeck BW: Fighting Corruption in Brazil: Transparency and Accountability in Infrastructure Projects. J. Infrastruct. Dev. 2011; 3(1): 45–63.\n\nTanzi V, Davoodi H: Corruption, Public Investment, and Growth. International Monetary Fund; 1997. IMF Working Paper WP/97/139.\n\nTesfaye B, Gebregziabher F: Financing large-scale infrastructure projects in Ethiopia: The challenges of cost overruns and delays. Afr. Dev. Rev. 2018; 30(3): 309–322.\n\nTeshome T: The Grand Ethiopian Renaissance Dam: Construction challenges and management practices. J. Constr. Eng. 2020; 45(1): 55–67.\n\nTransparency International: Corruption in Large Infrastructure Projects: The Role of Transparency and Accountability. Transparency International Reports.2021.\n\nTransparency International: Corruption Perceptions Index. Retrieved from Transparency International. 2022. Reference Source\n\nTransparency International: Corruption Perceptions Index (CPI) Report. Berlin: Transparency International; 2019.\n\nTsegaye G: Ethiopia’s anti-corruption efforts under Prime Minister Abiy Ahmed: A critical analysis. J. Afr. Stud. 2018; 34(2): 45–67.\n\nTsikata D: The political economy of land tenure reform in Ghana: The role of the state, communities, and the market. International Institute for Environment and Development. 2006. Reference Source\n\nVan de Walle N: African economies and the politics of permanent crisis, 1979–1999.Cambridge University Press; 2001. Publisher Full Text\n\nVerhoeven H: Water and conflict in Africa: The case of the Nile Basin. Water Alternatives. 2011; 4(3):319–338. Reference Source\n\nWang T: Sustainable development and its implementation: A global perspective.Sustain. Dev.2018; 26(5): 83–98. Publisher Full Text\n\nWiles J: Public participation in the governance of development.Int. Dev. Plan. Rev.2012; 34(4): 439–460. Publisher Full Text\n\nWorld Bank: Diagnosing Corruption in Ethiopia: Report. Washington, DC: World Bank; 2013.\n\nWorld Bank: Economic Impact of Corruption on Infrastructure Projects. Washington, D.C.: World Bank; 2020.\n\nWorld Bank: World development indicators. World Bank Publications; 2021. Reference Source\n\nWorld Bank: World development report 2019: The changing nature of work. World Bank Publications; 2019. Publisher Full Text Reference Source\n\nYehualashet D: Understanding the impact of social protection on poverty reduction in Ethiopia.Dev. Stud. Res.2017; 4(1): 42–56. Publisher Full Text\n\nYin RK: Case study research and applications: Design and methods. 6th ed.SAGE Publications; 2018. Reference Source" }	[ { "id": "343128", "date": "13 Dec 2024", "name": "Dr Garima Bhagat", "expertise": [ "Reviewer Expertise Corruption", "public construction management", "integrity risk management", "integrity climate", "public policy", "public procurement", "competition law", "anti-corruption investigation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, the work has intrinsic merits. The subject is important and corruption in large infrastructure projects is a very contemporary challenge, particularly for developing countries. However, in my view, the paper can be substantially improved, for which some suggestions may be considered by the authors.\n\n1. The background and context section can definitely be made more crisp. The basic themes presented in this section are repeated several times across the approximate 20 small paragraphs in this section. Once a theme has been identified and presented ('management inefficiencies' appears 4 times in different parts of this section), there is little value addition to the paper while compromising the economy of word length.\n\n2. In the recent times, there has been notable work in the domain of corruption in construction projects across different jurisdictions ( Owusu and Chan 2019 [Ref-1], Bhagat and Jha 2023 [Ref-2]). The discussion can be enriched by referring to latest literature and thereupon highlighting the gap in literature more emphatically.\n\n3. I would appreciate more justification for the sample size of 36 respondents. It appears small, with each sub group having 2-5 participants. With such small sub groups, how was bias addressed? Also, what was the criteria for the purposive sampling technique?\n4. The 'Results and Discussion' section is at the heart of a scholarly paper. I would advise to eschew devoting long paragraphs (in fact large parts of the entire section 4.1) to other works/ World Bank Report etc. Here, the reader is looking for the outcomes of your work. The former belongs to the introductory part of the paper.\n\n5. Was the objective of this research to confirm certain assertions about corruption in dam construction in Ethiopia? This is how the findings have been presented in the section. Was there any new/interesting finding revealed by this research? If so, please incorporate the same as that would add to the novelty of your work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "356296", "date": "21 Jan 2025", "name": "Norziaton Ismail Khan", "expertise": [ "Reviewer Expertise Forensic Accounting in Public Sector", "Fraud and Corruption", "Regulation & Political Connections", "Governance" ], "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 title \"Mega Corruptions in Mega Projects: Debating the Dynamics of Dam Construction in Ethiopia\" presents a compelling and highly relevant topic that delves into the intersection of corruption, large-scale infrastructure projects, and the socio-political context of Ethiopia. The focus on dam construction offers a specific lens through which to examine broader issues related to governance, economic development, and environmental impact. However, it can be enhanced by:\nPlease update the citations to the most recent World Bank data instead of using the ones from 2013. Each section should include additional quotes from the interviews for better clarity and depth. It is helpful to indicate which quotes come from each interviewee, as you have a total 36. Including more quotes will strengthen your arguments.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1179
https://f1000research.com/articles/12-142/v1	07 Feb 23	{ "type": "Research Article", "title": "Comparison of the antimicrobial reduction effect of photodynamic inactivation with the addition of chlorophyll and curcumin photosensitizer in Aggregatibacter actinomycetemcomitans and Enterococcus faecalis ", "authors": [ "Deny Arifianto", "Suryani Dyah Astuti", "Sarah Ratri Medyaz", "Septia Budi Lestari", "Samian Samian", "Dezy Zahrotul Istiqomah Nurdin", "Dita Ayu Hariyani", "Yunus Susilo", "Ardiansyah Syahrom", "Deny Arifianto", "Sarah Ratri Medyaz", "Septia Budi Lestari", "Samian Samian", "Dezy Zahrotul Istiqomah Nurdin", "Dita Ayu Hariyani", "Yunus Susilo", "Ardiansyah Syahrom" ], "abstract": "Background: Aggregatibacter actinomycetemcomitans and Enterococcus faecalis are pathogenic bacteria of the oral cavity that cause various diseases such as periodontitis and endodontics. These bacteria are easily resistant to antibiotics. Photodynamic inactivation (PDI) is a method of inactivating microorganisms that utilizes light to activate a photosensitizer agent (PS) that produces reactive oxygen species causing cell lysis. Methods: This study used the PDI method with a 405 nm diode laser at various energy density with the addition PS curcumin or chlorophyll Alfalfa, as much as 1.6 mg/ml on A. actinomycetemcomitans and E. faecalis bacteria. Results: The study on E. faecalis bacteria showed that the energy density diode laser irradiation of 1.59 J/cm² gave the percentage of E. faecalis bacteria death 36.7% without PS, 69.30% with the addition of chlorophyll Medicago sativa L and 89.42% with the addition of curcumin. Meanwhile, the bacteria A. actinomycetemcomitans showed that the energy density diode laser irradiation of 1.59 J/cm² gave the percentage of bacterial death 35.81% without PS, 64.39% with the addition of chlorophyll Medicago sativa L and 89.82% with the addition of curcumin. PS was critical to the success of the PDI. Conclusions: The addition of PS curcumin increased the effectiveness of reducing bacteria E. faecalis and A. actinomycetemcomitans compared to chlorophyll Medicago sativa L.", "keywords": [ "Aggregatibacter actinomycetemcomitans", "Enterococcus faecalis", "photodynamic inactivation", "diode laser", "diseases", "periodontitis", "curcumin", "chlorophyll" ], "content": "Introduction\n\nThe oral cavity is one of the most important parts of the body that must be maintained. Infectious diseases of the teeth and mouth that are often found are periodontitis and endodontics. Periodontitis is a bacterial infection of the teeth that causes inflammation of the supporting tissues of the teeth, which include the gingiva, ligaments, cement, and alveolar bone.1 Periodontitis is caused by pathogenic bacteria, predominantly gram-negative, anaerobic, or microaerophilic in the subgingival area.2 Aggregatibacter actinomycetemcomitans bacteria are found in dental plaque, periodontal pockets, and buccal mucosa in up to 36% of the normal population.3 Aggregatibacter actinomycetemcomitans bacteria can infect patients when the human immune system decreases and inhibits other organisms' growth in the oral mucosa, teeth, and nasopharynx.\n\nIn general, gram-positive bacteria, Enterococcus faecalis (E. faecalis), are found in the root canals of teeth. The bacterium Enterococcus faecalis is ovoid, with a diameter between 0.5 and 1 μm.4 These bacteria are facultative anaerobes and can survive in extreme environments such as highly alkaline pH and high salt concentration conditions. The number of these bacteria in the human body can be minimized by paying attention to the food consumed and environmental conditions such as humidity. Furthermore, E. faecalis bacteria resist calcium hydroxide and antibiotics such as tetracycline.5 Systemic treatment in the form of antibiotics has been widely used to treat periodontitis. However, several studies have reported cases of antimicrobial resistance to certain types of antibiotics. So alternative therapy is needed that is effective and does not cause antibiotic resistance.6 Therefore, the recommended alternative therapy in this study is photodynamic inactivation (PDI).\n\nPhotodynamic inactivation (PDI) is a method of inactivating microorganisms by utilizing light to activate a photosensitizer (PS) agent that produces reactive oxygen species (ROS), causing cell lysis.7,8 The suitability of the light spectrum with the PS absorption spectrum is the key to photophysical reactions, namely the absorption of light energy by PS agents, which will trigger photochemical and photobiological reactions to produce antimicrobial effects9,10 and biomodulation.11 PS is a light-sensitive molecule that plays a role in absorbing light energy. PS is divided into two types, namely endogenous and exogenous photosensitizers. The addition of exogenous PS aims to increase the effectiveness of light energy absorption.12 Some natural ingredients that are exogenous PS include chlorophyll and curcumin. Chlorophyll is a green substance found in green plants that photosynthesizes.13 In photosynthesis, chlorophyll acts as a light catcher, energy transfer, and light conversion and can absorb a maximum wavelength between 400-700 nm.14 Curcumin is a curcuminoid compound with yellow pigment in turmeric rhizome, which is antitumor, antioxidant, anticarcinogenic, anti-inflammatory, antiviral, antifungal, antispasmodic, and hepatoprotective.15 The absorption spectrum of curcumin is in the wavelength range of 375-475 nm.16\n\nPrevious studies have reported the effectiveness of using PS chlorophyll in alfalfa leaves with a blue LED activator of 20.48 J/cm2 for the inactivation of A. actinomycetemcomitans bacteria by 81%.17 The results of another study with the addition of PS curcumin and diode laser activator 403 nm 15.83 J/cm2 in Staphylococcus aureus resulted in a mortality rate of 85.48%.16 Then, another study using curcumin and blue LEDs on S. aureus bacteria resulted in a mortality rate of 91.49%.18 Continuing previous studies,15,16,18 this study aims to compare the effectiveness of antimicrobial reduction from photodynamic inactivation (PDI) on bacteria A. actinomycetemcomitans and E. faecalis with PS curcumin and chlorophyll Medicago sativa L. using a 405 nm diode laser. Diode laser irradiation was carried out at various lengths of irradiation time, namely (30, 60, 90, 120, 150, and 180) seconds.\n\n\nMethods\n\nBacteria A. actinomycetemcomitans ATCC 43718 and E. faecalis ATCC 29212 were cultured in Tryptone Soy Broth (TSB). Then, they were incubated for 24 hours at 37oC until the colonies reached ~108 CFU/mL or 1.0 McFarland standard. The culture was placed 100 L on 96-well microplates and incubated for 48 hours.\n\nChlorophyll was extracted from Medicago sativa L (K-Link liquid, Indonesia) and Curcuma standard (Sigma Aldrich) with a concentration of 1.6 mg/ml diluted with sterile normal saline. The absorption spectrum of chlorophyll was measured using Shimadzu UV-VIS 1800 spectrometer.\n\nThe light source of a laser diode is 405 nm, and characterization was carried out using Jasco CT–10 monochromators to determine the peak wavelength. The power output was 2.49 mW, measured with power meter OMM-6810B-220V. The spot beam area size was 0.28 cm2. Diode laser irradiation was carried out with variations in the length of the irradiation time of 30, 60, 90, 120, 150, and 180 seconds. The energy density value can be calculated using equation 19:\n\nThe treatment samples consisted of two types of bacteria, A. actinomycetemcomitans and E. faecalis. The bacterial PDI treatment consisted of a negative control group without treatment (T0), a positive control group with the addition of chlorophyll and curcumin (T1), a 405 nm diode laser treatment group at various energy densities of 0.26; 0.53; 0.79; 1.06; 1.32; 1.59 J/cm2 (S1), a 405 nm diode laser treatment group with the addition of chlorophyll Medicago sativa L 1.6 mg/ml (S2), and a 405 nm diode laser treatment group with the addition of curcumin PS 1.6 mg/ml (S3). In groups S2 and S3, samples were given chlorophyll or curcumin and they were incubated for 10 minutes, then irradiated with 405 nm diode laser with an exposure time (30, 60, 90, 120, 150, and 180 seconds). The treated samples were grown on TSA media, incubated for 24 hours at 37C, and the number of bacterial colonies grown was counted by the Total Plate Count method.\n\nEach treatment was calculated as CFU/ml using equation 2. Next, the percentage of bacterial reduction was calculated using equation 3 based on the control group. The results of bacterial reduction were statistically analyzed by ANOVA test using IBM SPSS Statistics Version 21.\n\n\nResults\n\nThe chlorophyll and curcumin extracts were tested using UV-Vis at a wavelength range of 325 nm to 705 nm to determine the absorption spectrum of light. Then, the results of the characterization of the absorption spectrum of chlorophyll and curcumin to light are obtained, as shown in Figures 1 and 2. Based on Table 1, the characterization results show the peak wavelength of the laser diode at 405 nm with the stability of the output power at a distance of 1 cm (2.49 ±0.07) mW. The temperature characterization showed the optimum temperature stability (26.60±0.01)oC for bacterial growth. Thus, the irradiation energy density of the laser diode is 405 nm with an output power of 2.49 mW and a beam area of 0.28 at various exposure times (30, 60, 90, 120, 150, 180) seconds are 0.26; 0.53; 0.79; 1.06; 1.32 and 1.59 J/cm2.\n\nAfter that, antibacterial tests were carried out on Aggregatibacter actinomycetemcomitans and Enterococcus faecalis bacteria, which were exposed to a diode laser with and without a photosensitizer. The viability of the bacteria Aggregatibacter actinomycetemcomitans and Enterococcus faecalis are shown in Figures 3 and 4. Based on bacterial viability, the percentages of death of A. actinomycetemcomitans and E. faecalis bacteria by diode laser irradiation with the addition of curcumin photosensitizer and Medicago sativa L chlorophyll treatment are shown in Figures 5 and 6.\n\nBased on the results of statistical tests, it was shown that diode laser irradiation with an energy density of 1.59 J/cm2 gave a percentage of E. faecalis bacteria death of 36.7% without adding a photosensitizer. Then, the percentage of death of E. faecalis bacteria was 69.30% with the addition of PS chlorophyll Medicago sativa L. and 89.42% with the addition of PS curcumin. Meanwhile, the results of statistical tests on bacteria A. actinomycetemcomitans with diode laser irradiation at an energy density of 1.59 J/cm2 gave the percentage of bacterial death of 35.81% without the addition of PS. Then, the death of A. actinomycetemcomitans was 64.39% with the addition of PS chlorophyll Medicago sativa L and 89.82% with the addition of PS curcumin.was 64.39% with the addition of PS chlorophyll Medicago sativa L and 89.82% with the addition of PS curcumin.\n\n\nDiscussion\n\nThis research was conducted using the PDI technique using a blue diode laser as a light source, chlorophyll Medicago sativa L and curcumin as PS to reduce bacteria E. faecalis and A. actinomycetemcomitans. The wavelength of light is an important factor in the photoinactivation process. The laser diode used in this study has a wavelength of 405 nm and output power of 2.49 mW. The results of the characterization of power against time and temperature show the stability of power and temperature so that the temperature factor does not cause the death of bacteria.\n\nPS is a light-sensitive molecule. Exogenous PS is PS that is added to assist the photoinactivation process. This study used exogenous PS chlorophyll Medicago sativa L and curcumin. Medicago sativa L chlorophyll absorbance used for a laser wavelength of 405 nm was 85.1% and for curcumin was 80.64%.18 The photoinactivation process occurs due to a photophysical mechanism initiated by the absorption of light by PS. The energy of the absorbed photon will cause the excitation of the electron to increase to a higher energy level. If the energy excitation state overlaps with the triplet excitation state, an intersystem crossing occurs, a spin reversal that places the electron in a triplet excited state and triggers a photochemical reaction.\n\nPhotochemical reactions are divided into two types. The first type is the transfer of electrons to a biological substrate in the form of a redox reaction and produces singlet oxygen. The second type is the transfer of energy to the triplet electrons to produce singlet oxygen. Singlet oxygen is radical. If attached to lipids and membrane proteins, it will cause peroxidation and damage cell membranes, causing leakage and cell lysis.18 The photochemical reactions in PDI are generally of the second type.\n\nThe study's results on E. faecalis bacteria showed a significant difference between treatments. Diode laser irradiation with an energy density of 1.59 J/cm2 gave the percentage of bacterial death of E. faecalis 36.7% without the addition of PS, 69.30% with the addition of PS chlorophyll Medicago sativa L and 89.42% with the addition of PS curcumin. Meanwhile, in A. actinomycetemcomitans bacteria with energy density diode laser irradiation 1.59 J/cm2, the percentage of bacterial death was 35.81% with the addition of PS, 64.39% with the addition of PS chlorophyll Medicago sativa L and 89.82% with the addition of PS curcumin.\n\nThe results showed that adding PS curcumin increased the effectiveness of reducing E. faecalis and A. actinomycetemcomitans bacteria. PDI with PS curcumin was effectively used to reduce bacteria because its absorption followed endogenous porphyrins.19 The addition of energy density will increase the reduction effect without and with the addition of PS Medicago sativa L17 and curcumin.18\n\n\nConclusion\n\nBased on statistical tests, the results of research on E. faecalis bacteria showed that laser irradiation with an energy density of 1.59 J/cm2 gave a percentage of E. faecalis bacteria mortality of 36.7% without the addition of PS, 69.30% with the addition of PS chlorophyll Medicago sativa L and 89.42% with the addition of PS curcumin. Meanwhile, A. actinomycetemcomitans showed that the energy density diode laser irradiation of 1.59 J/cm2 gave the percentage of bacterial death 35.81% without the addition of PS, 64.39% with the addition of PS chlorophyll Medicago sativa L and 89.82% with the addition of PS curcumin. So it can be concluded that the role of PS is significant for the success of PDI. The addition of PS curcumin increased the effectiveness of reducing bacteria E. faecalis and A. actinomycetemcomitans compared to chlorophyll Medicago sativa L.\n\n\nAuthor contributions\n\nDA contributes to the data curation, methodology, validation, original draft preparation of the work and editing of the work. SDA contributes to the conception, methodology, analysis, funding acquisitions, project administration, supervision, validation, review, original draft preparation of the work and editing of the work. SRM, SBL, DZIN, and DAH contribute to the conception, data curation, methodology, investigation, validation, original draft preparation of the work and editing of the work. S contributes to the conception, methodology, investigation, analysis, supervision, validation, review, original draft preparation of the work and editing of the work. YS contributes to the conception, data curation, methodology, investigation, validation, original draft preparation of the work and editing of the work. AS contributes to the conception, methodology, analysis, supervision, validation, review, original draft preparation of the work and editing of the work.", "appendix": "Data availability\n\nOpen Science Framework: Antimicrobial Reduction Effect of Photodynamic Inactivation with The Addition Photosensitizer. https://doi.org/10.17605/OSF.IO/BEZ2R. 20\n\nThis project contains the following files:\n\n- Table 1. Laser energy density at various time exposure.docx (The laser parameters used in this research)\n\n- Bacterial Treatment Group Aggregatibacter actinomycetemcomitant\n\n• CFU Calculation Aggregatibacter actinomycetemcomitant.xlsx\n\n• Excel of Bacterial Viability.xls\n\n• Graph of Bacterial Viability.jpg\n\n- Bacterial Treatment Group Enterococcus faecalis\n\n• CFU Calculation Bacterial Treatment Group Enterococcus faecalis.xlsx\n\n• Excel of Bacterial Viability.xls\n\n• Graph of Bacterial Viabilty.jpg\n\nOpen Science Framework: Antimicrobial Reduction Effect of Photodynamic Inactivation with The Addition Photosensitizer. https://doi.org/10.17605/OSF.IO/BEZ2R. 20\n\nThis project contains the following extended data:\n\n- Figure 1. Graph of curcumin absorption spectrum.jpg\n\n- Figure 2. Graph of Chlorophyll Absorption Spectrum.jpg.\n\n- Figure 3. Graph of bacterial viability of A. actinomycetemcomitans in various treatment.jpg.\n\n- Figure 4. Graph of bacterial viability of E. faecalis in various treatment.jpg.\n\n- Figure 5. Graph of the percentage of death of A. actinomycetemcomitans.jpg.\n\n- Figure 6. Graph of the percentage of death of E. faecalis.jpg\n\n- Equipment used during the research.docx\n\n- The materials used during the research.docx\n\n- Treatment process.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to thank Dr Riries Rulaningtyas for providing advice and supervision for this manuscript.\n\n\nReferences\n\nKönönen E, Gursoy M, Gursoy UK:Periodontitis: A multifaceted disease of tooth-supporting tissues. J. Clin. Med. Aug. 01, 2019; vol. 8(no. 8). MDPI. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang YL, der Liou J , Pan WL:Association between maternal periodontal disease and preterm delivery and low birth weight. Taiwan. J. Obstet. Gynecol. Mar. 2013; 52(1): 71–76. Publisher Full Text\n\nSetiawatie EM, Dyah Astuti S, Zaidan AH:An in vitro Anti-microbial Photodynamic Therapy Ernie Maduratna Setiawatie, and et al An in vitro Anti-microbial Photodynamic Therapy (aPDT) with Blue LEDs to Activate Chlorophylls of Alfalfa Medicago sativa L on Aggregatibacter actinomycetemcomitans.2016.Reference Source\n\nGoenawan M, Nugroho JJ, Anastasia CR, et al.:Effectivity of convex triangular and rectangular cross section instruments on decreasing the amount of root canal Enterococcus faecalis bacteria colonies. Journal of Dentomaxillofacial Science. Aug. 2016; 1(2): 120. Publisher Full Text\n\nSeguel N, Quezada-Aguiluz M, González-Rocha G, et al.:Antibiotic Resistance of Enterococcus faecalis from Persistent Endodontic Infections Resistencia Antibiótica de Enterococcus faecalis Provenientes de Infecciones Endodónticas Persistentes Antibiotic resistance of Enterococcus faecalis from persistent endodontic infections. Int. J. Odontostomat. 2020; 14(3): 448–456. Publisher Full Text\n\nVohra F, Akram Z, Safii SH, et al.:Role of antimicrobial photodynamic therapy in the treatment of aggressive periodontitis: A systematic review. Photodiagn. Photodyn. Ther. Mar. 01, 2016; vol. 13. Elsevier B.V. pp. 139–147. PubMed Abstract \| Publisher Full Text\n\nAstuti SD, Arifianto D, Drantantiyas ND, et al.:Efficacy of CNC-diode laser combine with chlorophylls to eliminate staphylococcus aureus biofilm. 2016 International Seminar on Sensors, Instrumentation, Measurement and Metrology (ISSIMM). IEEE. (pp. 57–61). Publisher Full Text\n\nCosta AC, Chibebe Junior J, Pereira CA, et al.:Susceptibility of planktonic cultures of Streptococcus mutans to photodynamic therapy with a light emitting diode. Braz. Oral Res. 2020; 24(4): 413–418. PubMed Abstract \| Publisher Full Text\n\nAstuti SD, Widya IW, Arifianto D, et al.:Effectiveness Photodynamic Inactivation with Wide Spectrum Range of Diode Laser to Staphylococcus aureus Bacteria with Endogenous Photosensitizer: An in vitro Study. J. Int. Dent. Med. Res. 2019; 12(2): 481–486.http://www.ektodermaldisplazi.com/journal.htm\n\nPlaetzer K, Krammer B, Berlanda J, et al.:Photophysics and photochemistry of photodynamic therapy: fundamental aspects. Lasers Med. Sci. 2009; 24(2): 259–268. PubMed Abstract \| Publisher Full Text\n\nLima PL, Pereira CV, Nissanka N, et al.:Photobiomodulation enhancement of cell proliferation at 660 nm does not require cytochrome c oxidase. J. Photochem. Photobiol. B Biol. 2019; 194: 71–75. PubMed Abstract \| Publisher Full Text\n\nMoslemi N, Azar SZ, Bahador A, et al.:Inactivation of Aggregatibacter actinomycetemcomitans by two different modalities of photodynamic therapy using Toluidine blue O or Radachlorin as photosensitizers: an in vitro study. Lasers Med. Sci. 2014; 30(1): 89–94. PubMed Abstract \| Publisher Full Text\n\nAstuti SD, Drantantiyas NDG, Putra AP, et al.:Photodynamic effectiveness of laser diode combined with ozone to reduce Staphylicoccus aureus biofilm with exogenous chlorophyll of Dracaena angustifolia leaves. Biomed. Photonics. 2019; 8(2): 4–13. Publisher Full Text\n\nAstuty SD, Suhariningsih AB, Astuti SD:The Efficacy of Photodynamic Inactivation of the Diode Laser in Inactivation of the Candida albicans Biofilms With Exogenous Photosensitizer of Papaya Leaf Chlorophyll. J. Lasers Med Sci. 2019; 10(3): 215–224. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAkram M, Shahab-Uddin AA, Usmanghani KHAN, et al.:Curcuma longa and curcumin: a review article. Rom. J. Biol. Plant. Biol. 2010; 55(2): 65–70.\n\nAstuti SD, Wibowo RA, Abdurachman NIDN, et al.:Antimicrobial photodynamic effects of polychromatic light activated by magnetic fields to bacterial viability. J. Int. Dent. Med. Res. 2017; 10(1): 111–117.\n\nSunarko SA, Ekasari W, Astuti SD:Antimicrobial effect of pleomeleangustifolia pheophytin A activation with diode laser to streptococcus mutans. J. Phys. Conf. Ser. IOP Publishing;2017; (Vol. 853(No. 1): p. 012039). Publisher Full Text\n\nSetiawatie EM, Astuti SD, Zaidan AH:An in vitro Anti-microbial Photodynamic Therapy (aPDT) with Blue LEDs to Activate Chlorophylls of Alfalfa Medicago sativa L on Aggregatibacter actinomycetemcomitans. J. Int. Dent. Med. Res. 9(2): 118–125.\n\nHakimiha N, Khoei F, Bahador A:The susceptibility of Streptococcus mutans to antibacterial photodynamic therapy: a comparison of two different photosensitizers and light sources. J. Appl. Oral Sci. 2014; 22(2): 80–84. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAstuti SD: Antimicrobial Reduction Effect of Photodynamic Inactivation with The Addition Photosensitizer. [Dataset].2022, December 13. Publisher Full Text" }	[ { "id": "221717", "date": "13 Feb 2024", "name": "Min Wu", "expertise": [ "Reviewer Expertise Light-based therapy for both bench work and clinical work" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 about comparison of the antimicrobial reduction effect of two PSs in different bacteria related to oral cavity causing various diseases such as periodontitis and endodontics.\n\nI think the purpose and design of this manuscript is quite clear but a little bit too simple.\n\nI think it would be better if in vivo study is included to make the work more solid. For in vitro study, I think the authors can also add different types of ROS probe and even perform the biofilm experiment to support their conclusions. This manuscript focused on two pathogens highly related to various oral diseases. They used photodynamic inactivation (PDI) to deal with these pathogens. The photosensitizer are chlorophyll and curcumin. The light source is aBL (405nm), and treatment is aPDI. The data only include CFU which is gold standard and survival rate. They compared between different groups including light alone and negative control. The conclusions are also very clear.\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?\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": "11154", "date": "13 Apr 2024", "name": "Suryani Dyah Astuti", "role": "Author Response", "response": "Thanks for valuable comments and suggestions for our manuscript. We have revised the manuscript according to the reviewers’ comments and answered them accurately. Some parts of the manuscript have been changed. 1. The purpose and design of this manuscript is quite clear but a little bit too simple. Provide further comments here: We would like to say thank you for your valuable suggestion and the opportunity to revise the manuscript. We already revised it. The purpose of this manuscript: Continuing previous studies [15,16,18], this study aims to compare the effectiveness of antimicrobial reduction from photodynamic inactivation (PDI) on bacteria A. actinomycetemcomitans and E. faecalis with PS curcumin and chlorophyll Medicago sativa L. using a 405 nm diode laser. Diode laser irradiation was carried out at various lengths of irradiation time, namely (30, 60, 90, 120, 150, and 180) seconds. In addition, this study aims to determine the effective laser irradiation time to reduce the bacteria A. actinomycetemcomitans and E. faecalis with PS curcumin and chlorophyll Medicago sativa L. The design of this manuscript: CFU/ml was calculated for each treatment using Equation 2. Furthermore, the percentage of bacterial reduction was calculated using Equation 3 based on the control group. The results of bacterial reduction were statistically analyzed using the Two Way Anova Factorial test using IBM SPSS Statistics Version 21 to determine the effect of each factor and its interaction between factors. The test usually requires distributed and at least interval scale data, with significant differences determined as P<α=0.05. Tukey's post hoc test and Kolmogorov-Smirnov test were used to check the normality of the data. 2. I think it would be better if in vivo study is included to make the work more solid. For in vitro study, I think the authors can also add different types of ROS probe and even perform the biofilm experiment to support their conclusions. Provide further comments here: We would like to say thank you for your valuable suggestion and the opportunity to revise the manuscript. We already revised it. The mechanism of Photodynamic Inactivation (PDI) is illustrated in Figure 7. Photochemical reactions are divided into two types. The first type is the transfer of electrons to a biological substrate in the form of a redox reaction and produces singlet oxygen. The second type is the transfer of energy to the triplet electrons to produce singlet oxygen. Singlet oxygen is a radical. Reactive Oxygen Species (ROS) can damage the bacterial cell membrane and cause lysis. This is the earliest stage in bacterial cell death. Photochemical activity generates ROS and triplet oxygen radicals that oxidize unsaturated fatty acids, producing hydroperoxides. These radicals interfere with the synthesis of saturated fatty acids, causing harmful hydroperoxides known as lipid peroxidation. This disruption of the bacterial cell wall leads to cell lysis [18]. The photochemical reactions in PDI are generally of the second type. In vivo studies are found in other journals [20,21]. The effect of bacterial photoinactivation on wounds in vivo due to photodynamic therapy in the red LED exposure group was 88%, the blue LED exposure group was 94%, and the red and blue LED combination exposure group was 95% [20]. Blue and red lasers combined with ozone treatment effectively accelerated wound healing of incisions infected with MRSA bacteria [21]. Thus, LED antimicrobial photodynamic therapy is effective for bacterial inactivation and accelerates wound healing in mice. Biofilm research is also found in other journals [22,23]. The difference in the reduction rate of PDT increased when ozone was added, thus helping biofilm reduction compared to PDT [22]. The results showed that the Chlo+Ozon+Laser combination treatment at 20 seconds of ozone exposure with 4 minutes irradiation time caused a decrease in biofilm activity by 80.26%, which was the highest efficacy of all treatment groups. The combination of laser, chlorophyll, and lower ozone concentration increased the effectiveness of photodynamic inactivation [24]." } ] } ]	1	https://f1000research.com/articles/12-142
https://f1000research.com/articles/13-1177/v1	09 Oct 24	{ "type": "Data Note", "title": "Morphological and Autofluorescence Dataset for ‘Touch’ Epidermal Cell Populations Collected with Imaging Flow Cytometry", "authors": [ "Arianna DeCorte", "Gabrielle Wolfe", "Nicole Dailey", "M. Katherine Philpott", "Amanda E. Gentry", "Christopher J. Ehrhardt", "Arianna DeCorte", "Gabrielle Wolfe", "Nicole Dailey", "M. Katherine Philpott", "Amanda E. Gentry" ], "abstract": "Background New methods for processing ‘touch’ or trace biological samples is an ongoing priority for forensic caseworking laboratories. These samples often contain materials from multiple individuals in varying quantities and/or degrees of degradation. Rapid characterization of cellular material before DNA profiling can allow laboratories to screen samples for the presence of multiple contributors or the amount of biological material present.\n\nMethods This dataset contains autofluorescence and morphological profiles of epidermal cell populations analyzed using Imaging Flow Cytometry. The epidermal samples were aged for varying amounts of time prior to analysis. Multiple samples from the same individual were also collected to assess profile variations within and across the contributors.\n\nConclusions This data set may be used to investigate variability in epidermal cell populations from different individuals and potential forensic signatures contained within the non-genetic components that comprise touch biological evidence.", "keywords": [ "Forensic Science", "Imaging Flow Cytometry", "Autofluorescence", "Forensic Biology", "Forensic DNA Profiling" ], "content": "Introduction\n\nOne of the most prevalent and challenging types of evidence submitted to forensic laboratories is ‘touch’ biological samples. These are created when one or more individuals handle a substrate and transfer cellular and/or genetic material onto its surface. As touch evidence is often composed of contributions from multiple individuals (e.g. Burrill et al., 2019, 2022), the resulting DNA profiles can be difficult to interpret, leading to delays in processing time and/or loss of the sample’s probative value. Autofluorescence profiling of cell populations may provide a way to rapidly detect when a sample contains cells from multiple individuals. Previous research has shown that epidermal cell populations from different individuals can show distinct variations in the intensity of autofluorescence at specific excitation wavelengths and emission channels (Stanciu et al., 2016). Furthermore, donor-specific autofluorescence signatures can be used to separate cells from different contributors prior to DNA profiling (Philpott et al., 2017). Using these studies as a foundation, we have built a dataset of a range of relevant sample types that have been characterized using Imaging Flow Cytometry (IFC): cell populations collected directly from the palm, as well as swabbings of handled items of known and unknown provenance (i.e. controlled and uncontrolled ‘touch’ samples). IFC collects both autofluorescence and morphological measurements from individual cells within a sample in a high-throughput manner. This can facilitate the development of forensic signatures for rapidly detecting whether an evidentiary sample contains biological deposits from multiple individuals or a single contributor, or to develop front-end methods for separating cells based on morphological or fluorescent properties. As part of this dataset, we included replicate samples from the same individual to assess intra-donor variability of autofluorescence/morphological characteristics, as well as samples aged for varying time intervals before IFC analysis to assess the impact that this may have on the individualizing features of epidermal cells.\n\n\nMethods\n\nAll procedures for collecting epidermal cell populations were reviewed and approved by the Virginia Commonwealth University Institutional Review Board (Protocol# HM2000454; Approved 4/3/23). Written informed consent was obtained from all participants. Samples were collected between 4/30/23 and 6/30/24. Samples were collected from participants either by swabbing the palmar surface using a pre-wetted cotton swab (Puritan, P/N) or by having individuals handle the substrate (e.g., a plastic tube or knife handle) for approximately 3 min. Samples were collected from the handled substrates in a similar manner (i.e., surface swabbed with a pre-wetted cotton swab). All swabs were placed in 1mL of sterile H2O and incubated for 15 min at room temperature. During this incubation step, the swabs were agitated every 5 min using a pulse vortex set at 3000 rpm. This facilitated the removal of cells from the cotton matrix of the swab into the solution. Next, the swab was removed and the resulting cell solution was centrifuged at 10,000 × g for 5 min to pellet the cells, decanted to remove the supernatant, and resuspended in 1mL of sterile H2O. This washing step was performed twice. During the final wash step, the cells were resuspended in 50 μL H2O prior to IFC.\n\nSamples were analyzed using the Amnis® Flowsight® imaging flow cytometer (Cytek Biosciences, Dallas, TX, USA) equipped with 405 nm, 488 nm, 642 nm, and 785 nm lasers in a dual channel configuration. The voltages were set to 100 mW, 60 mW, 100 mW, and 6.25 mW, respectively. Images of individual events were captured at 20× magnification in nine fluorescent detector channels, two bright field channels (channels 1 and 9), and a side-scatter channel (channel 6). Excitation lasers and emission channels were configured in a dual-channel arrangement such that the 488 nm and 785 nm excitation lasers were associated with channels 1-6 and the 405 nm and 642 nm excitation lasers were associated with channels 7-12. The emission wavelengths for each detector channel used for autofluorescence data collection were as follows: channel 2 (505–560 nm), channel 3 (560–595 nm), channel 4 (595–642 nm), channel 5 (642-745 nm); (745 nm), channel 7 (435–505); channel 8 (595–560 nm), channel 10 (595–642 nm), channel 11 (642–745 nm), and channel 12 (745–800 nm). The IFC data were saved in a raw image format (. rif). Alpha-numeric codes were used to designate data files from different individuals. The time between sample collection/deposition and IFC analysis is listed for each sample, along with whether the sample was taken by swabbing the individual’s hand or swabbing a substrate surface after handling by the individual.\n\nSamples were obtained from 57 unique individuals and aged between 0-3,650 days with some samples aged to different time points before analysis.\n\nN/A\n\nAll sampling procedures were reviewed and approved by the Virginia Commonwealth University Institutional Review Board (Protocol# HM2000454; Approved 4/3/23). Written informed consent was obtained from all participants.\n\n\nAuthor contributions\n\nCE conceived the study. CE, AG, and KP designed experiments. AD, GW, and ND conducted this research. CE prepared the first draft of the manuscript. CE, KP, and AG revised the manuscript.", "appendix": "Data availability\n\nFigshare: Morphological and Autofluorescence Dataset for ‘Touch’ Epidermal Cell Populations, DOI: https://doi.org/10.6084/m9.figshare.27068128.v3 (Ehrhardt et al., 2024).\n\nThe project contains the following underlying data:\n\n• Imaging Flow Cytometry source data were provided in the raw image format (. rif ).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe source data files were labeled with an anonymized sample ID number, date of analysis, and time between sample deposition and analysis. Epidermal cell populations taken from touched surfaces are labeled by anonymized ID and the type of substrate (e.g., conical tube, knife handle). Examples of image galleries for individual cells across bright field and fluorescence channels are provided in tiff format.\n\n\nAcknowledgements\n\nNone.\n\n\nReferences\n\nBurrill J, Daniel B, Frascione N: A review of trace “Touch DNA” deposits: Variability factors and an exploration of cellular composition. Forensic Sci. Int. Genet. 2019; 39: 8–18. PubMed Abstract \| Publisher Full Text\n\nBurrill J, Daniel B, Frascione N: Lysis and purification methods for increased recovery of DNA degraded from the touch-deposit swabs. Forensic Sci. Int. 2022; 330: 111102. PubMed Abstract \| Publisher Full Text\n\nEhrhardt C, et al.: Morphological and Autofluorescence Dataset for ‘Touch’ Epidermal Cell Populations. Dataset. figshare. 2024. Publisher Full Text\n\nPhilpott MK, Stanciu CE, Kwon Y, et al.: Analysis of cellular autofluorescence in touch samples by flow cytometry: implication for the front end separation of trace mixture evidence. Anal. Bioanal. Chem. 2017; 409(17): 4167–4179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStanciu CE, Philpott MK, Bustamante EE, et al.: Analysis of red autofluorescence (650-670nm) in epidermal cell populations and its potential for distinguishing contributors to ‘touch’ biological samples. F1000 Res. 2016; 5: 180. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "343846", "date": "11 Jan 2025", "name": "Dan Nana Osei Bonsu", "expertise": [ "Reviewer Expertise Forensic Biology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript and accompanying dataset potentially represent a valuable contribution to forensic science, particularly in the analysis of 'touch' epidermal cell populations and the growing interest in biological deconvolution for mixture analysis.\nHowever, the following limitations are evident:\nThe use of the .rif (raw image format) file type is a primary limitation, as it is not easily visualizable on Figshare. I was unable to obtain the necessary software for a comprehensive review, and the manuscript does not recommend tools to view these files, limiting accessibility and usability. The representative IFC images are insufficient. The manuscript, structured as a data descriptor, lacks sections on results, discussion, or conclusions although the methods section is comprehensive. This omission leaves readers without clear guidance on interpreting the data or conducting specific analyses, making it difficult to understand the individualizing features of epidermal cell populations or the effects of sample aging. If readers are expected to refer to other publications for data interpretation, these should be clearly indicated/cited, with their relevance explained.\nThe authors should provide additional guidance and preliminary analyses to help readers fully utilize this comprehensive epidermal cell population dataset.\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? No", "responses": [] } ]	1	https://f1000research.com/articles/13-1177
https://f1000research.com/articles/11-308/v1	14 Mar 22	{ "type": "Research Article", "title": "Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time", "authors": [ "Soichi Osozawa", "John Wakabayashi", "John Wakabayashi" ], "abstract": "We developed a new time-calibrated tree incorporating primarily endemic along with some cryptic Ryukyu islands cicada data, following the recent publication of global cicada data by Marshall et al. (2018), Łukasik et al. (2018), Simon et al. (2019), Price et al. (2019), and Hill et al. (2021). A total of 352 specimens were analyzed using BEAST v1. X software with a relaxed clock model. Fossil calibrations as old as Triassic were adopted largely following Johnson et al. (2018) and Moulds (2018), and a Quaternary geological event calibration was adopted following Osozawa et al. (2012, 2021b) and input into BEAST v1. X. Our timetree suggests that Tettigarctidae had a cicada basal lineage as old as 200.63 Ma, with Derotettiginae the next oldest lineage at 99.2 Ma. Tibicininae is a sister of the remaining subfamilies of Tettigomyiinae, Cicadettinae, and Cicadidae, and their species level differentiation and radiation began at 40.57 Ma. The Cicadinae clade consists of specific tribes with parapheletic relationship, and the vicariance and adaptive radiation generated many cryptic species in each tribe. We estimated base substitution rate as a function of age, and the result strongly indicates an exponential increase of base substitution rate in recent geologic time. The consequent increase in cicada biodiversity, including generation of cryptic species in the Ryukyu Islands and surroundings, may have been driven by the generation and spreading of C4 grasses and coeval Quaternary climate change.", "keywords": [ "fossil calibration", "geological event calibration", "exponentially increase", "base substitution rate", "increased biodiversity", "cryptic species", "ice age", "C4 grasses" ], "content": "Introduction\n\nA phylogenetic tree of worldwide cicada was recently constructed by Marshall et al. (2018) and Simon et al. (2019) applying five concatenated sequences of mitochondrial COI and COII, and nuclear ARD1, EF-1a, and 18S rRNA, and by Łukasik et al. (2019) applying whole mitochondrial sequences for representative species in Marshall et al. (2018), and family level phylogenetic relation has been clarified. Although Tettigarctinae is an old diverged lineage and Derotettiginae may be next, their worldwide phylogenetic trees were not dated trees. Price et al. (2019; restricted to Platypleurini) and Hill et al. (2021; restricted to Asian Cicadinae) built partial (not worldwide) dated trees using BEAST v.2.5 (Bouckaert et al. 2014) applying COI and other sequences, but much of global cicada evolution has not been tied to absolute time.\n\nThe latest version of BEAST (Bayesian Evolutionary Analysis Sampling Trees v1. X; v1.10.4 2021; Suchard et al. 2018) released on 10 June 2018 has a clear and simple age calibration protocol and function, updated from BEAST v.1. 7 (v1. X ≒ v.1. 8). This calibration involves applying times of the most recent common ancestors (tMRCAs) of the ingroup species, i.e., applying the node age of a specific clade as a minimum age, in the associated software of BEAUti (Bayesian Evolutionary Analysis Utility; BEAST is the platform software). The maximum age constraint normally considered in MCMCtree (4.9e 2017; Yang 2007) was not clearly defined (Benton & Donoghue 2007; Marshall 2008; Hill et al. 2021), and simply handled by ignoring the maximum age in BEAST v.1. X calibration (Osozawa & Wakabayashi 2021; Osozawa et al. 2021a). We sought the oldest fossil of the corresponding node of specific clade with an assumption that the oldest fossil age was equivalent to the minimum age and equivalent to “tMRCA” in BEAST v1. X. Moulds (2018) reviewed the ages of cicada fossils. These redefined ages, ranging from 16.45 ± 0.45 Ma to 244.5 ± 2.5 Ma, were available for our fossil-based time calibrations in BEAST v1. X.\n\nKlopfstein (2021) suggested that recent node dating approaches including Misof et al. (2014) and Montagna et al. (2019) have a credibility problem: different studies using the same molecular data and even the same sets of fossils regularly arrive at drastically different age estimates. She showed that a major reason for these differences is well known: even well-dated and firmly placed fossils can only provide a minimum age for a particular node. Therefore our fossil calibration applying solely minimum age (= tMRCA) was credible.\n\nAs shown by Osozawa et al. (2017a), Platypleura and some other endemic cicadas in Ryukyu Islands can be rigidly calibrated by a geological event calibration at 1.55 ± 0.15 Ma (Quaternary; Osozawa et al. 2012). As shown by Osozawa et al. (2021a), Meimuna opalifera and some other endemic cicadas on Hachijo-jima, Izu-Bonin islands, can be calibrated by a geological event calibration of emergent age at 0.24 Ma (Quaternary; Osozawa et al. 2021b).\n\nThrough these analyses, we corroborated the classification and some rearrangement of species into four subfamilies of Tibicininae, Tettigomyiinae, Cicadettinae, and Cicadinae included in a family Cicadidae by Marshall et al. (2018) and Łukasik et al. (2018), and then estimated the splitting dates of these subfamilies, tribes (especially Cicadinae tribes after Hill et al. 2021), and species (Figures 1–3). In the BEAST analyses, we included Derotettix, a relict species of new subfamily Derotettiginae with the oldest lineage in family Cicadidae (Simon et al. 2019), and attempted to estimate the crown age (Figure 2). Comparison to the entire Hemipteroid insect timetree (Johnson et al., 2018) and entire insect timetree (Misof et al. 2014) could be conducted as an extension of this analysis, by adding other Hemiptera species as outgroup (Figures 1–3).\n\nInserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by an Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.\n\nOUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.\n\nOUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0114 s/s/myr, the rate median shown on Tracer. Note that this rate is a little slower than that solely of COI in Figures 1 and 2, reflecting slower rate of 18S rRNA than COI (see Osozawa et al. 2017a).\n\nOur primary goal was to present the precise evolutionary history of all cicadas by constructing the BEAST timetree, and also taxonomic reconsiderations for Cicadinae tribes after Hill et al. (2021) and for Ryukyu endemic cicadas. Another BEAST v1. X function facilitates additional evaluation of the time variability of base substitution rates. Recent dating analyses employ a relaxed clock model, which allows each branch of a phylogenetic tree to have its own evolutionary rate (Drummond et al. 2012). Although the relaxed distribution can be set to lognormal in BEAUti, the rate of variability has not been documented prior to this study. The output figure of BEAST v1. X presents the base substitution rate and age at each node, and shows the acceleration of base substitution rates through the time.\n\n\nMethods\n\nThe present study did not concerned invertebrate experiments and did not involve endangered or protected species. We obtained permission of collection in the Taroko National Park, Taiwan, from the director (No. 0990012881; August 1 ~ 11, 2010), with a help of Bor-ming Jahn, and permission of collection in the Tokara islands, from the Toshima village headman, from August 29 ~ September 8, 2010. Collection in the Ryukyu islands was before the designation of National Park since 2016. No specific permission was required outside the national parks and private areas.\n\nMarshall et al. (2018), Simon et al. (2019), Łukasik et al. (2019) included comparatively few Asian cicada species in their analyses. We have previously published 70 isolate data from Platypleura primarily from the Japan, Ryukyu, and Taiwan islands (Osozawa et al. 2017a; our aim was the vicarince acted on each island population started at 1.55 Ma and the cryptic speciation), and 21 of these data were used in the present analyses by excluding duplicated sequence data. We also collected and analyzed cicada specimens, adding isolate data from 92 specimens. Accordingly, our own data total 21 + 92 = 113 specimens (Table 1). Note that we collected all the 35 species from Japan including the Ryukyu Islands, but excepting severely protected Platypleura albivannata (see Osozawa et al. 2017a; may be extinct without DNA sequence data) and Meimuna boninensis (see Osozawa et al. 2021a).\n\nWe incorporated representative sequence data from the GenBank/DDJB. This is because Tettigarctinae, Derotettiginae, Tibicininae, and Tettigomyiinae are not known from East Asia, and Cicadettinae has only two species of Kosemia in the Japan main islands. Thus to extend our analyses beyond East Asia, the Marshall et al. (2018) and Łukasik et al. (2019) data were essential for us. We combined our data from 113 East Asian specimens with data from 75 specimens from the studies of Marshall et al. (2018; including 20 East Asian specimens), and Łukasik et al. (2018; including 27 East Asia specimens). In addition, we incorporated data of 15 Platypleurini (other than Platypleura) from Price et al. (2019), and data of 149 Asian Cicadinae from recently published Hill et al. (2021). Accordingly we analyzed sequence data from 113 + 75 + 15 + 149 = 352 specimens.\n\nPlatypleura cicada (Osozawa et al. 2017a) experienced vicariance triggered by the 1.55 ± 0.15 Ma isolation of the Ryukyu, Japan, and Taiwan islands from Chinese continent (Osozawa et al. 2012), and we collected specimens from each island population for each Platypleura species. Similarly, we collected cicada specimens for the present analyses from each island population of Mogannia (Cicadettinae), and Cryptotympana, Graptopsaltria, Hyalessa, Pomponia, Meimuna, Tanna, and Euterpnosia (Cicadinae). Hyalessa maculaticollis was known to be affected by vicariance within China and Japan (Liu et al. 2018). Our 113 East Asian specimens consist primarily of these endemic and cryptic species inhabiting Japan, Taiwan, and the Ryukyu islands.\n\nCOI and 18S rRNA sequence data from our collected 113 isolates, including Platypleura in Osozawa et al. (2017a), are shown in Table 1. Primers used, amplifications, and sequencing are given in Osozawa et al. (2017a). These sequence data were aligned by ClustalW in MEGA 5 (Tamura et al. 2011). The COI sequence data comprise 1,534 bp, and the 18S rRNA sequence 874 bp, with high enough resolution to construct a phylogenetic tree, as we showed previous analyses of Platypleura (Osozawa et al. 2017a). We did not analyze calmodulin in Osozawa et al. (2017a), because the resolution was insufficient. The COI data in Marshall et al. (2018) comprised 1,485 pb, comparable to ours. The COI data in Price et al. (2019) comprised 940 bp, and Hill et al. (2021) comprised 648 bp, comparable to ours, so we incorporated these data into our present analyses. Nuclear 18S rRNA shows less variation with much slower base substitution rate compared to mitochondrial COI (Osozawa et al. 2017a; COI: 0.0270 substitutions/site/myr, 18S rRNA: 0.000492 s/s/myr; strict clock model; solely calibrated by 1.55 ± 0.15 Ma following Osozawa et al. 2012). The tree topology was unaffected by 18S rRNA (Osozawa et al. 2017a), but 18S rRNA was included in the analyses in this paper.\n\nWe used COI and 18S rRNA sequence data, from 352 total specimens (239 from GenBank/DDBJ + 113 of our own) for the COI timetree in Figures 1 and 2, and 155 total specimens (42 from GenBank/DDBJ + 113 of our own) for the COI +18S rRNA timetree in Figure 3. The COI and 18S rRNA data in table 1 in Marshall et al. (2018) contain missing and incomparable data, so some of their GenBank/DDBJ data were not applicable for our analyses. Whole mitochondrial sequence data by Łukasik et al. (2019) are included in our analyses as corresponding COI regions. Within COI sequence data in Marshall et al. (2018), 21 data for Cicadettinae and 14 data for Cicadinae were incorporated into our analyses. 18S rRNA sequence in Marshall et al. (2018) was used for only Nablistes heterochroma (Tettigomyiinae) and Platypedia putnami (Tibicininae). Only the COI sequence data in Price et al. (2019) for Platypleurini and in Hill et al. (2021) for Asian Cicadinae were applied to our study.\n\nNorth American Cryptotympanini were analyzed by Hill et al. (2015), applying 1,467 bp of COI and 783 bp of nuclear EF-1a with sufficient resolution. Cicadettini, primarily from Australia, was analyzed by Marshall et al. (2016), applying 1,492 bp of COI and 1,047 bp of nuclear EF-1a also with sufficient resolution. Some of these COI sequence data were included in our analyses.\n\nFor our initial analysis, we constructed a minimum age tree solely applying COI sequence data (Figures 1 and 2; 352 specimens) that covers Tettigomyiinae and Tibicininae species. Following this analysis, we constructed a minimum age tree by applying both COI and 18S rRNA sequences (Figure 3; 155 specimens, i.e., 352 − 155 = 197 specimens lack 18S rRNA sequences). These analyses showed that topology and ages associated with the analyses were not impacted by inclusion or exclusion of 18S rRNA sequence data.\n\nPrice et al. (2019) and Hill et al. (2021) employed BEAST v.2.5 (Bouckaert et al., 2014). We employed BEAST v.2.5 in Osozawa et al. (2016), but thereafter we changed to BEAST1. The calibration function in BEAUti in BEAST2 is similar to BEAST1 (see next section bellow), but note that “Taxa” in BEAST v1. X was combined with “Priors” in BEAST v.2.5. However, In BEAST2, applied sequence data should be concatenated as done in Price et al. (2019) and Hill et al. (2015, 2021). Otherwise, as in Osozawa et al. (2016), the calculation in BEAST2 for each applied sequence data (e.g., COI and nuclear 16S rRNA) is done separately (in this example, two BEAST runs are needed). The consequent two tree files must be combined into one by LogCombiner, but in the combined tree, branches are folded reflecting the discordant topology made by e.g., mitochondrial COI and nuclear 16S rRNA sequence data. BEAST v1. X is recommended to do combined gene analyses, and in general, concatenated gene analyses are not recommended.\n\nThe most recent BEAST 2.6 released in May 2019 did not change the protocols. A misunderstanding about tip dating is as follows (https://beast.community/first_tutorial). The “Tip Dates” panel in BEAST2 or the “Tips” panel in BEAST1 allows giving the taxa dates. However, taxon dates (or ‘tip dates’) are only important in certain cases, e.g., when sampled from rapidly evolving viruses or ancient fossil DNA material. In the case of the cicadas, we are analyzing a tree that represents millions of years of evolution, so the dates of the tips can be assumed to be zero. This should be the default, i.e., the taxa all have a date of zero and the “Use tip dates box” should not be selected.\n\nA Bayesian inference (BI) tree (Figures 1–3) was constructed using the software BEAST v1. X, running BEAUti, BEAST, TreeAnnotator, and FigTree, in ascending order. Before operating the BEAST software, the BEAGLE Library must be downloaded. Tracer v.1.6 was applied for checking the calculation status and estimating the median base substitution rate.\n\nFor graphic explanation of the operation of this software, see Osozawa (2021a; BEAST v1.X tutorial, in a case of four cicada genera) at: dx.doi.org/10.17504/protocols.io.bq6mmzc6.\n\nIn BEAUti, the following software settings were used (Appling Appendix BEAUti file, readers may run the platform software BEAST and check the protocol and reliability).\n\nPartitions: Loading fasta files was by using the Import Data or plus button. Partitions defined by the COI and 16S rRNA gene sequences appeared in the Partition box (For Figure 3; COI file only for Figures 1 and 2). Note that COI and 16S rRNA partitions automatically appear in Partitions without employing PartitionFinder, and the partitioning is performed simply by applying each COI and 18S rRNA sequence, instead of the concatenating of genes by SeaView (Gouy et al. 2010) as done by Price et al. (2019) and Hill et al. (2021). Additional partitioning by PartitionFinder 2 (Lanfear et al. 2016) in MCMCTree and BEAST2 analyses is not required in the present BEAST1 analyses.\n\nTaxa: Loading of taxa as ingroup was by using the plus button. The left screen: Taxon Set (monophyletic boxes were checked for all, and stem box were checked in case by case; see Table 2), and the right screen: Included monophyletic Taxa (= specific clade) and the resting Excluded Taxa in the central screen. As input in Figures 1–3, calibration dates were set in Priors bellow.\n\nThese are primarily fossil calibrations but include geological event calibrations. See main text and Figures 1–3.\n\nTips and Traits: Default (see above BEAST2 section).\n\nSites: Substitution Model: HKY (Hasegawa, Kishino and Yano) model, Base frequencies: Empirical, Site Heterogenety Model: Gamma, Number of Gamma Categories: 4, Partition into codon positions: Off. The GTR model generates similar topology.\n\nClocks: Clock Type: Uncorrected relaxed clock, Relaxed Distribution: Lognormal. Uncorrelated relaxed clocks allow each branch of a phylogenetic tree to have its own evolutionary rate under log-normal distribution, and the node rate is the rate median of three branches (Drummond et al. 2006).\n\nTrees: Tree Prior: Speciation: Yule Process.\n\nPriors: tMRCA (time of MRCA) was input from the calibration point date as Prior Distribution: Normal, and as the Mean and Standard deviation. See bellow for Priors as detailed setting of age calibration.\n\nOperators: Default.\n\nMCMC: Length of chain: 10,000,000.\n\nRunning BEAST was done by incorporating xml input file made by BEAUti. The consequent tree was drawn by FigTree v1.4.2, for that, the tree files were input into TreeAnnotator. The 95% highest posterior density for confidence intervals of ages can be output in FigTree, but not shown in Figures 1–3 to avoid visual complexity. In FigTree, posterior probability (“posterior”), posterior age (“Node ages”), and “rate median” (not constant) can be output, and these are shown at each node in Figures 2 and 3. This rate related function was not used in any previous paper, and we found in this paper variable base substitution rates the time as suggested by the relaxed clock model of BEAST (Drummond et al. 2012). Consequently, we made base substitution rate (“rate median” shown at each node in FigTree) vs age (“Node age” shown at each node in FigTree) diagram (Figures 1–3 inset) using a function of Excel.\n\nThe inset in Figures 1–3 shows that the base substitution rate was relatively slow until the Quaternary higher rate. To evaluate whether the slow rate reflected saturation, we examined the relation between pairwise distance and number of transition or transversion for each gene, using the MEGA5 function (Tamura et al. 2011; Figure 4).\n\nCalibrations points are shown on minimum age trees in Figures 1–3, and these dates were input in “Priors” in BEAUti as noted above; they are summarized below (Table 2). As noted above, corresponding ingroup species were included in ingroup taxa (= leaf node taxa in a specific clade) by Taxon Set on the Taxa screen in BEAUti.\n\nFossil calibrations are after Johnson et al. (2018) and Moulds (2018) (Table 2; Figures 1–3). For these fossil calibrations, some are based on radio-isotopic dating of the fossil-bearing strata, whereas others are based on biostratigraphy assigned to an age/stage on the geologic time scale, for which absolute age ranges are generally based on radio-isotopic dates of associated strata in key global localities. This time scale has been standardized by the International Commission on Stratigraphy (ICS) (www.stratigraphy.org) and the most recent version of the time scale is available at http://www.stratigraphy.org/index.php/ics-chart-timescale, and the explanatory paper related to the generation of the time scale is Cohen et al. (2013).\n\nCalibration points Q1 to Q6 and Q8 to Q12 are after our geological event calibration that adopts a 1.55 Ma date (Osozawa et al. 2012). This geologic event calibration was used in previous studies of Platypleura cicadas (Osozawa et al. 2017a) and four cicada groups (Osozawa et al. 2021a).\n\nThe specific calibration points are as follows: tMRCA of Mogannia minuta (Q1), M. hebes (Q2), Cryptotympana facialis (Q3), dark winged Platypleura (Q4) and right winged Platypleura (Q5; Osozawa et al. 2017a), Graptopsaltria nigrofuscata + G. bimaculata (Q6), Meimuna kuroiwae (Q8), M. oshimaensis + M. iwasakii + M. goshizana (Q9), Tanna japonensis + T. japonensis ishigakiana + T. sozanensis + T. sp. (Q10) Euterpnosia chibensis + E. chibensis daitoensis + E. chibensis okinawana (Q11), E. iwasakii + E. viridifrons + E. olivacea + E. gina + E. sp. (Q12): The date of the geological event, which records the isolation of the Ryukyu Islands from the Chinese mainland by the opening of the Okinawa trough that began (i.e., islands had separated from mainland and each other by this time) at 1.55 ± 0.15 Ma (Osozawa et al. 2012). The age assignment is from multiple biostratigraphic and radio-isotopic ages from the oldest marine strata on the landward side of the islands as well as the sides facing other islands, so that the age of such strata constrains the physical separation of the islands from the mainland and each other. There is no geologic evidence for land bridges that could have aided dispersal in the Ryukyu Islands.\n\nCalibration point Q7 (Meimuna opalifera) is distinct from the above 1.55 ± 0.15 Ma event calibration. Hachijo oceanic island is a part of the Izu volcanic arc, and we recently estimated the emergence time of Hachijo-jima as an island at 0.24 Ma (Osozawa et al. 2021b). This date is applicable for crown Meimuna opalifera on the Hachijo-jima + the Japan-Tokara islands (= Stem Meimuna opalifera on Hachijo-jima).\n\nWith the assumption that the oldest fossil age is equivalent tMRCA (= minimum age), the specific fossil calibration points and associated dates are as follows:\n\nCalibration point A1: Crown Hemiptera: Fossils of Aphidoidea were reported from the French Bundsandstein (Szwedo & Nel 2011; Bashkuev et al. 2012) of Anisian age (244.5 ± 2.5 Ma).\n\nA2: The oldest fossil Belostomatidae was reported from the Zagaje Formation, Poland (Popov 1996) of Hettangian age (200.3 ± 1.0 Ma).\n\nA3: Fossil Ledridae (Zhang 1997) and fossil Cercopidae (Hong 1982) were recovered from the Jehol Biota of northern China. The Jehol Biota horizon has been dated by the Ar-Ar method on associated silicic tuff at 130.7 ± 1.4 Ma (He et al. 2006).\n\nA4: Fossil Gerridae were recovered from French amber (Perrichot et al. 2005) of Albian age (107 ± 6 Ma).\n\nA5: Fossil Delphacidae were found in the Green River Formation, USA (Grande 1980). Ar-Ar dating on silicic tuff within the formation yields ages of 53.5 – 48.5 Ma (weighted average age of 51.25 ± 0.31 Ma; Smith et al. 2003).\n\nA6: Fossil Flatidae were found in the Maíz Gordo Formation, northwest Argentina (Petrulevičius 2011) of Paleocene age (61 ± 5 Ma).\n\nCalibration point B: Stem Tettigarctinae: Oldest fossil of Tettigarctinae were found in strata Dorset, England (Whalley 1985) of Hettangian age (203.1± 1.0 Ma).\n\nCalibration point C: Stem Derotettiginae: The preferred food of Derotettix mendosensis is Amaranthaceae in Argentina (Simon et al. 2019), and this worldwide C4 plant was phylogenetically studied by Piirainen et al. (2017). This plant fossil was reported by Zucol et al. (2018), and the fossil-bearing horizon was dated by the Ar-Ar method at 49.512 ± 0.019 Ma (Eocene; Woodburne et al. 2014). However, fossil Burmacicada protera were found from Burmese amber (Poinar & Kritsky 2011). Detrital zircons from the amber bearing matrix yielded a maximum depositional age U-Pb age of 98.79 ± 0.62 Ma, that was interpreted to closely approximate the actual depositional age on the basis of geologic relationships and associated fossils (Shi et al. 2012). We applied this older date of Burmese amber for stem Derotettiginae or crown Cicadidae.\n\nCalibration point D: Stem Platypedia putnami (= crown Tibicininae): Fossil Platypedia primigenia were found in the Florissant Formation, Colorado, USA, and the associated strata was dated by the Ar-Ar method at 35.15 ± 1.65 Ma (Mcintosh et al. 1992). However, we used an older crown date for crown Tibicininae based on fossil Davispia bearcreekensis that were found in the Fort Union Formation, Montana, USA (Cooper 1941). The age of the enclosing strata has been considered Thanetian in age (57.6 ± 1.6 Ma) (Flores & Bader 1999). Crown Cryptotympanini: Fossil Hadoa grandiose were also found in the Florissant Formation, Colorado, USA, but this calibration generated an unreasonable tree and was not adopted.\n\nCalibration point E: Crown Cicadettinae: Paracicadetta oligocenica (Boulard & Nel 1990) were recovered from deposits of Céreste, France, and this famous fossil locality was considered to be of Ruperian age (31 ± 2.9 Ma; Ducreux et al. 1985).\n\nCalibration point F: Stem Lyristes plebejus: Fossil Lyristes sp. were reported from Seifhennersdorf, Germany (Tietz et al. 1998), and associated strata was dated by the K-Ar method as 30.44 ± 1.52 Ma (Walther & Kvacek 2007).\n\nCalibration point G: Crown Cryptotympana: Fossil Cryptotympana incasa and C. miocenica (G1), and also Hyalessa lapidescens (G2) were found in Shanwang, Shandong, China (Zhang 1989; Zhang et al. 1994), and these strata are considered to be time correlative to the European MN5 mammalian unit (16.45 ± 0.45 Ma; Roček et al. 2011).\n\nCalibration point H: Crown Meimuna spp.: Fossil Meimuna protopalifera were found in the Itamuro Formation, Tochigi, Japan (Fujiyama 1969; Yoshikawa 2005), and the zircon fission track age of correlative terrestrial strata of the Nashino Formation of the Sendai area is 6.4 ± 0.4 Ma (Fujiwara et al. 2008).\n\n\nResults\n\nOur timetree spans a range as old as ca. 250 Ma, and there is no evidence of saturation of mutations (Figure 4), suggesting our minimum age tree is robust and reliable.\n\nBecause the topology is concordant between Figures 1 and 2 (COI) and Figure 3 (COI + 16S rRNA), the following description follows Figure 2 with 352 specimens. Our analyses was concordant to the subfamily classification of Marshall et al. (2018), Łukasik et al. (2019), and Simon et al. (2019). Figures 1 and 2 also include data in Price et al. (2019) and Hill et al. (2021).\n\nHemiptera, including Cicadoidea, has a single common ancestor of 242.96 Ma, as calibrated by the 244.5 ± 2.5 Ma age reviewed above as A1. The dated tree of the outgroup Hemiptera calibrated by A1 to A6 was concordant to Johnson et al. (2018) and Misof et al. (2014).\n\nIn the Cicadoidea ingroup, Tettigarctidae was an old lineage that differentiated from Cicadidae at 200.63 Ma, as calibrated by 200.3 ± 1 Ma (calibration point B), so Tettigarctidae is essentially a living fossil that has persisted since 200.63 Ma. We estimated a date of the common ancestor of two extant species of Tettigarcta tomentosa (Tasmania) and T. crinita (southeast Australia) at 13.96 Ma, and the youngest fossil of Tettigarctinae was reported from the Aquitanian (21.735 ± 1.295 Ma), southern New Zealand (Kaulfuss & Moulds 2015). However, Tettigarctidae includes 19 extinct genera according to Kaulfuss and Moulds (2015) and with many more genera according to Moulds (2018).\n\nSimon et al. (2019) proposed a new subfamily Derotettiginae consisting of a single species of Derotettix mendosensis, which is a sister of the remaining Cicadidae species and the oldest lineage species in Cicadidae dated at 99.2 Ma, as calibrated by point C at 98.79 ± 0.62 Ma. Łukasik et al. (2018) showed such a basal lineage of D. mendosensis in Cicadidae.\n\nOur timetree showed that Tibicininae is a sister of Tettigomyiinae + Cicadettinae + Cicadinae and differentiated at 66.15 Ma, and Tibicininae started differentiation at 57.31 Ma, as calibrated by point D at 57.6 ± 1.6 Ma. Tettigomyiinae is a sister of Cicadettinae and differentiated at 35.46 Ma, Tettigomyiinae + Cicadettinae is a sister of Cicadinae differentiated at 40.57 Ma. Cicadettinae started differentiation at 30.85 Ma, as calibrated by point E at 31 ± 2.9 Ma. Cicadinae started differentiation at 38.25 Ma. Differentiation of Tettigomyiinae + Cicadettinae took place simultaneously after 35.46 Ma.\n\nA single common ancestor of Cicadidae except Derotettiginae started differentiation and speciation into Tibicininae, Tettigomyiinae, Cicadettinae, and Cicadinae at 66.15 Ma. Although the pre-Miocene fossil Cicadidae collectively include ten extinct genera, comprising Davispia and Lithocicada for Tibicininae, Paracicadetta, Paleopsalta, Minyscapheus, and Miocenoprasia for Cicadettinae, and Burmacicada, Camuracicada, Tymocicada, Dominicicada for Cicadinae, the remaining 23 genera post-Oligocene fossil cicadas are extant (Moulds 2018). Cicadidae, consisted of only one species but coexisted with a Tettigarctidae species between 200.63 and 66.15 Ma, and cicada biodiversity was extremely low during this period except for extinct species and D. mendosensis.\n\nIn the Cicadettinae major clade, each tribe constitutes a distinct clade. In the Cicadinae major clade, apart from older five tribe clades containing only one specimen, six tribe clades of Platypleurini, Cryptotympanini, Psithyristriini, Dundubiini + Cosmopsaltriini, Polyneurini + Sonatini, and Leptopsaltriini + Gaeanini are recognized. Discrepancies are addressed by reconsideration of taxonomy in the discussion.\n\nThe geologic calibration points Q1 to Q12 at 1.55 ± 0.15 Ma (and 0.24 Ma) apply to multi furcations that were recognized for Mogannia minuta and other cicadas endemic to in the Ryukyu Islands and Taiwan (and in Hachijo-jima) as noted above. Each island or island group population was mostly genetically distinct, endemic, and cryptic, as shown for Platypleura in Osozawa et al. (2017a). This also applies to Meimuna opalifera on Hachijo oceanic island (Osozawa et al. 2021a,b). However, note that some cicadas were accidentally dispersed by super typhoons up to 1,000 km in modern and ancient times including Meimuna boninensis (Osozawa et al. 2021a).\n\nComparing base substitution rate vs age shows that the rate has not been constant; the rate appears to have exponentially increased into the Holocene. The data points, approximate curve, and associated equation are shown on the insets of Figures 1–3. The curves and associated rates are similar for analyses based on COI alone (Figures 1 and 2 insets), and combined COI + 18S rRNA (Figure 3 inset).\n\nFigure 4 shows that even mitochondrial COI gene with rapid base substitution rate (Osozawa et al. 2017a) is never saturated toward the ancient time up to ca. 250 Ma.\n\n\nDiscussion\n\nTibicininae is solely from North and South America with an exceptional occurrence from the Mediterranean region, but absent from Asia and Africa (+ Australia). The stem age is estimated at 66.15 Ma (Figures 1 and 2), and if we assume that Tibicininae was generated by vicariance its differentiation may have been influenced by the formation of the Atlantic Ocean. Marine magnetic anomalies on the Atlantic Ocean floor can be used to ascertain spreading history and separation of continents that resulted from this spreading. The configuration at Chron34 (84Ma) after the Cretaceous magnetic quiet zone (long normal polarity epoch; superchron K-T at 118-84 Ma) was shown by Moulin et al. (2010), and the south Atlantic Ocean spread over 500 km (minimum distance between Africa and South America) at Chron 34 (84 Ma). The date of 84 Ma can be considered to be a starting date of continent level vicariance, which may have triggered the Tibicininae differentiations relative to especially Cicadinae shown in Figures 1 and 2.\n\nIn Cicadettinae, Prasiini is a sister of Cicadettini. Muda kuroiwae in Prasiini (Hayashi & Saisho 2011) is endemic and restricted to Okinawa-jima and Kume-jima, and represents as a sister of the similar species of Katoa taibaiensis on the Chinese mainlamd.\n\nIn the Moganniini clade, Nipponosemia terminalis (Matsumura 1913) (synonym: Vagitanus terminalis) is a sister of Mogannia spp. N. terminalis has been documented from the Yaeyama islands and Miyako-jima (endangered and protected), Ryukyu, and Taiwan (Figure 2 from the Taiwan specimen; another species of N. virecens is known from the Kaoshun peninsula, southern most Taiwan; Lee & Hayashi 2004), but Yang & Wei (2013) reported N. terminalis and other three Nipponosemia from China. A detailed phylogenetic study for these Nipponosemia species would be useful. The genitalia and morphological character are similar to Mogannia (Hayashi & Saisho 2011), concordant to the sister relationship with Mogannia. See Osozawa et al. (2021a) for the Mogannia minuta vicariant speciation on the Ryukyu Islands and the accidental typhoon dispersals in recent and also ancient times. Mogannia hebes in northern Taiwan and in southern China has sister relationship reflecting vicariance by the Taiwan strait (Osozawa et al. 2011), and this species in southern Taiwan was differentiated relative to the northern Taiwan species reflecting vicariance triggered by the physical barriers of the Yilan basin and Lanyang valley (Osozawa et al. 2017b; http://kawaosombgi.livedoor.blog/?p=26 and others).\n\nWe combined East Asian Platypleura data after Osozawa et al. (2017a) with mostly African Platypleurini data excluding Platypleura after Price et al. (2019), and the terminal node of the East Asian Platypleura in the Platypleurini clade suggests the possibility of a Gondwanan origin and dispersal to Far East of Japan and Ryukyu, and Taiwan (Price et al. 2019). See Osozawa et al. (2017a) for the Platypleura vicariant speciation (see below for the cryptic speciation) on the Ryukyu Islands.\n\nTacua speciosa (Tacuini) represents the basal lineage of Cryptotympanini concordant with Marshall et al. (2018). In the Cryptotympanini clade, Auritibicen in Japan is the basal lineage, and Lyristes plebejus (synonym: Tibicen plebejus) in Croatia is the next. Asian Cryptotympana species is a sister of North American Noetibicen species (Hill et al. 2015). Intercontinental dispersal by way of a Bering land bridge during Oligocene to Miocene climatic optima (Wu et al. 2015) was proposed for Papilionoidea butterflies feeding on Magnoliidae.\n\nZammara smaragdina, Costa Rica, represents the basal lineage of the remaining major clades that are paraphyletic each other. Distantalna splendida, renamed from Tosena splendida by Boulard (2009; referred in Hill et al. 2015), is represented by Tosenini, as a next basal lineage, distinct from another Tosenini of Tosena melanopteryx in the Psithyristriini composite clade. Tosena (Tosenini) and Pomponia (Psithyristriini) has a sister relationship, and these are similar tribes (species level transfer may be needed; Duffels & Hayashi, 2006). Pomponia backanensis, northern Vietnam, was described by Pham et al. (2015). Pomponia linearis on the Yaeyama islands and Taiwan, mildly differentiated each other as cryptic species, was renamed P. yayeyamana based on Kato (1932). The original P. linearis was reported from primarily Indochina, and has been treated as the P. linearis complex, including cryptic Chinese and Indian populations (Hayashi & Saisho 2011). Unipomponia decem (Psithyristriini?) was renamed Pomponia decem (Lee & Sanborn 2010).\n\nMegapomponia (Lee & Sanborn 2010) was associated with the genera from Dundubiina (Hill et al. 2021), and included in the Dundubiini clade. Oceanian Cosmopsaltriini is a sister of Asian Dundubiini, reflecting large scale vicariance driven by bio-geographic barrier of the Wallacea line, as well as endemism within the islands by Oceanian arc fragmentations (Boer & Duffels 1996). In the Dundubiini clade, see Osozawa et al. (2021a) for the vicariant and cryptic speciation of Meimuna kuroiwae on the Ryukyu islands and the accidental typhoon dispersals in recent and ancient times (including Meimuna boniensis on the oceanic Bonin islands). See Osozawa et al. (2021a) for the vicariant and cryptic speciation of Meimuna opalifera on the oceanic Hachijo-jima island (Osozawa et al. 2021b) by the accidental typhoon dispersal from the Japan continental islands. Meimuna mongolica in Korea and China is the basal lineage relative to the sympatric M. opalifera. Meimuna oshimensis endemic on the Amami and Okinawa islands (cryptic species), Meimuna iwasakii endemic on the Yaeyama islands and Taiwan (no specimen collected from Taiwan specimen; cryptic species), and Meimuna goshizana and M. gakokizana, other endemic species on Taiwan, were vicariantly speciated or adaptively radiated in Taiwan.\n\nHyalessa is in Sonatini was renamed from Oncotympana in the distinct Oncotympanini. Hyalessa maculaticollis in Japan and China (Liu et al. 2018) is deeply differentiated. Sonatini is a sister of Polyneurini (once included in Tosenini; noted in Hayashi & Saisho 2011), and these constitute the Polyneurini + Sonatini clade. Graptopsaltria nigrofuscata in Japan and G. bimaculata on the Amami and Okinawa islands were vicariantly speciated.\n\nTerpnosia cf. graecina was synonymised with Leptopsaltriina (discussed in Hill et al. 2021) constitutes the basal lineage with Thailand Leptopsaltriini in the Leptopsaltriini-Gaeanini major clade. Kalabita operculata, Malaysia, was a member of above-mentioned Platypleurini known to have diversified in Africa (Price et al. 2019), but this Asian species is included in the Leptopsaltriini + Gaeanini clade. Trilar (2006) presented an adult photo of K. operculata showing that it lacks the pronotum that characterizes Platypleurini. Furthermore, the spectrogram - oscillogram of its song is similar to those of Euterpnosia spp., Leptopsaltriini, shown in Hayashi and Saisho (2011). Platypleurini both in African and Asia are monophyletic as noted above, and an exception is unreasonable. Hill et al. (2021) transferred Kalabita Moulton, 1923 from Platypleurini to Leptopsaltriini. Tosena paviei is a member of Tosenini, but is a sister of Callogaeana guanxiensis in Gaeanini, and renamed as Vittagaeana paviei in Gaeanini by Hill et al. (2021). Both the species are from Vietnam, and constitute a Gaeanini clade with another Vietnam species of Balinta cf. tenebricosa of Gaeanini. An interesting result is that Gaeanini including T. paviei is not monophyletic, and paraphyletic in the Leptopsaltriini major clade. Hill et al. (2021) showed wing phenotypes of Gaeanini- Tosenini, which are distinct from phenotypes of Leptopsaltriini. Note that Gaeana (Gaeanini) is also a sister of Tanna (Leptopsaltriini) with different wing and chest phenotypes. Tanna japonensis is differentiated between Japan and the isolated population on the Amami-Oshima island, and further differentiated from the isolated Tanna japonensis ishigakiana population on Ishigaki-jima island. Taiwan yields Tanna sozanensis (sister of T. japonensis ishigakiana) and the other seven Tanna species (Chen 2011), might have adaptively radiated within the island. Tanna in China is a sister of T. sozanensis. According to Hill et al. (2021), Cicadmallus micheli is characterised by an unusual ‘hammer-head’ morphology but otherwise bears morphological relationships to Leptopsaltriini, and represents the basal lineage of Indochina Terpnosia (Thai & Yang 2009) and East Asian Euterpnosia of the Leptopsaltriini clade. See Osozawa et al. (2021a) for the vicariant and cryptic speciation for Euterpnosia for the northern population on Japan-Amami-Okinawa and the southern population on Yaeyama-Taiwan, as well as accidental typhoon dispersal in ancient times (Euterpnosia chibensis daitoensis on the oceanic Daito islands from Tokuno-shima continental island). Taiwan yields Euterpnosia gina, E. olivacea, E. viridifrons, and other 12 Euterpnosia species (Chen 2011), and may have adaptively radiated within the island.\n\nHemipteroid insects of Psocodea, Thysanoptera, and the subject of this study, Hemiptera, include 120,000 described species which comprise over 10% of known insect diversity; they date back to 400 Ma (Hemiptera: 300 Ma; Johnson et al. 2018). Johnson et al. (2018) estimated that differentiation into species took place primarily in the Cretaceous, including Cercopoidea, Gerriidea, Flatidae, and Cicadoidea, which are common to our analyses. However, they analyzed only two to nine taxa, in contrast to the 344 taxa of Cicadoidea and 8 taxa for other Hemiptera of our analyses. Misof et al. (2014) estimated mostly pre-Paleogene dates of differentiation into species including Cercopoidea, Aphididae, and Delphacidae, concordant with our analyses, with less than 13 taxa analyzed. Their higher-level phylogeny suggested long branches and an old lineage of each super family species concordant with ours, but did not suggest the geologically recent increase in insect diversity apparent from our analyses of 352 Hemiptera taxa (Figure 2).\n\nIn Figure 2, ingroup Cicadidae, excluding Derotettiginae, underwent extensive differentiation into 341 taxa after 66.15 Ma, mostly after 40.57 Ma, leading to increasing biodiversity of Cicadidae, although Price et al. (2019) suggested that number of lineages saturated in the Pleistocene. Cicadidae consisted of only two species including D. mendosensis between 99.2 and 66.15 Ma, although Cicadidae contains many extinct species that remain to be identified as fossils (Moulds 2018).\n\nCryptic species on each island of Ryukyu chain are typical examples of increased biodiversity. For example, Platypleura kaempferi in the Amami and Okinawa islands has light colored wings, contrasting with dark colored wings in Japan-Korea-China and Taiwan, and the clades are distinct from each other (Osozawa et al. 2017a). P. kaempferi is not a single species but includes at least two cryptic species of light or dark winged Platypleura. Cicadas calibrated by other Quaternary calibration points include cryptic species, which also contributed to increasing biodiversity. The Okinawa trough is currently spreading (widening) and the Ryukyu islands are separating from the Chinese mainland. Accordingly vicariant speciation and radiation is in progress, which is also contributing increasing biodiversity. On the Chinese mainland, Hyalessa maculaticollis and Platypleura hilpa extensively radiated to form cryptic species (Liu et al. 2018, 2020).\n\nFigures 1–3 insets show a large range of base substitution rates for different time periods, at variance with the constant molecular clock hypothesis (relatively constant rate over time; Ho 2008). The trend in base substitution rates shows an exponential increase into the Holocene.\n\nSuch an increase in base substitution rate was first shown for taxa such as primates by Ho et al. (2005) who showed that a Quaternary calibration date resulted in a more a rapid base substitution rate than that associated with an older calibration date. They employed an older version of BEAST (v1. 3; Drummond & Rambaut 2003) that required repeated runs, applying a date at each calibration point. In contrast, BEAST v1. X, used in our analyses, can simultaneously apply multiple calibration points, as we have done using dates ranging from the Triassic to the Quaternary. As a result, the calculated increasing rate of base substitution in our analyses is not an artifact of a Quaternary calibration, but is constrained by multiple age calibrations across a wide range of geologic time. Therefore, although the base substitution rate trendlines and associated equations of Ho et al. (2005) are similar to ours, their timetrees do not reflect the changing of base substitution rates through time, but rather reflect a constant base substitution rate as if constrained by a strict molecular clock. A similar analysis was done for beetles in the Aegean region by Papadopoulo et al. (2010).\n\nThe increasing base substitution rate is apparently associated with the recently increasing cicada diversity, expansion, and radiation (in Figure 2 timetree) that started at 40.57 Ma. The timing of the most rapid diversification coincides with Quaternary environmental change, marked by the start of glacial-inter glacial cycles. The initiation of Quaternary glaciations may have been triggered by rapid expansion of land grasses (Poales), that led to increased carbon fixation that decreased atmospheric CO2 concentrations, because of the high efficiency of CO2 fixation of such C4 plants (Sage 2004; Taira 2007). C4 Poales appeared and began diversification during the Oligocene (23 – 33.9 Ma) based on molecular clock approach, and after 14.5 Ma based on fossil evidence (Sage 2004). We estimated 20.35 Ma by our Angiospermae timetree, that also employed BEAST v1. X with robust plant fossil calibrations (Osozawa et al. 2021c).\n\nFood plants of D. mendosensis are, however, C4 dicots of Amaranthaceae (see figure 9 in Sage 2004) and Chenopodiaceae in degraded salt-plain habitats in arid regions of central Argentina (Simon et al. 2019). These dicot fossils and C4 monocot fossils of Poales grass (Chloridoidae) were reported from the Eocene in Patagonia by Zucol et al. (2018), and the fossil horizon was dated by the Ar-Ar method at 49.512 ± 0.019 Ma (Woodburne et al. 2014). The C4 photosynthetic pathway began at ca. 50 Ma in South America, earlier than elsewhere. For Chloridoideae, however, transition from C3 to C4 photosynthesis occurred in the Oligocene (23~33.9 Ma) as reported by Christin et al. (2008), consistent with our estimate for C4 dicots at 31.92 Ma (Osozawa et al. 2021c), whereas Sage (2004) suggested a fossil date at 14.5 Ma as noted above.\n\nThe trigger of increasing biodiversity may have been the generation and radiation of C4 plants and development of grass lands on the Earth since the Oligocene or perhaps more definitively since middle Miocene, by decreasing atmospheric CO2 concentrations. This may have led to the start of Quaternary ice ages and resultant adaptive radiation and increasing base substitution (≒ mutation) rates. Thus, biologic activity, including spreading C4 grasses may have significantly impacted Earth's environment.\n\n\nData availability\n\nSequence data in Table 1 are found in GenBank/DDBJ by incorporating the accession number.", "appendix": "Acknowledgements\n\nWe thank Chris Simon and David Marshall for privately offering Tettigarcta sequence data (later released in GenBank/DDBJ). David Marshall also privately offered Asian Cicadinae sequence data of Hill et al. (2021) and reprint of Price et al. (2019). We pay our respects to their extensive and perfect taxon samplings including in protected countries with necessary permissions. We thank the collectors shown in Table 1. Bor-ming Jahn (Taiwan University; deceased 1 December, 2016), Ping-Shih Yang (Taiwan University), Chin-Ho Tsai (National Dong Hwa University), and Jen-Zon Ho (deceased 2018) and Hua-Te Fang (Endemic Species Research Institute) supported sample collections and obtained permission to collect in Taiwan. This project was partly financed through the Osozawa Fund (former), Tohoku University. We thank Keiji Nunohara (Nunohara Office for Geological Survey), Kohei Sugawara (Ecofarm GSK), Atsushi Momose (Mitsubishi Material Techno Corporation), CTI Engineering Co., Ltd., and NEWJEC, Inc. for contributing to this fund. This work was supported by Japan Society for the Promotion of Science, “Extrusion Wedge of the Sambagawa High P-T Metamorphic Rocks,” in the form of a grant awarded to the senior author (20540441).\n\n\nReferences\n\nBenton MJ, Donoghue PCJ: Paleontological evidence to date the tree of life. Mol. Biol. Evol. 2007; 24: 26–53. PubMed Abstract\n\nBenton MJ, Donoghue PCJ, Asher RJ, et al.: Constraints on the timescale of animal evolutionary history. Palaeontol. Electron. 2015; 18.1.1FC: 1–106. Publisher Full Text\n\nBashkuev A, Se J, Aristov D, et al.: Insects from the Buntsandstein of Lower Franconia and Thuringia. Paläontol. Z. 2012; 86: 175–185. Publisher Full Text\n\nBouckaert R, Heled J, Kühnert D, et al.: BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 2014; 10: e1003537. PubMed Abstract \| Publisher Full Text\n\nBoulard M: Distantalna genre nouveau pour les Tosenini (Rhynchota, Cicadomorpha, Cicadidae). Nouvelle Revue d’Entomologie (N.S.). 2009; 25: 325–328.\n\nBoulard M, Nel A: Sur deux cigales fossiles des terrains tertiaires de la France (Homoptera, Cicadoidea). Revue Francaise d’Entomologie. 1990; 12: 37–45.\n\nChen CH: A field guide to cicadas in Taiwan. Taipei: Bookzone; 2011; 206p. (In Chinese)\n\nChristin PA, Besnard G, Samaritani E, et al.: Oligocene CO2 decline promoted C4 photosynthesis in grasses. Curr. Biol. 2008; 18: 37–43.\n\nCohen KM, Finney SC, Gibbard PL, et al.: The ICS International Chronostratigraphic Chart. Episodes. 2013; 36: 199–204. Publisher Full Text\n\nCooper KW: Davispia bearcreekensis Cooper, A new cicada from the Paleocene, with a brief review of the fossil Cicadidae. Am. J. Sci. 1941; 239: 286–304. Publisher Full Text\n\nde Boer AJ , Duffels JP: Historical biogeography of the cicadas of Wallacea, New Guinea and the West Pacific: a geotectonic explanation. Palaeogeogr. Palaeoclimatol. Palaeoecol. 1996; 124: 153–177. Publisher Full Text\n\nDrummond AJ, Suchard MA, Xie D, et al.: Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012; 29: 1969–1973. PubMed Abstract \| Publisher Full Text\n\nDucreux J, Hugueney M, Truc G: La formation des Calcaires et Lignites de Sigonce (Oligocene moyen, bassin de Forcalquier, Alpes-de-Haute- Provence): datation a l'aide des mammiferes; reconstitution des milieux de depots. Geobios. 1985; 18: 109–114. Publisher Full Text\n\nDuffels JP, Hayashi M: On the identity of the cicada species Pomponia picta (Walker) (=P. fusca (Olivier)) and P. linearis (Walker) (Hemiptera: Cicadidae). Tijdschrift voor Entomologie. 2006; 149: 189–201. Publisher Full Text\n\nFlores RM, Bader LR: Fort Union coal in the Powder River Basin, Wyoming and Montana: A synthesis. U.S. Geol. Surv. Prof. Pap. 1999; 1625-A: 1–71.\n\nFujiyama I: A Miocene Cicada from Nasu, with an additional record of a Pleistocene cicada from Shiobara, Japan. Bulletin of the National Science Museum, Tokyo. 1969; 12: 863–875.\n\nFujiwara O, Yanagisawa Y, Irizuki T, et al.: Chronological data for the Middle Miocene to Pliocene sequence around the southwestern Sendai Plain, with special reference to the uplift history of the Ou Backbone Range. Bulletin of Geological Survey Japan. 2008; 59: 423–438. Publisher Full Text\n\nGrande L: Paleontology of the Green River Formation with a review of the fish fauna. The Geological Survey of Wyoming Bulletin. 1980; 63: 1–333.\n\nGouy M, Guindon S, Gascuel O: SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 2010; 27: 221–224. PubMed Abstract \| Publisher Full Text\n\nHayashi M, Saisho Y: The Cicadidae of Japan. Tokyo: Seibundo-Sinkosha; 2011; 223. (In Japanese).\n\nHe HY, Wang XL, Jin F, et al.: The 40Ar/39Ar dating of the early Jehol Biota from Fengning, Hebei Province, northern China. Geochem. Geophys. Geosyst. 2006; 7: Q04001. Publisher Full Text\n\nHill KBR, Marshall DC, Moulds MS, et al.: Molecular phylogenetics, diversification, and systematics of Tibicen Latreille, 1825 and allied cicadas of the tribe Cryptotympanini, with three new genera and emphasis on species from the USA and Canada (Hemiptera: Auchenorrhyncha: Cicadidae). Zootaxa. 2015; 3985: 219–251. PubMed Abstract \| Publisher Full Text\n\nHill KRB, Marshall DC, Marathe K, et al.: The molecular systematics and diversification of a taxonomically unstable group of Asian cicada tribes related to Cicadini Latreille, 1802 (Hemiptera: Cicadidae). Invertebr. Syst. 2021; 2021(35): 570–601.\n\nHo S: The molecular clock and estimating species divergence. Nature Education. 2008; 1: 168.\n\nHo SY, Phillips MJ, Cooper A, et al.: Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 2005; 2: 1561–1568.\n\nHong YC: Mesozoic Fossil Insects of Jiuquan Basin in Gansu Province. Clapham; 1982. In Chinese.\n\nJohnson KP, et al.: Phylogenomics and the evolution of hemipteroid insects. Proc. Natl. Acad. Sci. U. S. A. 2018; 115: 12775–12780. PubMed Abstract \| Publisher Full Text\n\nKato M: Monograph of Cicadidae. Tokyo, Japan: Sanseido; 1932; 450 pp. (In Japanese partly supplemented by English).\n\nKaulfuss U, Moulds M: A new genus and species of tettigarctid cicada from the early Miocene of New Zealand: Paratettigarcta zealandica (Hemiptera, Auchenorrhyncha, Tettigarctidae). ZooKeys. 2015; 484: 83–94. PubMed Abstract \| Publisher Full Text\n\nKing B, Rücklin M: Tip dating with fossil sites and stratigraphic sequences. PeerJ. 2020; 8: e9368. PubMed Abstract \| Publisher Full Text\n\nKlopfstein K: The age of insects and the revival of the minimum age tree. Austral Entomol. 2021; 60: 138–146. Publisher Full Text\n\nLanfear R, Frandse PB, Wright AM, et al.: PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 2016. Publisher Full Text\n\nLee YJ, Hayashi M: Taxonomic Review of Cicadidae (Hemiptera, Auchenorrhyncha) from Taiwan, Part 3. Dundubiini (Two Other Genera of Cicadina), Moganiini, and Huechysini with a New Genus and Two New Species. J. Asia Pac. Entomol. 2004; 7: 45–72. Publisher Full Text\n\nLee YJ, Sanborn AF: Three new species of the genus Megapomponia (Hemiptera: Cicadidae) from Indochina, with a key to the species of Megapomponia. J. Asia Pac. Entomol. 2010; 13: 31–39. Publisher Full Text\n\nLiu Y, Qiu Y, Wang X, et al.: Morphological variation, genetic differentiation and phylogeography of the East Asia cicada Hyalessa maculaticollis (Hemiptera: Cicadidae). Syst. Entomol. 2018; 43: 308–329. Publisher Full Text\n\nLiu Y, Pham HT, He Z, et al.: Phylogeography of the cicada Platypleura hilpa in subtropical and tropical East Asia based on mitochondrial and nuclear genes and microsatellite markers. Int. J. Biol. Macromol. 2020; 151: 529–544. PubMed Abstract \| Publisher Full Text\n\nŁukasik P, Nazario K, Van Leuven JT, et al.: Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas. Proc. Natl. Acad. Sci. U. S. A. 2018; 115: E226–E235. PubMed Abstract \| Publisher Full Text\n\nŁukasik P, Chong RA, Nazario K, et al.: One hundred mitochondrial genomes of cicadas. J. Heredity. 2019; 110: 247–256. Publisher Full Text\n\nMarshall DC: A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 2008; 171: 726–742. PubMed Abstract \| Publisher Full Text\n\nMarshall DC, Hill KBR, Moulds MS, et al.: Inflation of molecular clock rates and dates: Molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini). Syst. Biol. 2016; 65: 16–34. PubMed Abstract \| Publisher Full Text\n\nMarshall DC, Moulds M, Hill KBR, et al.: A molecular phylogeny of the cicadas (Hemiptera: Cicadidae) with a review of tribe and 926 subfamily classification. Zootaxa. 2018; 4424: 1–64. PubMed Abstract \| Publisher Full Text\n\nMisof B, et al.: Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014; 346: 763–767. PubMed Abstract \| Publisher Full Text\n\nMontagna M, Tong KJ, Magoga G, et al.: Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction. Proceedings of the Royal Society of London Series B-Biological Sciences. 2019; 286: 20191854.\n\nMoulin M, Aslanian D, Unternehr P: A new starting point for the south and equatorial Atlantic Ocean. Earth Sci. Rev. 2010; 98: 1–37. Publisher Full Text\n\nMcintosh WC, Geissman JW, Chapin CE, et al.: Calibration of the latest Eocene-Oligocene geomagnetic polarity time scale using 40Ar/39Ar dated ignimbrites. Geology. 1992; 20: 459–463. Publisher Full Text\n\nMoulds MS: Cicada fossils (Cicadoidea: Tettigarctidae and Cicadidae) with a review of the named fossilised Cicadidae. Zootaxa. 2018; 4438: 443–470. PubMed Abstract \| Publisher Full Text\n\nOsozawa S: BEAST v1.X tutorial, in a case of four cicada genera. protocols.io.2021. Publisher Full Text\n\nOsozawa S, Wakabayashi J: Geologically calibrated mammalian tree and the corresponding global events, including birth of human. Research Square. 2021. Publisher Full Text\n\nOsozawa S, Shinjo R, Armig R, et al.: Palaeogeographic reconstruction of the 1.55 Ma synchronous isolation of the Ryukyu Islands, Japan, and Taiwan and inflow of the Kuroshio warm current. Int. Geol. Rev. 2012; 54: 1369–1388. Publisher Full Text\n\nOsozawa S, Vuong NV, Tich VV, et al.: Reactivation of a collisional suture by Miocene transpressional domes associated with the Red River and Song Chay detachment faults, northern Vietnam. J. Asian Earth Sci. 2015; 105: 252–269. Publisher Full Text\n\nOsozawa S, Fukuda H, Kwon HY, et al.: Quaternary vicariance of tiger beetle, Cicindela chinensis, in Ryukyu, Japan, Taiwan and Korea—China. Entomol. Res. 2016; 46: 122–127.\n\nOsozawa S, Shiyake S, Fukuda H, et al.: Quaternary vicariance of Platypleura (Cicadidae) in Japan, Ryukyu, and Taiwan islands. Biol. J. Linn. Soc. 2017a; 121: 185–199. Publisher Full Text\n\nOsozawa S, Sato F, Wakabayashi J: Quaternary vicariance of lotic Coeliccia in the Ryukyu-Taiwan islands contrasted with lentic Copera. J. Hered. 2017b; 108: 280–287. PubMed Abstract \| Publisher Full Text\n\nOsozawa S, Kanai K, Fukuda H, et al.: Phylogeography of Ryukyu insular cicadas: Extensive vicariance by island isolation vs accidental dispersal by super typhoon. PLoS One. 2021a; 16(5): e0244342. Publisher Full Text\n\nOsozawa S, Ito H, Nakazato H, et al.: 4D volcanic geology of Hachijo-jima islet, Izu-Bonin arc. Int. Geol. Rev. 2021b; 63. Publisher Full Text\n\nOsozawa S, Nakejima C, Wakabayashi J: Post-Triassic Spermatophyta timetree adding the Quaternary radiated Asarum wild gingers. Research Square. 2021c. Publisher Full Text\n\nPapadopoulo A, Anastasiou I, Vogler AP: Revisiting the insect mitochondrial molecular clock: The mid-Aegean trench calibration. Mol. Biol. Evol. 2010; 27: 1659–1672. PubMed Abstract \| Publisher Full Text\n\nPerrichot V, Nel A, Néraudeau D: Gerromorphan bugs in Early Cretaceous French amber (Insecta: Heteroptera): first representatives of Gerridae and their phylogenetic and palaeoecological implications. Cretac. Res. 2005; 26: 793–800. Publisher Full Text\n\nPetrulevičius JF: Paleogene insects from Maíz Gordo Formation, northwest Argentina: Taphonomy, diversity and paleobiogeography.Salfity JA, Marquillas RA, editors. Cenozoic Geology of the Central Andes and Argentina SCS. 2011; 337–347.\n\nPham HT, Lee YJ, Constant J: Cicada genus Pomponia Stål, 1866 (Hemiptera: Cicadidae) from Vietnam andCambodia, with a new species, a new record, and a key to the species. Zootaxa. 2015; 3925: 562–572. PubMed Abstract \| Publisher Full Text\n\nPiirainen M, Liebisch O, Kadereit G: Phylogeny, biogeography, systematics and taxonomy of Salicornioideae (Amaranthaceae/Chenopodiaceae) – A cosmopolitan, highly specialized hygrohalophyte lineage dating back to the Oligocene. Taxon. 2017; 66: 109–132. Publisher Full Text\n\nPoinar G Jr, Kritsky G: Morphological conservatism in the foreleg structure of cicada hatchlings, Burmacicada protera n. gen., n. sp. in Burmese amber, Dominicicada youngi n. gen., n. sp. in Dominican amber and the extant Magicicada septendecim (L.) (Hemiptera: Cicadidae). Hist. Biol. 2011; 1: 1–6.\n\nPopov YA: The first record of a fossil water bug from the Lower Jurassic of Poland (Heteroptera: Nepomoprha: Belostomatidae). Polskie Pismo Entomologiczne. 1996; 65: 101–105.\n\nPrice BJ, Marshall DC, Barker NP, et al.: Out of Africa? A dated molecular phylogeny of the cicada tribe Platypleurini Schmidt (Hemiptera: Cicadidae), with a focus on African genera and the genus Platypleura Amyot & Audinet-Serville. Syst. Entomol. 2019; 44: 842–861. Publisher Full Text\n\nRoček Z, Dong L, Přikry T, et al.: Fossil frogs (Anura) from Shanwang (Middle Miocene; Shandong Province, China). Geobios. 2011; 44: 499–518.\n\nSage RF: The evolution of C4 photosynthesis. New Phytol. 2004; 161: 341–370. Publisher Full Text\n\nShi G, Grimaldi DA, Harlow GE, et al.: Age constraint on Burmese amber based on U-Pb dating of zircons. Cretac. Res. 2012; 37: 155–163. Publisher Full Text\n\nSimon C, Gordon ERL, Moulds MS, et al.: Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas. Biol. J. Linn. Soc. 2019; 128: 1076. Publisher Full Text\n\nSmith ME, Singer B, Carroll A: 40 Ar/39 Ar geochronology of the Eocene Green River Formation, Wyoming. Geol. Soc. Am. Bull. 2003; 115: 549–565. Publisher Full Text\n\nSuchard MA, Lemey P, Baele G, et al.: Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus. Evolution. 2018; 4: vey016. Publisher Full Text\n\nSzwedo J, Nel A: The oldest Aphid insect from the Middle Triassic of the Vosges, France. Acta Palaeontol. Pol. 2011; 56: 757–766. Publisher Full Text\n\nTaira A: Search the Earth History, Geology 3. Tokyo: Iwanami Shoten, Publishers; 2007; 396. (in Japanese).\n\nTamura K, Peterso D, Peterson N, et al.: MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011; 28: 2731–2739. PubMed Abstract \| Publisher Full Text\n\nThai PH, Yang JT: A contribution to the Cicadidae fauna of Vietnam (Hemiptera: Auchenorrhyncha), with one new species and twenty new records. Zootaxa. 2009; 2249: 1–19. Publisher Full Text\n\nTietz O, Berner T, Matting E: Insekten aus dem Unteroligozan von Seifhennersdorf in der Oberlausitz. Abhandlungen und Berichte des Naturkundemuseums, Gorlitz. 1998; 70: 139–154.\n\nTrilar T: Frequency modulated song of the cicada Kalabita operculata (Auchenorrhyncha: Cicadoidea) from Borneo. Russ. Entomol. J. 2006; 15: 341–346.\n\nWalther H, Kvacek Z: Early Oligonene flora of Seifhennersdorf (Saxiny). Acta Musei Nationalis Pragae, Series B, Historia Naturalis. 2007; 63: 85–174.\n\nWhalley PES: The systematics and palaeogeography of the Lower Jurassic insects of Dorset, England. Bulletin of the British Museum of Natural History (Geology). 1985; 39: 107–189.\n\nWoodburne MO, Goin FJ, Raigemborn MS, et al.: Revised timing of the South American early Paleogene land mammal ages. J. S. Am. Earth Sci. 2014; 54: 109–119. Publisher Full Text\n\nWu LW, Yen SH, Lees DC, et al.: Phylogeny and historical biogeography of Asian Pterourus butterflies (Lepidoptera: Papilionidae): A case of intercontinental dispersal from North America to East Asia. PLoS One. 2015; 10: e0140933. PubMed Abstract \| Publisher Full Text\n\nYang M, Wei C: On the cicada genus Nipponosemia Kato, with description of one new species from China (Hemiptera, Cicadidae). ZooKeys. 2013; 293: 19–39. Publisher Full Text\n\nYang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007; 24: 1586–1591.\n\nYoshikawa T: Paleoenvironmental change and age of the Miocene Kanomatazawa Formation in the Shiobara area, Tochigi Prefecture, central Japan. J. Geol. Soc. Jpn. 2005; 111: 39–49. In Japanese with English abstract. Publisher Full Text\n\nZhang JF: Fossil insects from Shanwang, Shandong, China. Jinan: Shandong Science and Technology; 1989; 459.\n\nZhang JF, Sun B, Zhang XY: Miocene insects and spiders from Shanwang, Shandong. Beijing: Science Press; 1994; 298.\n\nZhang H: Early Cretaceous insects from the Dalazi Formation of the Zhixin Basin, Jilin Province, China. Palaeoworld. 1997; 7: 75–103.\n\nZucol AF, Krause JM, Brea M, et al.: Emergence of grassy habitats during the greenhouse–icehouse systems transition in the Middle Eocene of southern South America. Ameghiniana. 2018; 55: 451–482. Publisher Full Text" }	[ { "id": "179259", "date": "30 Jun 2023", "name": "Sungsik Kong", "expertise": [ "Reviewer Expertise Phylogenetics" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe main objective of this study is to present a time-calibrated tree of cicada species reconstructed using BEAST v1.X. The trees contain crypic cicada species from Ryukyu islands in addition to the existing data presented in the previous studies. The authors show improved taxonomy of some of the major cicada groups. Moreover the authors suggest an exponential increase of base substitution rate in recent geologic time. While the content of the manuscript is interesting, it requires substantial improvement and is not ready for indexing. The following comments elaborate some places where the improvements can be made.\nIn general, the manuscript is not easy to understand. It is understandable that English may not be the authors' first language, however, an academic manuscript must be written clearly. For example, the last sentence of Abstract seems to be not connecting with the previous sentences. The first sentence of Introduction is excessively long.\n\nIn figure 1, is is not clear what it means by \"maximum\" COI sequence. It is not clear what is the inserted figure. I assume it is the plot on the left side with white background. These are also called as 'incets' later in the manuscript. How about labeling these as a) and b)? Here, y-axis is not labeled. It is not clear what it means by the intersection for the curve and what it represents biologically. Green or red starts and the values corresponding to it is never explained in the caption.\n\nBasically figure 2 is an identical tree as what is presented in figure 1. Again, the caption is very difficult to understand. Red and green stars and the values associated with them are never explained. The three values at the node in the tree are never explained.\n\nFigure 3 has similar problems. More work is needed in presenting the trees. Also, the authors mention in the caption of Figure 3 that the rate is a 'little' slower than that of in Figures 1 and 2, but it is what it means by 'a little', which is a subjective description.\n\nThe authors mention that the tree topology (based on COI) was unaffected by 18S rRNA. In other words, Figures 1, 2, and 3 are the same trees. If this is true, I am not sure presenting three identical trees is a good practice. Moreover, the authors must explore if the congruence occurred because they actually are congruent or simply the signals in 18S rRNA is too small to override the signals in COI. It would be interesting to explore the tree based on 18S rRNA.\n\ntypo {Abstract} parapheletic -> paraphyletic.\n\ntypo {Figure 2} OUTs -> OTUs.\n\nsubstrituions/site/myr and s/s/myr are used interchangeably. It would be a good idea to define for the first time and stick to the abbreviated version.\n\nTable 1 has a header labeled as 'country', but in fact, 'sampling locality' might be a better description of the content. Also, it might be a better to specify what accession numbers the authors are referring to, GenBank?\n\nTable 2 caption must be improved.\n\nIt is unclear how the authors decided to use HKY model for the BEAST analysis.\n\nThe authors mentioned that the 95\\% highest posterior density for confidence intervals of ages are not shown in Figure 1--3 to avoid visual complexity. Is it going to be available in supplementary material? This is important information to verify authors' claims regarding the node ages in the manuscript.\n\nFigure 4 mentions the number of base changes for whole mitochondrial gene, but the two plots are based only on COI and 18S rRNA. It's confusing which is correct. The caption needs improvement.\n\nIn results, the authors refer to Figure 3 as COI + 16S rRNA. It seemed like the authors were working on 18S rRNA. It's confusing which is correct.\n\nThe authors mentioned that the rate has exponentially increased into Holocene based on the incets of Figure 1--3. But no Holocene was labeled anywhere in these figures. Also, the authors stated the curves and rates are similar for the incets in Figure 1,2 and 3, but it is hard to understand how the authors concluded that they are 'similar', which is a very subjective description.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9858", "date": "20 Jul 2023", "name": "Soichi Osozawa", "role": "Author Response", "response": "copyright 30 Jun 2023 \| for Version 1 Sungsik Kong, University of Wisconsin-Madison, Madison, Wisconsin, USA format_quote Cite this report speaker_notes Responses(0) NOT APPROVED info_outline The main objective of this study is to present a time-calibrated tree of cicada species reconstructed using BEAST v1.X. The trees contain crypic cicada species from Ryukyu islands in addition to the existing data presented in the previous studies. The authors show improved taxonomy of some of the major cicada groups. Moreover the authors suggest an exponential increase of base substitution rate in recent geologic time. While the content of the manuscript is interesting, it requires substantial improvement and is not ready for indexing. The following comments elaborate some places where the improvements can be made. Thank you for your review, and we appreciate your attention to our main insight and new finding regarding the exponential increase of base substitution rate in recent geologic time. Although we acknowledge that our experience with BEAST v1. X and the calibration method is limited, we recommend that you become a BEAST v1.X user, as it will provide you with the tools and resources to address your queries effectively. Utilizing BEAST v1.X will enable you to delve deeper into the subject matter and gain a better understanding of the findings we presented. In general, the manuscript is not easy to understand. It is understandable that English may not be the authors' first language, however, an academic manuscript must be written clearly. We appreciate your confidence in the writing quality of the present manuscript. Considering that John Wakabayashi is a native English speaker, it is likely that the manuscript is indeed well-written. However, we understand your desire for a thorough review of the English language in the R1 manuscripts. For example, the last sentence of Abstract seems to be not connecting with the previous sentences. “We estimated base substitution rate as a function of age, and the result strongly indicates an exponential increase of base substitution rate in recent geologic time.” Is connected to next sentence “The consequent increase in cicada biodiversity, including generation of cryptic species in the Ryukyu Islands and surroundings, may have been driven by the generation and spreading of C4 grasses and coeval Quaternary climate change.” The first sentence of Introduction is excessively long. It is crucial to emphasize the specific type of gene used in the phylogenetic analyses, and our current COI and 18S rRNA sequence data may not be sufficient for our study. Addressing these concerns, we reviewed here the significance of utilizing an appropriate and comprehensive set of genes for the recent trend of phylogenetic analyses for cicadas. In figure 1, is not clear what it means by \"maximum\" COI sequence. “1,534 bp in maximum”, not “maximum COI sequence”. We will revise in R1 manuscript. It is not clear what is the inserted figure. I assume it is the plot on the left side with white background. These are also called as 'inserts' later in the manuscript. How about labeling these as a) and b)? Here, y-axis is not labeled. The inset was made by node data shown in Fig. 2. In R1, we will improve the expression. Y axis is Ma, or you questioned no species name? It is not clear what it means by the intersection for the curve and what it represents biologically. To draw the approximate curve, better to apply the intersection data, and we applied rate median obtained from Tracer. Green or red starts and the values corresponding to it is never explained in the caption. You will find the captions within Fig. 1, but we will enlarge the caption in R1. Basically figure 2 is an identical tree as what is presented in figure 1. We acknowledge the feedback provided by Jessica Ware, a reviewer of our dragonfly manuscript, regarding Figure 2 being overly crowded. To address this concern, we have made revisions by dividing the scientific content of Figure 2 into simplified and full version figures, namely Figures 1 and 2, respectively. It is important to note that both figures are identical, as you correctly pointed out. By providing simplified and full versions of the figure, we aim to improve the clarity and readability of the scientific information presented. This division allows readers to quickly grasp the main concepts in the simplified version, while still having access to the more detailed information in the full version if desired. We appreciate the valuable input from Jessica Ware and are grateful for her suggestion to enhance the visual presentation of our manuscript. Thank you for highlighting this issue, and we hope these revisions address the concern effectively. Again, the caption is very difficult to understand. Red and green stars and the values associated with them are never explained. The three values at the node in the tree are never explained. You will find the captions within Fig. 2, but we will enlarge the caption in R1. Probably see also main text. Figure 3 has similar problems. More work is needed in presenting the trees. Fig. 3 was presented to compare COI + 18S rRNA tree vs solely COI tree in Figs. 1 and 3. Allow us here too busy figure without simplified figure. Also, the authors mention in the caption of Figure 3 that the rate is a 'little' slower than that of in Figures 1 and 2, but it is what it means by 'a little', which is a subjective description. Rate median 0.0114 in Fig. 3 inset is a little slower than 0.0128 in Figs. 1 and 2, reflecting Fig. 3 was considered slower rated (not sensitive) 18S rRNA data. The authors mention that the tree topology (based on COI) was unaffected by 18S rRNA. In other words, Figures 1, 2, and 3 are the same trees. If this is true, I am not sure presenting three identical trees is a good practice. Moreover, the authors must explore if the congruence occurred because they actually are congruent or simply the signals in 18S rRNA is too small to override the signals in COI. It would be interesting to explore the tree based on 18S rRNA. Note that COI tree is for 352 specimens and tips, and COI + 18S rRNA tree is for 1492 specimens and tips, and not strictly identical and congruent. 18S rRNA tree is “low resolution” and discordant COI tree. Seealso “Why was BEAST2 not used”. typo {Abstract} parapheletic -> paraphyletic. In R1, we revise. typo {Figure 2} OUTs -> OTUs. In R1, we revise. substrituions/site/myr and s/s/myr are used interchangeably. It would be a good idea to define for the first time and stick to the abbreviated version. We will delete later appeared “substrituions/site/myr”. Some journal ask to offer abbreviations, but now not a case. Table 1 has a header labeled as 'country', but in fact, 'sampling locality' might be a better description of the content. Also, it might be a better to specify what accession numbers the authors are referring to, GenBank? In GenBank/DDJB “country” is requested to use. Also our data with accession numbers are found in GenBank/DDBJ. Table 2 caption must be improved. In R1, we will check English. It is unclear how the authors decided to use HKY model for the BEAST analysis. Default setting. The authors mentioned that the 95\\% highest posterior density for confidence intervals of ages are not shown in Figure 1--3 to avoid visual complexity. Is it going to be available in supplementary material? This is important information to verify authors' claims regarding the node ages in the manuscript. Please consider adding 95% highest posterior density (HPD) bars to represent confidence intervals for ages on each node in Figure 2. The figure becomes further busy. We believe they may not add significant meaning. Figure 4 mentions the number of base changes for whole mitochondrial gene, but the two plots are based only on COI and 18S rRNA. It's confusing which is correct. The caption needs improvement. Vertical axis is COI numbers of base changes and 18S rRNA numbers of base changes, respectively in left sided COI and right sided 18S rRNA figures. In results, the authors refer to Figure 3 as COI + 16S rRNA. It seemed like the authors were working on 18S rRNA. It's confusing which is correct. We found four mistakes of 16S rRNA in page 11 including Osozawa et al. (2016), and we collect as 18S rRNA and Osozawa et al. (2017a) in R1. The authors mentioned that the rate has exponentially increased into Holocene based on the incets of Figure 1--3. But no Holocene was labeled anywhere in these figures. Also, the authors stated the curves and rates are similar for the incets in Figure 1,2 and 3, but it is hard to understand how the authors concluded that they are 'similar', which is a very subjective description. The Holocene is the most recent epoch of the Quaternary period, following the boundary at 0.0117 Ma. We acknowledge the difficulty in accurately labeling the time point at 0.0117 Ma in Figures 1 to 3. Compare formula in the same one in Fig. 1 and 2, and the distinct one in Fig. 3. We were hoping your constructive review about increasing rate, factor, and affect. 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? Yes 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 Competing Interests No competing interests were disclosed. Reviewer Expertise Phylogenetics I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above." } ] }, { "id": "184588", "date": "02 Aug 2023", "name": "David A Duchêne", "expertise": [ "Reviewer Expertise Phylogenetic modelling", "molecular evolution", "molecular dating." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study, Osozawa and Wakabayashi examine the timing of the splits within the Cicadas using a Bayesian framework for phylogenetic analysis. The motivation for the study and data are well presented. However, the methods have large amounts of superfluous information that makes them appear confusing. Overall, the manuscript is going in a good direction, but requires substantial streamlining.\nMy main comment is on the description of BEAST. For the purposes of this study, BEAST v1 and 2 should make very little difference. In fact, it would be surprising to find any difference in results whatsoever, unless the analyses failed to converge to stationarity. The differences highlighted by the authors, such as in the BEAUti interface, are not meaningful to the analyses. Therefore, the authors should consider removing any comparison between the software, and only mention BEAST once and very briefly in the methods.\nFar more important is the models chosen for analysis using BEAST. At the moment these details seem buried in between the discussion about the software versions. I suggest the authors replace any sections about the BEAST versions, and exclude BEAST from section headings, leaving simply a section on \"Molecular dating\". Importantly, the authors do not mention how they assessed convergence of the MCMC chain to stationarity (e.g., effective sample sizes, multiple runs, and visual assessment, or similar).\nThere is substantial redundancy in the figures, which is confusing to the untrained eye. The authors should consider using a single main tree figure with the primary results and icons to indicate which analyses were congruent. This would make the study far more succinct and intuitive.\nThe excessive emphasis on the software versions obscures the true emphasis of the study: Cicada evolution. The authors should consider re-framing the Abstract and Introduction to focus on the previous biological findings on the topic. The methodological considerations are secondary and should be left to the methods. Otherwise, the study appears to primarily focus on a debate about methods, which is not the case. The emphasis should be on the novel molecular and fossil data, which are the true major source of novel insights in the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10036", "date": "24 Aug 2023", "name": "Soichi Osozawa", "role": "Author Response", "response": "copyright 02 Aug 2023 \| for Version 1 David A Duchêne Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Capital Region of Denmark, Denmark In this study, Osozawa and Wakabayashi examine the timing of the splits within the Cicadas using a Bayesian framework for phylogenetic analysis. The motivation for the study and data are well presented. However, the methods have large amounts of superfluous information that makes them appear confusing. Overall, the manuscript is going in a good direction, but requires substantial streamlining. Thank you for your review and approval. I plan to compare MCMCTree to BEAST v1 and eagerly await the MCMCTree GUI for Mac. If you are involved in the development of MCMCTree, I appreciate your contributions to the field. My main comment is on the description of BEAST. For the purposes of this study, BEAST v1 and 2 should make very little difference. In fact, it would be surprising to find any difference in results whatsoever, unless the analyses failed to converge to stationarity. The differences highlighted by the authors, such as in the BEAUti interface, are not meaningful to the analyses. Therefore, the authors should consider removing any comparison between the software, and only mention BEAST once and very briefly in the methods. Regarding the comparison to BEAST v2, I understand that it has undergone significant modifications and is distinct from v1, even though they share some developers. If you prefer, you may choose to use BEAST v1 for this study. Far more important is the models chosen for analysis using BEAST. At the moment these details seem buried in between the discussion about the software versions. I suggest the authors replace any sections about the BEAST versions, and exclude BEAST from section headings, leaving simply a section on \"Molecular dating\". Importantly, the authors do not mention how they assessed convergence of the MCMC chain to stationarity (e.g., effective sample sizes, multiple runs, and visual assessment, or similar). Title \"Molecular dating\" may be a suggestion to avoid negative review for us, but I would like to describe details. It is important to emphasize that a larger sample size and genome size, along with an increased MCMC chain, is unrelated to dating and calibrating the tree. The MCMC chain is retained at its default settings. There is substantial redundancy in the figures, which is confusing to the untrained eye. The authors should consider using a single main tree figure with the primary results and icons to indicate which analyses were congruent. This would make the study far more succinct and intuitive. I have simplified Fig. 1 to the best of my ability. The node data, including base substitution rates, may be visualized in FigTree, created also by MCMCTree. The excessive emphasis on the software versions obscures the true emphasis of the study: Cicada evolution. The authors should consider re-framing the Abstract and Introduction to focus on the previous biological findings on the topic. The methodological considerations are secondary and should be left to the methods. Otherwise, the study appears to primarily focus on a debate about methods, which is not the case. The emphasis should be on the novel molecular and fossil data, which are the true major source of novel insights in the study. I am emphasizing the increase in base substitution rate towards the present. To achieve this, the fossil dating process in BEAST v1 is thoroughly described. However, it is important to note that dating by MCMCTree and BEAST v2 does not align with our results, possibly due to the impact of maximum age assumptions." } ] } ]	1	https://f1000research.com/articles/11-308
https://f1000research.com/articles/13-1165/v1	08 Oct 24	{ "type": "Systematic Review", "title": "Management of Pulmonary Mucormycosis: A Systematic Review", "authors": [ "Tarig Fadelelmoula", "Navas Ayyalil", "Nandini Doreswamy", "Navas Ayyalil", "Nandini Doreswamy" ], "abstract": "Background Mucormycosis is a life-threatening fungal infection. Rhino-orbito-cerebral mucormycosis (ROCM) and pulmonary mucormycosis (PM) are the most common presentations. This systematic review focuses on the management of PM. Although the mortality from PM has improved over the last few decades, it is still high, at 49.8% (Muthu, Agarwal, et al., 2021).\n\nObjective The objective is to identify and map the management of PM.\n\nDesign This review is designed for knowledge synthesis, with a systematic approach to identifying, synthesizing, and mapping treatment protocols for the management of PM.\n\nMethods This systematic review provides a clear, reproducible methodology. It is reported in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). Inclusion criteria were defined: peer-reviewed journal articles published in English from 2018 to 2023 relating to treatment protocols for PM, where the full text of the article was available. Exclusion criteria were also defined - articles that focus on limited treatment regimens, such as the use of amphotericin B only, or topics not relevant to the research question, such as fungal infections and pulmonary diseases unrelated to mucormycosis.\n\nResults The results span six years, from 2018 to 2023, with 355 articles identified. After removing duplicates, 227 papers remained. Inclusion and exclusion criteria were applied, with 202 articles excluded as a result. The remaining 19 articles were deemed relevant. In addition, seven relevant articles were identified via citation tracking and two articles identified by hand search. Thus, a total of 28 articles thus reviewed. The management of PM was mapped in tabular and diagrammatic form.\n\nConclusion The results indicate that early diagnosis, early and aggressive surgery, and effective antifungals may improve survival. There is a shift away from using Am-B and a clear preference for L-AmB as a first-line antifungal. Posaconazole and Isavuconazole are the drugs of choice for stepdown, maintenance, and salvage therapy, and as alternative therapies. The control of co-morbidities is a crucial aspect of treatment. Cytokines and hyperbaric oxygen may be beneficial. The therapeutic value of iron chelators, zinc, and nebulized amphotericin B (NAB) merit further study.", "keywords": [ "pulmonary mucormycosis", "pulmonary fungal infections", "COVID-19 associated pulmonary mucormycosis", "CAPM", "management of pulmonary mucormycosis", "management of pulmonary mucormycosis", "mucormycosis", "Mucorales." ], "content": "Background\n\nMucormycosis is a life-threatening fungal disease caused by 11 genuses and 27 species of the order Mucorales (Gomes et al., 2011). Rhizopus arrhizus is the commonest cause, followed by Lichtheimia, Apophysomyces, Rhizomucor, Mucor and Cunninghamella species (Gomes et al., 2011; Roden et al., 2005). Humans usually contract mucormycosis by inhaling sporangiospores or, occasionally, by consuming contaminated food or through traumatic inoculation (Ribes et al., 2000; Richardson, 2009). Mucorales species have significant angio-invasive characteristics, which results in rapid local progression and substantial morbidity (Lee et al., 1999; Moreira et al., 2016; Prakash et al., 2019). Most patients with mucormycosis also have significant co-morbidities. The most common underlying conditions are malignancies (63.4%), diabetes mellitus (17.1%) and solid organ transplantation (9.8%) (Rüping et al., 2010).\n\nDespite treatment with antifungal therapy and surgical debridement, the mortality rate is around 50% (Muthu, Singh, et al., 2021).The incidence of mucormycosis is rising globally (Ambrosioni et al., 2010; Bitar et al., 2009; Pana et al., 2016; Torres-Narbona et al., 2007). Although the mortality rate of this disease has improved over time, it is still high (Muthu, Agarwal, et al., 2021). Therefore, this systematic review aims to shed light on recent treatment protocols for PM. A systematic review is appropriate because many of these treatments are new or emerging.\n\nThe most usual form of the disease is rhino-orbito-cerebral mucormycosis (ROCM), where the sites of infection include the nasal cavities, sinuses, orbits, intracranial spaces and structures, and compartments of the neck. and pulmonary mucormycosis (PM). The lungs are the second most common site of infection mucormycosis – a form of the disease known as pulmonary mucormycosis (PM). The rhino-orbito-cerebral form of the disease is more common in patients with diabetes, whereas the lungs are more like to be affected in patients with hematologic malignancies. This systematic review focuses on the pulmonary form of the disease, seeking to identify and map recent treatment protocols for PM. For PM, haematological malignancy is the major risk factor (32–40%), followed by diabetes mellitus (32–56%), haematopoietic stem cell transplant (1–9.8%) and solid organ transplant (6.5–9%), and renal disease (13–18%) (Feng & Sun, 2018; Tedder et al., 1994).\n\nThe clinical presentation, radiological presentation, and risk factors of PM are often very similar to acute Invasive Pulmonary Aspergillosis (IPA) (Agrawal et al., 2020). Both PM and IPA have devastating tissue-destructive effects. One of the most remarkable signs of PM is tissue necrosis, which is often a result of vascular thrombosis. In immunocompromised hosts, the primary route of infection is the inhalation of sporangiospores, which leads to pulmonary infection (Roden et al., 2005). PM tends to occur in patients with high neutropenia (Roden et al., 2005). A definitive diagnosis of PM relies on histopathology of pulmonary tissue, culture of sputum secretions, bronchoalveolar lavage, fine needle aspiration, or a combination of these diagnostic methods (Mir et al., 2018).\n\nThe incidence of PM increased dramatically during the COVID-19 pandemic, with most cases seen in India. Uncontrolled diabetes and the use of glucocorticoids in India, and ICU stays elsewhere, are the main factors associated with this increase (Hoenigl et al., 2022). COVID-19-associated PM (CAPM) is difficult to diagnose because its clinical presentation is often the same as COVID-19 itself (Hoenigl et al., 2022). It is diagnosed at the same time as COVID-19 or within 3 months of virologically confirmed infection (Muthu et al., 2022). Any patient with COVID-19 who has haemoptysis, or expectorates brownish or black sputum, should be investigated for CAPM (Pruthi et al., 2022).\n\nBefore the advent of the antifungal amphotericin B deoxycholate (Am-B) in 1959, mucormycosis in all its forms carried a mortality of 84%, but the use of Am-B led to a dramatic improvement – by the 1990s, the mortality rate fell to 47% (Roden et al., 2005). A review conducted in 2021 shows how mortality from PM, specifically, has improved over time – before the year 2000, it was as high as 72.1%, dropping to 58.3% between 2000 and 2009, and decreasing even further, to 49.8%, between 2010 and 2020 (Muthu, Agarwal, et al., 2021).\n\nWhile Am-B has been the mainstay of antifungal treatment for decades, its use has often been limited by a high degree of dose-dependent toxicity. It has now largely been replaced by liposomal amphotericin B, a lipid-based form of the drug, which has a significantly better toxicity profile. Other drugs, such as triazoles, have been found to be effective – posaconazole, introduced in 2006 (Brigmon et al., 2021), and isuvaconazole, approved for use in 2015 (Greenberg et al., 2006; van Burik et al., 2006) have not only been deployed as primary therapies, usually in combination with L-AmB, but also as stepdown, maintenance, and salvage therapies.\n\nAdjunctive immune therapies have also looked promising in recent years – granulocyte transfusions, cytokines such as interferon-gamma (IFN-γ), and recombinant granulocyte-macrophage colony-stimulating factor (GM-CSF) and granulocyte colony-stimulating factor (G-CSF) (Spellberg & Ibrahim, 2010). Hyperbaric oxygen may also be a useful adjunct (John et al., 2021). In addition, there has been some debate about whether iron chelators and zinc have a role to play in the treatment of mucormycosis.\n\nAlthough mucormycosis was considered to be a community-acquired disease, nosocomial mucormycosis has been increasingly reported from many hospitals worldwide (Rammaert et al., 2012; Saegeman et al., 2010). The most common clinical presentations of mucormycosis are rhino-orbito-cerebral (34%) and pulmonary (21%), the lungs being the second most common site of involvement in patients with mucormycosis (Jeong et al., 2019; Prakash et al., 2019). The main sites of infection are the lungs (19%), skin and soft tissues (19%), paranasal sinus/sino-orbital region (15.8%), and rhino-cerebral (7.9%) (Pana et al., 2016). A combination of prompt diagnosis, appropriate medical therapy and early aggressive surgical intervention could reduce the mortality to 25% (Ibrahim et al., 2012; John et al., 2021). However, the mortality of mucormycosis remains high, perhaps because of delayed diagnosis, the high cost of managing the disease, and limited treatment options (Skiada et al., 2018).\n\nThe incidence of mucormycosis is rising globally (Ambrosioni et al., 2010; Bitar et al., 2009; Pana et al., 2016; Torres-Narbona et al., 2007). Significant risk factors include uncontrolled diabetes mellitus in ketoacidosis, other forms of metabolic acidosis, treatment with glucocorticoids, organ or bone marrow transplantation, neutropenia, trauma and burns, malignant hematologic disorders, and deferoxamine therapy in patients receiving hemodialysis (Ibrahim et al., 2003; Spellberg et al., 2005; Sugar, 1990). For PM, haematological malignancy is the major risk factor (32–40%), followed by diabetes mellitus (32–56%), haematopoietic stem cell transplant (1–9.8%) and solid organ transplant (6.5–9%), and renal disease (13–18%) (Feng & Sun, 2018; Tedder et al., 1994). There are recent changes in the epidemiology of the disease, especially in Asia, where tuberculosis and chronic renal failure are emerging risks (Prakash & Chakrabarti, 2019).\n\nDuring the pandemic, there was a surge in mucormycosis in patients with COVID-19 and in those who recovered from COVID-19 (Ghazi et al., 2021). COVID-19-associated PM (CAPM) has been described in patients infected with SARS-CoV-2. Several factors have been implicated in the development of CAPM, including the use of glucocorticoids, poor glycaemic control, and viral-induced lymphopenia (Pal et al., 2021). Thromboembolic events are also seen in COVID-19, including pulmonary embolism, deep vein thrombosis (DVT), cerebrovascular accidents (CVA), and myocardial infarction (Abbas et al., 2021). The resultant hyper-coagulability and distal ischemia may well contribute to mucormycosis, although definitive proof for this remains elusive. The prime site of infection depends on the type of Mucorales and the comorbidity of the affected individual (Jeong et al., 2019; Lanternier et al., 2012; Skiada et al., 2011). Bone and joint infections, peritonitis, and nephritis are rare forms of mucormycosis (Serris et al., 2019). Endocarditis is also rare and is usually only seen in intravenous drug users (Serris et al., 2019).\n\nClimate change plays a role in the emergence of diseases (El-Sayed & Kamel, 2020). It may result in a surge in known fungal diseases and the emergence of new fungal diseases as well (Garcia-Solache & Casadevall, 2010). Climate change is defined by the United Nations Framework Convention on Climate Change (FCCC) as “a change of climate which is attributed directly or indirectly to human activity that alters the composition of the global atmosphere and which is in addition to natural climate variability observed over comparable time periods” (Pielke, 2004).\n\nThe geographic range of fungal pathogens is expanding because of the increase in temperature at higher latitudes (Gadre et al., 2022). Many fungal species are capable of developing thermotolerance and, as a result, fungi previously harmless to humans may become pathogenic (Gadre et al., 2022). Sivagnanam et al. (2017) reported patient clusters with sino-pulmonary mucormycosis associated with changes in climatic conditions, such as changes in precipitation and temperature. Extreme climate events may also exacerbate the incidence of fungal disease - for instance, there are reports of necrotizing fasciitis caused by mucormycosis after the Indian Ocean tsunami of 2004 (Andresen et al., 2005) and the Missouri tornado of 2011 (Neblett Fanfair et al., 2012).\n\nThe incidence of mucormycosis in India and Pakistan is a hundred times higher than the rest of the world combined (van Rhijn & Bromley, 2021). The higher incidence of co-morbidities such as diabetes mellitus accounts for some proportion of this significant difference in incidence (Ghazi et al., 2021). However, even before the advent of Covid-19, there was an increase in the number of cases of mucormycosis in these South Asian countries, and the higher incidence of diabetes mellitus alone does not account for the increase (van Rhijn & Bromley, 2021). Climate change in South Asia could be a contributing factor because fungi thrive at higher temperatures and in conditions of increasing humidity (Pörtner et al., 2022; Safdar et al., 2019; van Rhijn & Bromley, 2021).\n\nIndividuals with defective immunity or increased available serum iron are more susceptible to mucormycosis. However, the disease has also been reported in healthy hosts (Larsen et al., 2003; LeCompte & Meissner, 1947). Symptoms of PM include dyspnea, cough, chest pain, and fever is present in most reported cases (Tedder et al., 1994). Angioinvasion leads to the necrosis of the pulmonary parenchyma, which may lead to cavitation and hemoptysis. This can be fatal if a major blood vessel is involved (Harada et al., 1992; Watts, 1983). Although most patients with PM present with a fulminant and rapidly progressive disease, some patients only present with chronic symptoms (Agarwal et al., 2006).\n\nEarly diagnosis is a cornerstone of successful management (Fernandez et al., 2013). Clinical diagnostic methods have low sensitivity and specificity, which makes the diagnosis of PM challenging (Skiada et al., 2018). Therefore, diagnosis requires a high index of suspicion, recognition of host factors, and analysis of the clinical presentation. Diplopia in a diabetic patient or pleuritic pain in a patient with neutropenia should arouse the suspicion of mucormycosis. The prompt use of imaging, as well as histology, microbiology, and advanced molecular methods underpin successful diagnosis and management (Skiada et al., 2018).\n\nMolecular diagnosis\n\nIn 2014, Gebremariam et al. investigated host immune responses to Mucorales. They discovered the genes for proteins that encode spore coatings – the CotH genes, which are only found in Mucorales (Gebremariam et al., 2014). A 2018 study by Baldin et al. showed that CotH could be used as a target for the early diagnosis of mucormycosis (Baldin et al., 2018). In this study, mice infected with Rhizopus delemar, Lichtheimia corymbifera, Cunninghamella bertholettiae, and Mucor circinelloides, were positive for CotH, detected through polymerase chain reaction (PCR), in 3/3, 1/3, 2/2, and 3/3 urine samples, respectively (Baldin et al., 2018).\n\nReal-time qualitative polymerase chain reaction (qPCR) can now be used to detect Mucorales DNA in blood samples. qPCR is non-invasive and allows mucormycosis to be diagnosed up to eight days before mycological diagnosis (Bourcier et al., 2017; Millon et al., 2016; Millon et al., 2013; Springer et al., 2016). In 2022, Alinaghi et al. (2022) found that when mucormycosis occurred as a co-infection alongside COVID-19, the mortality rate was 33.6%. Furthermore, mucormycosis was diagnosed between 3 and 45 days after the diagnosis of COVID-19, and other co-infections such as aspregillosis occasionally occurred (Alinaghi et al., 2022).\n\nChest X-ray\n\nRadiology may only show peribronchial ground-glass opacity in the early stages, but later, pulmonary nodules, isolated masses, lobar consolidation, or cavitation may be found (Kawakami et al., 2004; Lin et al., 2017; McAdams et al., 1997). Wedge-shaped pulmonary infarcts may also be found. These infarcts are usually seen when there is thrombosis of the pulmonary vessels, following fungal angioinvasion (Marchevsky et al., 1980).\n\nChest CT scan\n\nHigh-resolution chest CT scans are the preferred method to detect the extent of PM. These scans may show evidence of a Mucorales infection earlier than a chest X-ray. If an expanding mass is found, or a consolidation across tissue planes, especially towards the great vessels of the mediastinum, it is highly suggestive of mucormycosis (Reimund & Ramos, 1994). Other suggestive findings include 10 or more nodules with pleural effusion (Skiada et al., 2018). When a reverse halo sign is found on CT, it is more suggestive of PM than IPA (Agrawal et al., 2020).\n\nBronchoscopy\n\nThe use of bronchoscopy in obtaining tissue biopsy for microscopic histological examination and culture seems to be safe in capitating lung lesions, despite its potential risk factors (e.g., pneumothorax) (Smith & Kauffman, 2012). Bronchoscopic guided Trans-Bronchial Lung Biopsy (TBLB) is the most common modality used to obtain lung tissue for diagnosis (Krishna et al., 2022). As far back as 1999, Lee, Mossad, and Adal undertook a 30-year review of patients with mucormycosis – of the 35 patients reviewed, bronchoscopy was required in more than 70% for a definitive diagnosis (Lee et al., 1999). Bronchoscopy remains a mainstay of diagnosis even today. In 2022, the Delphi panel recommended early bronchoscopy in all suspected cases of this life-threatening disease (Muthu et al., 2022).\n\nHistology, Molecular Tests, and Biopsy\n\nThe diagnosis of mucormycosis is based on both histopathological findings of tissue invasion by hyphae and cultures isolating pathogens of the order Mucorales, most commonly Rhizopus, Mucor, and Rhizomucor species (Smith & Lee, 2022). Many molecular based tests can be used either for detection or identification of mucorales, these tests include polymerase chain reaction (PCR) (Hsiao et al., 2005), restriction fragment length polymorphism analyses (RFLP) (Kumar et al., 2022; Page et al., 2021), DNA sequencing of defined gene regions (Nyilasi et al., 2008; Springer et al., 2016), and melt curve analysis of PCR products (Kasai et al., 2008).\n\nWhile transbronchial lung biopsy (TBLB) is the most common method of obtaining lung tissue for diagnosis, specimen tissue can also be obtained by video-assisted thoracoscopic surgery (VATS) and open lung biopsy in patients undergoing surgical treatment (Krishna et al., 2022). In patients with haematologic disease, it can be a challenge to perform a diagnostic biopsy early. In a study of 28 haematologic patients, Potenza et al. (2011) demonstrated that Mucorales-specific T cells were only detected in patients with proven invasive mucormycosis – these cells neither detected before the onset of infection nor after the infection was fully resolved. Therefore, when early diagnostic biopsy is a challenge, Mucorales-specific T cells can be an effective surrogate diagnostic marker.\n\nArtificial intelligence (AI)\n\nSyed-Abdul et al. (2022) showed that Artificial Intelligence-based models may be able to predict the risk of mucormycosis after COVID-19. AI models may be able to identify high-risk patients and flag predisposing factors such as obesity, anosmia, de novo diabetes, myalgia, and nasal discharge. Such models may enable protocols during and after COVID-19 that prevent co-infection with Mucorales (Agrawal et al., 2020).\n\nThe effective management of depends on early suspicion or recognition of PM. Early diagnosis is critical to effective treatment. The essential components of the management of this disease include the reversal of underlying risk factors, such as correcting hyperglycemia or tapering glucocorticoids; early and aggressive surgical resection, if possible; and optimal anti-fungal therapy (Pandey et al., 2020; Patel et al., 2020). Amphotericin B is a reliable antifungal that is used for primary anti-fungal therapy, with L-AmB widely in use as a less toxic form of the drug. The triazoles posaconazole and isuvaconazole are also effective against mucormycosis, and are used as primary therapies and in stepdown, maintenance, and salvage therapies (Smith & Lee, 2022).\n\nSurgical treatment\n\nPM usually progresses rapidly. Surgery is often a necessity because of the massive amount of tissue necrosis that occurs during the disease. Treating the disease and killing these highly virulent fungi may not prevent or reverse the tissue necrosis (Ibrahim et al., 2005). While surgery and anti-fungal therapies are the primary modalities of treatment, clear-cut guidelines regarding the extent and timing of surgical resection are yet to be defined. However, a successful attempt at methodological management of PM was made by the authors in the previously reported surgical series (Pulle et al., 2021). Aggressive surgical resection with clear margins should be offered whenever feasible, as anti-fungal therapy alone may have sub-optimal outcomes. Surgical resection should be synergised with peri-operative anti-fungal therapy to improve long-term survival (Kumar et al., 2022).\n\nAntifungal therapy\n\nAmphotericin B (Am-B) has been in use from 1959, as a reliable antifungal that is effective in treating progressive and potentially fatal fungal infections (Cavassin et al., 2021). It is still an important option in the treatment of mucormycosis. However, Am-B has a high dose-dependent toxicity that can manifest as nephrotoxicity (Deray, 2002) or reactions to infusions (Cavassin et al., 2021). Am-B is only recommended now in settings where resources are limited, or it is the only treatment option available (Cornely et al., 2019).\n\nThere is sufficient evidence in the literature to merit the early initiation of the lipid-based amphotericin B formulation, liposomal amphotericin-B (L-AmB), instead of Am-B, as the first line of treatment, in doses of 5 to 10 mg per kilogram per day (Kontoyiannis & Lewis, 2006; Lewis & Wiederhold, 2003). Nephrotoxicity and infusion-related reactions are significantly less with L-AmB (Hamill, 2013). Its peak plasma level is much higher than Am-B and the area under the concentration-time curve is larger (Hamill, 2013). It is smaller in size and carries a negative charge, so it avoids substantial recognition and uptake by the mononuclear phagocyte system (Hamill, 2013).\n\nRecently, posaconazole and isuvaconazole have been used as primary therapies, usually in conjunction with L-AmB. Intravenous isuvaconazole, intravenous posaconazole, or delayed release posaconazole tablets are also recommended as salvage treatments, in moderate doses (Cornely et al., 2019; Kohno et al., 2023). They are also used as stepdown or maintenance therapies, or as alternative therapies in patients who are unable to tolerate amphotericin B in any form (Smith & Lee, 2022). It is worth noting that fluconazole, voriconazole and itraconazole have no activity on Mucorales (Sun et al., 2002).\n\nIron chelating agents\n\nLike many bacteria and fungi, Mucorales produce compounds known as siderophores that have a high affinity for iron – these compounds provide the fungus with the ability to acquire iron from the host (Tahiri et al., 2023). Rhizoferrin is the most specific siderophore that Mucorales produce (Tahiri et al., 2023). A recent experimental study in a murine model showed that rhizoferrin may increase fungal virulence (Alejandre-Castañeda et al., 2022). Mucorales also produce permeases that have a high affinity for iron (Stearman et al., 1996). These permeases can form copper-oxidase-ferrous-permease complexes to capture soluble iron and make it available to the fungus (Stearman et al., 1996).\n\nIron chelators are medications that bind iron. There is increasing evidence that they may have a role to play in the management of mucormycosis, in starving the fungus of iron, which is essential for its high virulence and growth. (Boelaert et al., 1994; Symeonidis, 2009). Mucorales species have a very high affinity for iron. Therefore, iron chelators that do not capture and bind iron as efficiently as the pathogen, may “donate” iron to the fungus, thereby increasing a patient’s susceptibility to mucormycosis. Indeed, haemodialysis patients treated with the iron chelator deferoxamine (DFO) are more susceptible to mucormycosis (Mahalmani et al., 2021). However, there are new iron chelators, deferiprone and deferasirox, are even more efficient at binding iron than Mucorales fungi. In clinical practice, these new medications are used to treat patients with conditions such as thalassemia without increasing the susceptibility to mucormycosis (Divakar Jose et al., 2021; Neufeld, 2006).\n\nDeferiprone and deferasirox not only exhibit a very high affinity for iron, they also have a stable chemical structure and low molecular mass – these properties render them impervious to fungal iron uptake systems (Boelaert et al., 1994; Symeonidis, 2009). The fungus is unable to “steal” iron from these molecules the way it is able to with older iron chelators like DFO (Boelaert et al., 1994; Symeonidis, 2009). It is possible that these new iron chelators bind iron so strongly that they are actually able to detach iron from fungal iron uptake to inhibit fungal growth (Symeonidis, 2009). This has been proven in vivo, using animal models (Symeonidis, 2009). There is anecdotal support as well – a case report in 2006 showed that salvage treatment with deferasirox had clear therapeutic benefits in rhino-cerebral mucormycosis (Reed et al., 2006). However, Spellberg et al. (2012) found that a combination of L-AmB and deferasirox increased mortality in haematological malignancies. Even so, Sipsas et al. (2018) note thatdeferasirox may be beneficial in diabetic patients with mucormycosis, especially in ketoacidosis where an acidic pH increases unbound tissue iron. Further study is warranted to evaluate the role of iron chelators in the management of mucormycosis.\n\nCytokines, Granulocyte Transfusions and Hyperbaric Oxygen\n\nCytokines, granulocyte transfusions, and hyperbaric oxygen are promising new therapies. Cytokines such as IFN-γ, G-CSF, and GM-CSF enhance host immunity by activating granulocytes that damage fungal cells (Spellberg et al., 2009). IFN- gamma and GM-CSF are also known to enhance the activity of polymorphonuclear leukocytes to augment the damage to fungal hyphae (Gil-Lamaignere et al., 2005). In neutropenic hosts, granulocyte transfusions can help, as they can deliver polymorphonuclear leukocytes to the site of the infection (Spellberg et al., 2009). L-AmB acts synergistically with polymorphonuclear leukocytes to damage the hyphae of some Rhizopus species (Simitsopoulou et al., 2008).\n\nHyperbaric oxygen (HBO) enhances the oxidative action of amphotericin B by correcting lactic acidosis, at pressures over 10 atmospheres absolute (ATA) (Gebremariam et al., 2014; Siddiqui et al., 1997). HBO may enhance leukocyte-mediated phagocytoses and tissue repair (Chakrabarti & Singh, 2020). However, there is a paucity of data on the use of HBO in PM (Grigull et al., 2006; John et al., 2021; Spellberg et al., 2009). It has been used as adjunctive therapy for rhino-orbital-cerebral mucormycosis and soft tissue infections, but it is much less commonly used for PM and other manifestations of the disease (John et al., 2021). The recommended dose of hyperbaric oxygen therapy consists of two sessions of 90–120-min each, at 2–3 ATA, per day (Chakrabarti & Singh, 2020). HBO reportedly benefits patients with diabetes or in trauma, but is less effective in stem cell transplantation and in patients with haematological malignancies (Chakrabarti & Singh, 2020). Randomized controlled trials may prove the efficacy of HBO in mucormycosis (Brunet & Rammaert, 2020).\n\n\nMethods\n\nThis systematic review identifies and maps recent treatment protocols for PM. It provides a clear, reproducible methodology (Sucharew & Macaluso, 2019) and is reported in accordance with the framework and recommendations by Peters et al. (2015). Although the mortality rate of this disease has improved over time, it is still high (Muthu, Agarwal, et al., 2021). The objective of this review is to systematically identify and map the management of pulmonary mucormycosis. Therefore, a systematic review is appropriate here.\n\nThis systematic review was designed to answer the following research question:\n\n○ What recent treatment protocols have been reported in the literature that can be deployed in the management of pulmonary mucormycosis?\n\nAll articles relating to treatment protocols for PM were included. The concept is treatment protocols in the context of PM. The population of interest is the human population. The following inclusion criteria were applied:\n\n• Articles published in English.\n\n• Peer-reviewed journal articles.\n\n• Articles where the full text was available.\n\n• Publications from 2018 to 2023.\n\nArticles that focus on limited treatment regimens or topics that are not relevant to the research question, were excluded. For example, articles focusing on the following topics were excluded:\n\n• Articles that only mention limited treatment regimens for PM, such as the use of amphotericin B only.\n\n• Fungal infections other than mucormycosis.\n\n• Covid-19 treatments and sequelae unrelated to mucormycosis.\n\n• Pulmonary disease unrelated to mucormycosis.\n\nFour electronic search systems were identified: Scopus, PubMed, ScienceDirect, and Web of Science. Scopus offers excellent coverage (Falagas et al., 2008; Kulkarni et al., 2009) and is the most effective search engine for the overview of a topic (Tober, 2011). ScienceDirect is also a highly effective, second only to Scopus as a search engine (Tober, 2011). PubMed, a subset of Scopus, is the optimal search system for biomedical topics - it is the most frequently updated and includes early releases of articles (Falagas et al., 2008; Kulkarni et al., 2009; Samadzadeh et al., 2013). PubMed was included for this reason, to ensure a more precise and in-depth search.\n\nScience Direct is second only to PubMed in terms of precision, recall, and relevance of search results (Samadzadeh et al., 2013). Therefore, ScienceDirect was also selected as an appropriate search engine for this systematic review. Web of Science has a well-documented performance in tracking citation counts (Falagas et al., 2008; Kulkarni et al., 2009) and was therefore selected as a suitable search engine for this review. While Google Scholar is also effective in terms of recall and relevance, the search results it provides are inconsistent, and citation information is often inadequate or not updated (Falagas et al., 2008; Kulkarni et al., 2009). Therefore, Google Scholar was not selected for this systematic review.\n\nFor each of the four search systems selected, search strategy/search terms were defined (Table 1). Within these search systems, all databases were included in the search. After the search results were assessed and articles relevant to the research question identified, citation tracking (snowball search) was also undertaken – a search of references within the relevant articles identified.\n\nThe second and third authors reviewed this. The extracted data was cross-checked by all authors to minimise personal bias (Page et al., 2021). Any disagreements on data extraction and the categorisation of articles were resolved through detailed discussions, leading to a consensus between the authors.\n\nAll three authors developed the concept and idea for this systematic review. The first author provided expert guidance on this review and verified the methods and results. The second and third authors conducted the search, identified, and removed duplicates from search results, and read the abstract and titles of the remaining articles, reading the full text of those articles where abstracts were unavailable. The second and third authors then applied the exclusion and inclusion criteria to the remaining articles, to ensure that only relevant articles were selected.\n\nThe selected articles were analysed to identify broad qualitative themes. A descriptive analysis was also undertaken to:\n\n• identify recent treatment protocols mentioned in the literature reviewed; and\n\n• map the results in tabular form.\n\nThe authors confirm that this paper is an accurate and transparent account of the systematic review conducted. The review’s design and analysis were not preregistered.\n\n\nResults\n\nThe selected articles were reviewed in detail, with a focus on identifying and mapping treatment protocols for PM. The results span six years, from 2018 through 2023. Overall, 355 articles were identified in the four electronic search systems. 128 duplicates were removed. The titles and abstracts of the remaining 227 articles were screened and exclusion criteria applied. This process resulted in the exclusion of 202 articles. All the authors read the full text of the remaining 25 articles, applying the inclusion criteria. 19 articles were found to be relevant to the research question. Citation tracking was then undertaken – a snowball search of all references within these 19 articles. This process identified seven more relevant articles. Two more articles were identified by hand search. Thus, a total of 28 relevant articles were included.\n\nTable 1 lists the search systems, databases and search terms used to identify relevant articles. Figure 1 (Fadelelmoula et al., 2024a) shows the PRISMA flow diagram of article screening and selection. Supplementary Table 1 (Fadelelmoula et al., 2024d) lists the key features of selected articles, listed by date of publication. Figure 2 (Fadelelmoula et al., 2024b) shows the treatment modalities for PM in diagrammatic form. Supplementary Table 2 (Fadelelmoula et al., 2024e) lists the co-morbidities mentioned in the articles selected and Figure 3 (Fadelelmoula et al., 2024c) illustrates these co-morbidities. Supplementary Table 3 (Fadelelmoula et al., 2024f) sets out the PRISMA checklist for this review.\n\nSearch conducted on 1 December 2023.\n\nThe key results relevant to the research question are presented below.\n\n• Of the primary therapies recommended for PM, liposomal amphotericin B (L-AmB) was recommended in 21 articles, surgery in 20, amphotericin B in eight, posaconazole in 10, Isavuconazole in three, bronchoscopy or BAL in two, and antibiotics in one. Three articles mention echinocandins, but these antifungals had no therapeutic benefit in the treatment of PM.\n\n• Stepdown, maintenance, or salvage therapy with posaconazole was mentioned in 10 articles, and isavuconazole in six articles.\n\n• Combination therapy was recommended in eight articles, but the authors of three other articles did not find combination therapy helpful.\n\n• Adjunctive therapies are recommended in four of the selected articles.\n\n• Alternative therapies are mentioned in 12 articles – Am-B and Digital Subtraction Angiography in one article each, posaconazole and isavuconazole in four articles each, and iron chelators in five.\n\n• Early diagnosis is underlined as the key to survival and low morbidity in 10 articles.\n\n• Eight articles recommend the effective control of predisposing factors and co-morbidities.\n\n• Multidisciplinary teams and a multimodal approach are recommended in four articles.\n\n• Four articles mention the use of glucocorticoids such as dexamethasone in patients with COVID-19 but stress the need for caution.\n\n• Two articles recommend checking for drug-drug interactions, particularly when triazoles are used for treatment.\n\n• One article stated that combination therapy with L-AmB and NAB is not useful but recommends that nebulized amphotericin B (NAB) merits further investigation, as other doses and formulations may be of use.\n\n• Two articles recommend against voriconazole.\n\n• One article stated that zinc therapy may be protective, but another states that zinc does not have any therapeutic use in the treatment of this disease.\n\n\nDiscussion\n\nThe incidence of PM is rising globally, particularly since the advent of COVID-19. Climate change could also be a contributing factor, as fungi thrive at higher temperatures and in conditions of increasing humidity. Although survival and recovery from PM has improved over time, this disease still carries a high mortality – around 50%. Till the end of the twentieth century, the three mainstays of managing PM were surgery, where feasible; Am-B, the preferred first-line antifungal; and the control of underlying factors such as hyperglycaemia, ketoacidosis, and neutropenia. However, there seems to be a gradual but noticeable shift in the management of PM – not only because more efficacious antifungals are now available, but also because there is a more considered approach to diagnosis and therapy. An analysis of the articles included in this review point to four broad themes: early diagnosis; first-line or primary therapy; stepdown, maintenance, or salvage therapies; and adjunctive therapies.\n\nEarly diagnosis, early surgery, and a multidisciplinary approach: Early diagnosis may be the key to survival and low morbidity. However, as Wu states, early diagnosis may present a challenge – in many instances, patients with PM have nonspecific symptoms that may point to the possibility of COVID-19 or bacterial pneumonia, instead (Wu et al., 2023). Today, the emphasis is on a high index of suspicion, recognition of predisposing factors, and analysis of the clinical presentation. For instance, pleuritic pain in a patient with neutropenia should arouse the suspicion of PM. Urgent and early imaging, histology, microbiology, and advanced molecular methods can confirm the diagnosis early, and make all the difference to survival. In terms of the approach, multidisciplinary teams and a multimodal approach are important pieces of the puzzle that improve the chances of achieving early diagnosis and instituting effective therapy (Elgarten et al., 2018; Pruthi et al., 2022; Ramirez et al., 2018; Seifert et al., 2020).\n\nPrimary therapies: Surgery and L-AmB are the mainstays of primary therapy. Posaconazole also seems to be gaining traction as a first-line antifungal, either on its own or in combination with L-AmB. Posaconazole and isuvaconazole are the keys to successful stepdown, maintenance, or salvage therapy. While surgery remains a recommended first-line treatment, there seems to be a shift in thinking on whether, and when, surgery is required in PM. There is a growing recognition that early and aggressive surgical resection may significantly reduce mortality (Choi et al., 2019; Cornely et al., 2019; Dantis et al., 2021; Elgarten et al., 2018; Guo et al., 2019; Kanj et al., 2023; Liang et al., 2021; Mehta et al., 2022; Mills et al., 2018; Muthu et al., 2022; Muthu, Singh, et al., 2021; Pruthi et al., 2022; Pulle et al., 2021; Ramirez, 2018; Rana et al., 2021; Sipsas et al., 2018; Skiada et al., 2018; Yang et al., 2023). In addition, bronchoscopy and bronchoalveolar lavage (BAL) may be useful in removing retained secretions and necrotic tissue (Liang et al., 2021; Seifert et al., 2020).\n\nAlongside early diagnosis, a multidisciplinary approach, and early and aggressive surgery, new antifungal drugs and formulations with a higher safety index are now preferred. The lipid-based L-AmB is the most widely used first-line antifungal, with the older and more toxic Am-B now reserved for use in settings where resources are limited. Posaconazole is being used in primary antifungal therapy as well, both in conjunction with L-AmB and as a monotherapy. Isuvaconazole is also being used as a primary therapy in clinical settings, but as it has only been available since 2015, it remains to be seen whether its clinical efficacy can be established more firmly, in time. Combination therapy with more than one antifungal was recommended by the authors of 11 articles (Choi et al., 2019; Cornely et al., 2019; Ding et al., 2020; Guo et al., 2019; Hanks et al., 2023; Hoenigl et al., 2022; Manjunath et al., 2018; Meena et al., 2023; Rana et al., 2021; Seifert et al., 2020; Yang et al., 2023). However, Kanj et al. (2023), Muthu et al. (2023) and Yuan et al. (2021), did not find combination therapy useful in the treatment of PM.\n\nStepdown, maintenance, salvage, and alternative therapies: For stepdown, maintenance, and salvage therapy, posaconazole is now the antifungal of choice (Elgarten et al., 2018; van Burik et al., 2006). However, based on a 2006 review of 91 patients treated with posaconazole as salvage therapy, Elgarten et al. (2018) concluded that while posaconazole can be effective, treatment failures are not unknown. Isuvaconazole can also be used for salvage. Posaconazole and isuvaconazole are also preferred alternative therapies for patients who cannot tolerate L-AmB.\n\nControlling co-morbidities and contributing factors: The control of co-morbidities continues to be a crucial aspect of effective treatment. Of the articles included, twenty-six mention co-morbidities – the details are listed in Supplementary Table 1 (Fadelelmoula et al., 2024d). Diabetes mellitus was the most common co-morbidity and is reported in fourteen articles, followed by COVID-19, which is stated in seven. Chronic kidney disease (CKD), hematological malignancies, immunosuppression, the use of glucocorticoids, hyperglycemia, and renal transplant are each mentioned in three or more articles. It is worth noting that in patients with COVID-19, glucocorticoids should be reserved for those with hypoxia, as these drugs can increase susceptibility to mucormycosis (Rana et al., 2021). Prolonged Intensive Care Unit (ICU) stays, ketoacidosis, chronic liver disease, a history of tuberculosis, pulmonary artery pseudoaneurysm (PAP), pulmonary compromise, high sequential organ failure assessment (SOFA) scores, and hypoproteinemia are some of the other contributing factors mentioned in the articles included in this review. Kontoyiannis and Lewis mention many of the same contributing factors in their recommendations for the treatment of mucormycosis, and state that the relative contribution of each of these factors is unknown (Kontoyiannis & Lewis, 2011).\n\nAdjunctive therapies: Selected articles also mention promising new adjunctive therapies that may well improve the prognosis of this disease. Hanks et al. (2023) suggest that ECMO may be useful as an adjunctive therapy, while Yuan et al. (2021) state that mucolytic agents such as ambroxol may be helpful adjuncts. Sipsas et al. (2018) recommends monoclonal antibodies, GM-CSF, IFN-γ, and white blood cell transfusions. Skiada et al. (2018) suggest that hyperbaric oxygen, GM-CSF, IFN-γ, and ergosterol synthesis inhibitor (VT-1161) may be useful. Sipsas et al. (2018) also postulate that emerging therapies may offer promise in improving survival rates and decreasing the morbidity currently associated with PM – these authors state argue that targeted immunotherapy, reversal of tissue hypoxia, and host-specific immunological and metabolic profiling, all merit further study.\n\nPotential therapies with insufficient or conflicting evidence: Five articles mention iron chelators, but there does not seem to be sufficient evidence or consensus, yet, of their efficacy in clinical practice. Meena et al. note that the DEFEAT Mucor study, a randomized trial, showed that combination therapy with the iron chelator, deferasirox, and L-AMB actually increased the 90-day mortality (Meena et al., 2023; Spellberg et al., 2012). However, Meena et al. (2023) still recommend that iron chelators merit consideration – larger studies may be required for definitive proof of therapeutic benefit or harm. In their view, diabetic patients with COVID-19 may benefit more from iron chelators than neutropenic patients with haematological malignancies. Skiada et al. (2018) note that the DEFEAT Mucor study had several limitations; they state that there are many case reports to show that deferasirox may be a useful adjunctive therapy in patients with diabetes. However, they state that its therapeutic role is yet to be established through prospective, randomized clinical trials (Skiada et al., 2018). Sipsas et al. (2018) state that the combination of deferasirox and L-AmB increases mortality in haematological malignancies, but may be beneficial in diabetic patients with mucormycosis, especially in ketoacidosis, where an acidic pH increases unbound tissue iron.\n\nMuthu et al. (2023) state that adjunctive therapy with zinc supplements is helpful. However, Rana et al. (2021) state that zinc does not have any therapeutic use in this disease. Muthu et al. (2023) also found that NAB was not helpful as an adjunctive therapy, but postulate that a different dose or formulation may prove beneficial and warrants further investigation.\n\nTherapies that are not recommended: Elgarten et al. (2018) and Manjunath et al. (2018) found no therapeutic benefit from echinocandins such as micafungin, used in combination with either L-AmB, or both L-AmB and posaconazole. Seifert et al. (2020) also used micafungin in combination with L-AmB to treat a patient with PM, but the patient did not survive. Yuan et al. (2021) does not recommend fluconazole or itraconazole because cultures from specimens obtained through bronchoscopy were not sensitive to these triazoles. There are clear recommendations against the use of voriconazole. Meena et al. (2023), Hanks et al. (2023), and Manjunath et al. (2018) state that PM does not respond to voriconazole. As early as 2007, a multicenter study (Trifilio et al., 2007) found that voriconazole-associated mucormycosis carried a 73% mortality rate. Pongas et al. (2009) state that the prophylactic use of voriconazole leads to selection pressure, which increases the risk of Mucorales infections and contributes to poorer outcomes. It is an open question as to whether there is a direct link between the hypervirulence of Mucorales and the use of voriconazole, or if is this a causal association (Meena et al., 2023).\n\nPromising new therapies: Mucorales species are developing resistance to amphotericin B, posaconazole, and isavuconazole (Cornely et al., 2014; Dannaoui, 2017; Roden et al., 2005; Schwarz et al., 2019). There is an urgent need for new antifungal therapies that are effective and safe. There are innovative therapies emerging, currently, that hold great potential in the treatment of this disease. Among these novel therapies, the humanized clone VX01 may be the most promising. It is created by humanizing a mouse monoclonal antibody (C2 MAb). In the murine model, VX01 targets CotH3, a spore coat protein specific to Mucorales species. VX01 has an affinity for this protein and binds it, resulting in the loss of CotH3. Therefore, the fungus is rendered non-invasive, and its virulence is attenuated. Other promising therapies for PM include nanoemulsions such as NB-201, silver nanoparticles (AgNPs), and zirconium oxide nanoparticles (ZrO2NPs) (León-Buitimea et al., 2021). These nanomaterials are currently in the experimental, in vitro phase of development (George et al., 2011).\n\nTransparency: The authors of this systematic review have endeavoured to use transparent and robust methods. The framework described by Peters et al. (2015) guided this review. The authors undertook an initial exploration to identify appropriate search systems, which had disciplines and subjects relevant to the research question. Four electronic search systems were thus identified, and the search strategy consisted of searching all available databases within each of these four systems, as well as citation tracking (snowball search) and a hand search.\n\nLimitations: There are limitations to this review. It only includes peer-reviewed journal articles published between 2018 and 2023, in English. A search of other databases and systems may have provided additional results. But still relevant papers may have been missed because of these limitations.\n\n\nConclusion\n\nThe objective of this systematic review was to identify and map the management of pulmonary mucormycosis. Four broad themes were identified, that are not only critical to survival, but also to lowering the burden of morbidity associated with this disease. The four themes are: early diagnosis; first-line or primary therapy; stepdown, maintenance, or salvage therapies; and adjunctive therapies. Recommended approaches and modalities of treatment were identified and mapped within each of these themes.\n\nThe results indicate that early diagnosis, and early and aggressive surgery, may hold the key to effective management. The results also indicate that a multidisciplinary, multimodal approach may improve the chances of achieving an early diagnosis and a prompt decision to operate. In addition, the results show that there has been a shift away from the use of Am-B as an antifungal, except in resource-limited settings. There is a clear preference for L-AmB as a first-line antifungal, with posaconazole used either in combination with L-AmB or as a first-line monotherapy. Posaconazole and isavuconazole are the drugs of choice for stepdown, maintenance, and salvage therapy, and as alternatives for patients who are unable to tolerate L-AmB. The control of co-morbidities such as diabetes continues to be a crucial aspect of effective management.\n\nThe results highlight new adjunctive therapies that may well improve the chances of surviving this deadly disease – immunomodulators such as IFN-γ and GM-CSF, hyperbaric oxygen, and ergosterol synthesis inhibitor (VT-1161). The results also highlight potential therapies such as iron chelators, zinc, and NAB that do not, yet, have sufficient evidence for their use, or have conflicting evidence. The results indicate that there is considerable debate about the role of iron chelators such as deferasirox, but no broad consensus yet for their use in clinical settings. However, as many Mucorales species depend on iron for both growth and virulence, iron chelators seem to offer substantial promise as future therapies.\n\n\nEthics approval and consent to participate\n\nNot applicable.\n\n\nConsent for publication\n\nNot applicable.\n\n\nAuthor contributions\n\nAll three authors were responsible for developing the concept of this systematic review. The first author provided expert guidance, provided critical revisions of intellectual content, and verified methods and results. The second and third authors conducted the search, extracted the data, performed the analysis, and drafted the manuscript. All the authors read and approved the final version of the manuscript for publication.\n\n\nAuthor note\n\nThis review has not been published and is not under consideration for publication elsewhere. Correspondence concerning this article should be addressed to Tarig Fadelelmoula, Head of the Department of Internal Medicine, College of Medicine and Health sciences, National University of Science and Technology, Sohar, Sultanate of Oman. Email: tarigeltoum@nu.edu.om\n\n\nRegistration\n\nThis systematic review did not entail any preregistered protocols.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: Management of Pulmonary Mucormycosis: A Systematic Review, DOI: https://doi.org/10.6084/m9.figshare.26362093.v1, https://doi.org/10.6084/m9.figshare.26362099.v1, https://doi.org/10.6084/m9.figshare.26362519.v2, https://doi.org/10.6084/m9.figshare.26362600.v1 (Fadelelmoula et al., 2024b, 2024c, 2024d, 2024e, 2024f).\n\nThis project contains the following underlying data:\n\n• Supplementary Table 1 lists the key features of selected articles, listed by date of publication.\n\n• Figure 2 shows the treatment modalities for PM in diagrammatic form.\n\n• Supplementary Table 2 lists the co-morbidities mentioned in the articles selected\n\n• Figure 3 illustrates Co-morbidities, underlying conditions, and contributing factors in pulmonary mucormycosis\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nFigshare: Management of Pulmonary Mucormycosis: A Systematic Review, DOI https://doi.org/10.6084/m9.figshare.26362480.v2, https://doi.org/10.6084/m9.figshare.26362585.v1 (Fadelelmoula et al., 2024f), (Fadelelmoula et al., 2024a).\n\nThis project contains the following underlying data:\n\n• Supplementary Table 3 - PRISMA 2020 Checklist\n\n• FIGURE 1 - PRISMA Flow Diagram\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nThis systematic review has been reported in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) (Page et al., 2021).\n\n\nAcknowledgements\n\nNot applicable.\n\n\nReferences\n\nAbbas Z, Chaudhary A, Chaudhary MA: COVID-19 associated coagulopathy resulting in cerebral venous thrombosis and pulmonary embolism. Cureus. 2021; 13(11). Publisher Full Text\n\nAgarwal R, Kumar V, Gupta D: Pulmonary mucormycosis: two of a kind. Eur. J. Intern. Med. 2006; 17(1): 63–65. PubMed Abstract \| Publisher Full Text\n\nAgrawal R, Yeldandi A, Savas H, et al.: Pulmonary mucormycosis: risk factors, radiologic findings, and pathologic correlation. Radiographics. 2020; 40(3): 656–666. PubMed Abstract \| Publisher Full Text\n\nAlejandre-Castañeda V, Patiño-Medina JA, Valle-Maldonado MI, et al.: Secretion of the siderophore rhizoferrin is regulated by the cAMP-PKA pathway and is involved in the virulence of Mucor lusitanicus. Sci. Rep. 2022; 12(1): 10649. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlinaghi S, Karimi SA, Amirali B, et al.: Mucormycosis infection in patients with COVID-19: A systematic review. Health Sci. Rep. 2022; 5(2): e529. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmbrosioni J, Bouchuiguir-Wafa K, Garbino J: Emerging invasive zygomycosis in a tertiary care center: epidemiology and associated risk factors. Int. J. Infect. Dis. 2010; 14: e100–e103. PubMed Abstract \| Publisher Full Text\n\nAndresen D, Donaldson A, Choo L, et al.: Multifocal cutaneous mucormycosis complicating polymicrobial wound infections in a tsunami survivor from Sri Lanka. Lancet. 2005; 365(9462): 876–878. Publisher Full Text\n\nBaldin C, Soliman SS, Jeon HH, et al.: PCR-based approach targeting mucorales-specific gene family for diagnosis of mucormycosis. J. Clin. Microbiol. 2018; 56(10). 00746-00718. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBitar D, Van Cauteren D, Lanternier F, et al.: Increasing incidence of zygomycosis (mucormycosis), France, 1997–2006. Emerg. Infect. Dis. 2009; 15(9): 1395–1401. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoelaert JR, Van Cutsem J, de Locht M , et al.: Deferoxamine augments growth and pathogenicity of Rhizopus, while hydroxypyridinone chelators have no effect. Kidney Int. 1994; 45(3): 667–671. PubMed Abstract \| Publisher Full Text\n\nBourcier J, Heudes PM, Morio F, et al.: Prevalence of the reversed halo sign in neutropenic patients compared with non-neutropenic patients: Data from a single-centre study involving 27 patients with pulmonary mucormycosis (2003-2016). Mycoses. 2017; 60(8): 526–533. PubMed Abstract \| Publisher Full Text\n\nBrigmon MM, Ochoa B, Brust K: Successful long-term therapy of mucormycosis with isavuconazole.Baylor University Medical Center Proceedings.2021.\n\nBrunet K, Rammaert B: Mucormycosis treatment: Recommendations, latest advances, and perspectives. J. Mycol. Médicale. 2020; 30(3): 101007. PubMed Abstract \| Publisher Full Text\n\nCavassin FB, Baú-Carneiro JL, Vilas-Boas RR, et al.: Sixty years of amphotericin B: an overview of the main antifungal agent used to treat invasive fungal infections. Infect. Dis. Ther. 2021; 10: 115–147. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChakrabarti A, Singh S: Management of Mucormycosis. Curr. Fungal Infect. Rep. 2020; 14(4): 348–360. Publisher Full Text\n\nChoi H, Lee H, Jeon K, et al.: Factors affecting surgical resection and treatment outcomes in patients with pulmonary mucormycosis. J. Thorac. Dis. 2019; 11(3): 892–900. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCornely O, Arikan-Akdagli S, Dannaoui E, et al.: ESCMID and ECMM joint clinical guidelines for the diagnosis and management of mucormycosis 2013. Clin. Microbiol. Infect. 2014; 20: 5–26. PubMed Abstract \| Publisher Full Text\n\nCornely OA, Alastruey-Izquierdo A, Arenz D, et al.: Global guideline for the diagnosis and management of mucormycosis: an initiative of the European Confederation of Medical Mycology in cooperation with the Mycoses Study Group Education and Research Consortium. Lancet Infect. Dis. 2019; 19(12): e405–e421. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDannaoui E: Antifungal resistance in mucorales. Int. J. Antimicrob. Agents. 2017; 50(5): 617–621. Publisher Full Text\n\nDantis K, Rathore V, Kashyap NK, et al.: SARS-CoV-2 sequel: pulmonary mucormycosis with a mycotic aneurysm in a transplant recipient. Tuberc. Respir. Dis. 2021; 84(4): 335–337. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeray G: Amphotericin B nephrotoxicity. J. Antimicrob. Chemother. 2002; 49(suppl_1): 37–41. Publisher Full Text\n\nDing X-L, Li H-M, Du J: Successful treatment of cutaneous mucormycosis disseminated from pulmonary mucormycosis with liposomal amphotericin B and posaconazole. Chin. Med. J. 2020; 133(14): 1747–1748. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDivakar Jose RR, Delhikumar C, Ram Kumar G: Efficacy and safety of combined oral chelation with deferiprone and deferasirox on iron overload in transfusion dependent children with thalassemia–A Prospective Observational Study. Indian J. Pediatr. 2021; 88: 330–335.\n\nEl-Sayed A, Kamel M: Climatic changes and their role in emergence and re-emergence of diseases. Environ. Sci. Pollut. Res. 2020; 27: 22336–22352. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElgarten CW, Levy EM, Mattei P, et al.: Successful treatment of pulmonary mucormycosis in two pediatric hematopoietic stem cell transplant patients. Pediatr. Transplant. 2018; 22(7): e13270. PubMed Abstract \| Publisher Full Text\n\nFadelelmoula T, Navas AA, Doreswamy N: Figure 1 - PRISMA flow diagram.2024a. Publisher Full Text\n\nFadelelmoula T, Navas AA, Doreswamy N: Figure 2 - Treatment modalities for pulmonary mucormycosis.2024b. Publisher Full Text\n\nFadelelmoula T, Navas AA, Doreswamy N: Figure 3 - Co-morbidities, underlying conditions, and contributing factors in pulmonary mucormycosis.2024c. Publisher Full Text\n\nFadelelmoula T, Navas AA, Doreswamy N: Supplementary Table 1 - Key features of selected articles listed by date of publication.2024d. Publisher Full Text\n\nFadelelmoula T, Navas AA, Doreswamy N: Supplementary Table 2 - Co-morbidities mentioned in the articles selected.2024e. Publisher Full Text\n\nFadelelmoula T, Navas AA, Doreswamy N: Supplementary Table 3 - PRISMA 2020 Checklist.2024f. Publisher Full Text\n\nFalagas ME, Pitsouni EI, Malietzis GA, et al.: Comparison of PubMed, Scopus, web of science, and Google scholar: strengths and weaknesses. FASEB J. 2008; 22(2): 338–342. PubMed Abstract \| Publisher Full Text\n\nFeng J, Sun X: Characteristics of pulmonary mucormycosis and predictive risk factors for the outcome. Infection. 2018; 46: 503–512. PubMed Abstract \| Publisher Full Text\n\nFernandez JF, Maselli DJ, Simpson T, et al.: Pulmonary mucormycosis: what is the best strategy for therapy? Respir. Care. 2013; 58(5): e60–e63. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGadre A, Enbiale W, Andersen LK, et al.: The effects of climate change on fungal diseases with cutaneous manifestations: A report from the International Society of Dermatology Climate Change Committee. J. Climate Change Health. 2022; 6: 100156. Publisher Full Text\n\nGarcia-Solache MA, Casadevall A: Global warming will bring new fungal diseases for mammals. MBio. 2010; 1(1). 00061-00010. Publisher Full Text\n\nGebremariam T, Liu M, Luo G, et al.: CotH3 mediates fungal invasion of host cells during mucormycosis. J. Clin. Invest. 2014; 124(1): 237–250. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGeorge C, Kuriakose S, George S, et al.: Antifungal activity of silver nanoparticle-encapsulated β-cyclodextrin against human opportunistic pathogens. Supramol. Chem. 2011; 23(8): 593–597. Publisher Full Text\n\nGhazi BK, Rackimuthu S, Wara UU, et al.: Rampant increase in cases of mucormycosis in India and Pakistan: a serious cause for concern during the ongoing COVID-19 pandemic. Am. J. Trop. Med. Hyg. 2021; 105(5): 1144–1147. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGil-Lamaignere C, Simitsopoulou M, Roilides E, et al.: Interferon- gamma and granulocyte-macrophage colony-stimulating factor augment the activity of polymorphonuclear leukocytes against medically important zygomycetes. J. Infect. Dis. 2005; 191(7): 1180–1187. PubMed Abstract \| Publisher Full Text\n\nGomes MZ, Lewis RE, Kontoyiannis DP: Mucormycosis caused by unusual mucormycetes, non-Rhizopus,-Mucor, and-Lichtheimia species. Clin. Microbiol. Rev. 2011; 24(2): 411–445. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGreenberg R, Mullane K, Van Burik J-A, et al.: Posaconazole as salvage therapy for zygomycosis. Antimicrob. Agents Chemother. 2006; 50(1): 126–133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrigull L, Beilken A, Schmid H, et al.: Secondary prophylaxis of invasive fungal infections with combination antifungal therapy and G-CSF-mobilized granulocyte transfusions in three children with hematological malignancies. Support. Care Cancer. 2006; 14: 783–786. PubMed Abstract \| Publisher Full Text\n\nGuo S, Liu H, Tang X, et al.: Clinical characteristics and prognoses of pulmonary mucormycosis in four children. Pediatr. Investig. 2019; 3(04): 223–227. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHamill RJ: Amphotericin B formulations: a comparative review of efficacy and toxicity. Drugs. 2013; 73(9): 919–934. PubMed Abstract \| Publisher Full Text\n\nHanks J, Unai S, Bribriesco A, et al.: Successful treatment of pulmonary mucormycosis (Lichtheimia spp.) in a post-partum patient with COVID-19 ARDS requiring extra-corporeal membrane oxygenation using salvage therapy. Perfusion. 2023; 38(6): 1315–1318. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarada M, Manabe T, Yamashita K, et al.: Pulmonary mucormycosis with fatal massive hemoptysis. Pathol. Int. 1992; 42(1): 49–55. Publisher Full Text\n\nHoenigl M, Seidel D, Carvalho A, et al.: The emergence of COVID-19 associated mucormycosis: a review of cases from 18 countries. Lancet Microbe. 2022; 3: e543–e552. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHsiao CR, Huang L, Bouchara J-P, et al.: Identification of medically important molds by an oligonucleotide array. J. Clin. Microbiol. 2005; 43(8): 3760–3768. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIbrahim A, Edwards J, Filler S: Zygomycosis. Clinical mycology. New York, NY: Oxford University Press; 2003; 241–251. Publisher Full Text\n\nIbrahim AS, Spellberg B, Avanessian V, et al.: Rhizopus oryzae adheres to, is phagocytosed by, and damages endothelial cells in vitro. Infect. Immun. 2005; 73(2): 778–783. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIbrahim AS, Spellberg B, Walsh TJ, et al.: Pathogenesis of mucormycosis. Clin. Infect. Dis. 2012; 54(suppl_1): S16–S22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJeong W, Keighley C, Wolfe R, et al.: The epidemiology and clinical manifestations of mucormycosis: a systematic review and meta-analysis of case reports. Clin. Microbiol. Infect. 2019; 25(1): 26–34. PubMed Abstract \| Publisher Full Text\n\nJohn TM, Jacob CN, Kontoyiannis DP: When uncontrolled diabetes mellitus and severe COVID-19 converge: the perfect storm for mucormycosis. J. Fungi. 2021; 7(4): 298. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKanj SS, Haddad SF, Meis JF, et al.: The battle against fungi: lessons in antifungal stewardship from COVID 19 times. Int. J. Antimicrob. Agents. 2023; 62(1): 106846. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKasai M, Harrington SM, Francesconi A, et al.: Detection of a molecular biomarker for zygomycetes by quantitative PCR assays of plasma, bronchoalveolar lavage, and lung tissue in a rabbit model of experimental pulmonary zygomycosis. J. Clin. Microbiol. 2008; 46(11): 3690–3702. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKawakami K, Watanabe Y, Kadowaki S: Early onset invasive pulmonary zygomycosis following allogeneic peripheral blood stem cell transplantation in a patient with therapy-related myelodysplastic syndrome. [Rinsho Ketsueki]. 2004; 45(4): 319–321. PubMed Abstract\n\nKohno S, Izumikawa K, Takazono T, et al.: Efficacy and safety of isavuconazole against deep-seated mycoses: A phase 3, randomized, open-label study in Japan. J. Infect. Chemother. 2023; 29(2): 163–170. PubMed Abstract \| Publisher Full Text\n\nKontoyiannis DP, Lewis RE: Invasive zygomycosis: update on pathogenesis, clinical manifestations, and management. Infect. Dis. Clin. 2006; 20(3): 581–607, vi. PubMed Abstract \| Publisher Full Text\n\nKontoyiannis DP, Lewis RE: How I treat mucormycosis. Blood. 2011; 118(5): 1216–1224. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKrishna V, Bansal N, Morjaria J, et al.: COVID-19-associated pulmonary mucormycosis. J. Fungi. 2022; 8(7): 711. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKulkarni AV, Aziz B, Shams I, et al.: Comparisons of citations in Web of Science, Scopus, and Google Scholar for articles published in general medical journals. JAMA. 2009; 302(10): 1092–1096. PubMed Abstract \| Publisher Full Text\n\nKumar A, Pulle MV, Asaf BB, et al.: Covid-associated pulmonary mucormycosis. Lung India. 2022; 39(2): 100–101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLanternier F, Dannaoui E, Morizot G, et al.: A global analysis of mucormycosis in France: the RetroZygo Study (2005–2007). Clin. Infect. Dis. 2012; 54(suppl_1): S35–S43. PubMed Abstract \| Publisher Full Text\n\nLarsen K, Buchwald C v, Ellefsen B, et al.: Unexpected expansive paranasal sinus mucormycosis. ORL. 2003; 65(1): 57–60. PubMed Abstract \| Publisher Full Text\n\nLeCompte PM, Meissner WA: Mucormycosis of the central nervous system associated with hemochromatosis: report of a case. Am. J. Pathol. 1947; 23(4): 673–677. PubMed Abstract\n\nLee FY, Mossad SB, Adal KA: Pulmonary mucormycosis: the last 30 years. Arch. Intern. Med. 1999; 159(12): 1301–1309. Publisher Full Text\n\nLeón-Buitimea A, Garza-Cervantes JA, Gallegos-Alvarado DY, et al.: Nanomaterial-Based Antifungal Therapies to Combat Fungal Diseases Aspergillosis, Coccidioidomycosis, Mucormycosis, and Candidiasis. Pathogens. 2021; 10(10). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLewis RE, Wiederhold NP: The solubility ceiling: a rationale for continuous infusion amphotericin B therapy?. Clin. Infect. Dis. 2003; 37(6): 871–872. PubMed Abstract \| Publisher Full Text\n\nLiang Y, Chen X, Wang J, et al.: Oral posaconazole and bronchoscopy as a treatment for pulmonary mucormycosis in pediatric acute lymphoblastic leukemia patient: A case report. Medicine. 2021; 100(6): e24630. Publisher Full Text\n\nLin E, Moua T, Limper AH: Pulmonary mucormycosis: clinical features and outcomes. Infection. 2017; 45: 443–448. Publisher Full Text\n\nMahalmani V, Sarma P, Prakash A, et al.: Role of Iron Chelators in Mucormycosis. Indian J. Pharm. 2021; 53(4): 261–263. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nManjunath M, Prajapat D, Sharma RK, et al.: Refractory bronchovascular pleuropulmonary mucormycosis: Case report and difficulties in management. Lung India. 2018; 35(1): 70–72. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarchevsky AM, Bottone EJ, Geller SA, et al.: The changing spectrum of disease, etiology, and diagnosis of mucormycosis. Hum. Pathol. 1980; 11(5): 457–464. PubMed Abstract\n\nMcAdams HP, Rosado de Christenson M, Strollo DC, et al.: Pulmonary mucormycosis: radiologic findings in 32 cases. AJR Am. J. Roentgenol. 1997; 168(6): 1541–1548. PubMed Abstract \| Publisher Full Text\n\nMeena DS, Kumar D, Bohra GK: Combination therapy in Mucormycosis: Current evidence from the world literature, a mini review. J. Med. Mycol. 2023; 33(1): 101332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMehta RM, Bansal S, Kalpakkam H: Critical COVID-19-associated pulmonary mucormycosis: The underreported life-threatening spectrum of the mucormycosis epidemic. Lung India. 2022; 39(2): 187–190. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMillon L, Herbrecht R, Grenouillet F, et al.: Early diagnosis and monitoring of mucormycosis by detection of circulating DNA in serum: retrospective analysis of 44 cases collected through the French Surveillance Network of Invasive Fungal Infections (RESSIF). Clin. Microbiol. Infect. 2016; 22(9): 810.e1–810.e8. PubMed Abstract \| Publisher Full Text\n\nMillon L, Larosa F, Lepiller Q, et al.: Quantitative polymerase chain reaction detection of circulating DNA in serum for early diagnosis of mucormycosis in immunocompromised patients. Clin. Infect. Dis. 2013; 56(10): e95–e101. PubMed Abstract \| Publisher Full Text\n\nMills SEA, Yeldandi AV, Odell DD: Surgical treatment of multifocal pulmonary mucormycosis. Ann. Thorac. Surg. 2018; 106(2): e93–e95. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMir I, Basnet S, Ellsworth D, et al.: Pulmonary Mucormycosis in chronic lymphocytic leukemia and Neutropenia. Case Rep. Infect. Dis. 2018; 2018: 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoreira J, Ridolfi F, Almeida-Paes R, et al.: Cutaneous mucormycosis in advanced HIV disease. Braz. J. Infect. Dis. 2016; 20: 637–640. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuthu V, Agarwal R, Dhooria S, et al.: Has the mortality from pulmonary mucormycosis changed over time? A systematic review and meta-analysis. Clin. Microbiol. Infect. 2021; 27(4): 538–549. PubMed Abstract \| Publisher Full Text\n\nMuthu V, Agarwal R, Patel A, et al.: Definition, diagnosis, and management of COVID-19-associated pulmonary mucormycosis: Delphi consensus statement from the Fungal Infection Study Forum and Academy of Pulmonary Sciences, India. Lancet Infect. Dis. 2022; 22(9): e240–e253. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuthu V, Gogineni RR, Agarwal R, et al.: Treatment of pulmonary mucormycosis with adjunctive nebulized amphotericin B (MUCONAB trial): Results of an open-label randomized controlled trial. Mycoses. 2023; 66: 688–696. PubMed Abstract \| Publisher Full Text\n\nMuthu V, Singh H, Gorsi U, et al.: Large pulmonary artery pseudoaneurysm in mucormycosis: successfully managed with surgery and amphotericin. BMJ Case Rep. 2021; 14(1). Publisher Full Text\n\nNeblett Fanfair R, Benedict K, Bos J, et al.: Necrotizing cutaneous mucormycosis after a tornado in Joplin, Missouri, in 2011. N. Engl. J. Med. 2012; 367(23): 2214–2225. PubMed Abstract \| Publisher Full Text\n\nNeufeld EJ: Oral chelators deferasirox and deferiprone for transfusional iron overload in thalassemia major: new data, new questions. Blood. 2006; 107(9): 3436–3441.\n\nNyilasi I, Papp T, Csernetics Á, et al.: High-affinity iron permease (FTR1) gene sequence-based molecular identification of clinically important Zygomycetes. Clin. Microbiol. Infect. 2008; 14(4): 393–397. PubMed Abstract \| Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. Int. J. Surg. 2021; 88: 105906. PubMed Abstract \| Publisher Full Text\n\nPal R, Singh B, Bhadada SK, et al.: COVID-19-associated mucormycosis: an updated systematic review of literature. Mycoses. 2021; 64(12): 1452–1459. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPana ZD, Seidel D, Skiada A, et al.: Invasive mucormycosis in children: an epidemiologic study in European and non-European countries based on two registries. BMC Infect. Dis. 2016; 16: 1–9. Publisher Full Text\n\nPandey N, Kaushal V, Puri GD, et al.: Transforming a general hospital to an infectious disease hospital for COVID-19 over 2 weeks. Front. Public Health. 2020; 8: 382. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPatel A, Kaur H, Xess I, et al.: A multicentre observational study on the epidemiology, risk factors, management and outcomes of mucormycosis in India. Clin. Microbiol. Infect. 2020; 26(7): 944.e9–944.e15. Publisher Full Text\n\nPeters MD, Godfrey CM, Khalil H, et al.: Guidance for conducting systematic scoping reviews. JBI Evidence Implementation. 2015; 13(3): 141–146.\n\nPielke RA: What is Climate Change? Energy Environ. 2004; 15(3): 515–520. Publisher Full Text\n\nPongas GN, Lewis RE, Samonis G, et al.: Voriconazole-associated zygomycosis: a significant consequence of evolving antifungal prophylaxis and immunosuppression practices? Clin. Microbiol. Infect. 2009; 15(s5): 93–97. PubMed Abstract \| Publisher Full Text\n\nPörtner H, Roberts D, Tignor M, et al., editors. Climate change 2022: Impacts, adaptation, and vulnerability. Contribution of Working Group II to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press; 2022. In Press. Reference Source\n\nPotenza L, Vallerini D, Barozzi P, et al.: Mucorales-specific T cells emerge in the course of invasive mucormycosis and may be used as a surrogate diagnostic marker in high-risk patients. Blood. 2011; 118(20): 5416–5419. PubMed Abstract \| Publisher Full Text\n\nPrakash H, Chakrabarti A: Global epidemiology of mucormycosis. J. Fungi. 2019; 5(1): 26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrakash H, Ghosh AK, Rudramurthy SM, et al.: A prospective multicenter study on mucormycosis in India: Epidemiology, diagnosis, and treatment. Med. Mycol. 2019; 57(4): 395–402. PubMed Abstract \| Publisher Full Text\n\nPruthi H, Muthu V, Bhujade H, et al.: Pulmonary artery pseudoaneurysm in COVID-19-associated pulmonary mucormycosis: case series and systematic review of the literature. Mycopathologia. 2022; 187(1): 31–37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPulle MV, Puri HV, Asaf BB, et al.: Outcomes of early anti-fungal therapy with aggressive surgical resection in pulmonary mucormycosis. Lung India. 2021; 38(4): 314–320. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamirez JL, Urisman A, Kukreja J, et al.: Surgical Management of Pulmonary Mucormycosis in Third-Trimester Pregnancy. Thorac. Cardiovasc. Surg. Rep. 2018; 07: e27–e29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRammaert B, Lanternier F, Zahar J-R, et al.: Healthcare-associated mucormycosis. Clin. Infect. Dis. 2012; 54(suppl_1): S44–S54. PubMed Abstract \| Publisher Full Text\n\nRana G, Gautam S, Mawari G, et al.: Massive hemoptysis causing mortality in a post COVID-19 infected Asian male patient: Presenting as pulmonary mucormycosis, pulmonary tuberculosis and later sino-nasal mucormycosis. Respir. Med. Case. Rep. 2021; 34: 101511. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReed C, Ibrahim A, Edwards JE Jr, et al.: Deferasirox, an iron-chelating agent, as salvage therapy for rhinocerebral mucormycosis. Antimicrob. Agents Chemother. 2006; 50(11): 3968–3969. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReimund E, Ramos A: Disseminated neonatal gastrointestinal mucormycosis: a case report and review of the literature. Pediatr. Pathol. 1994; 14(3): 385–389. PubMed Abstract\n\nRibes JA, Vanover-Sams CL, Baker DJ: Zygomycetes in human disease. Clin. Microbiol. Rev. 2000; 13(2): 236–301. Publisher Full Text\n\nRichardson M: The ecology of the Zygomycetes and its impact on environmental exposure. Clin. Microbiol. Infect. 2009; 15: 2–9. PubMed Abstract \| Publisher Full Text\n\nRoden MM, Zaoutis TE, Buchanan WL, et al.: Epidemiology and outcome of zygomycosis: a review of 929 reported cases. Clin. Infect. Dis. 2005; 41(5): 634–653. PubMed Abstract \| Publisher Full Text\n\nRüping MJGT, Heinz WJ, Kindo AJ, et al.: Forty-one recent cases of invasive zygomycosis from a global clinical registry. J. Antimicrob. Chemother. 2010; 65(2): 296–302. PubMed Abstract \| Publisher Full Text\n\nSaegeman V, Maertens J, Meersseman W, et al.: Increasing incidence of mucormycosis in University Hospital, Belgium. Emerg. Infect. Dis. 2010; 16(9): 1456–1458. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSafdar F, Khokhar MF, Arshad M, et al.: Climate change indicators and spatiotemporal shift in monsoon patterns in Pakistan. Adv. Meteorol. 2019; 2019: 1–14. Publisher Full Text\n\nSamadzadeh GR, Rigi T, Ganjali AR: Comparison of four search engines and their efficacy with emphasis on literature research in addiction (prevention and treatment). Int. J. High Risk Behav. Addict. 2013; 1(4): 166–171. PubMed Abstract \| Publisher Full Text\n\nSchwarz P, Cornely OA, Dannaoui E: Antifungal combinations in Mucorales: A microbiological perspective. Mycoses. 2019; 62(9): 746–760. PubMed Abstract \| Publisher Full Text\n\nSeifert S, Wiley J, Kirkham J, et al.: Pulmonary mucormycosis with extensive bronchial necrosis and bronchomediastinal fistula: a case report and review. Respir. Med. Case. Rep. 2020; 30: 101082. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSerris A, Danion F, Lanternier F: Disease entities in mucormycosis. J. Fungi. 2019; 5(1): 23. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSiddiqui A, Davidson JD, Mustoe TA: Ischemic tissue oxygen capacitance after hyperbaric oxygen therapy: a new physiologic concept. Plast. Reconstr. Surg. 1997; 99(1): 148–155. PubMed Abstract \| Publisher Full Text\n\nSimitsopoulou M, Roilides E, Maloukou A, et al.: Interaction of amphotericin B lipid formulations and triazoles with human polymorphonuclear leucocytes for antifungal activity against Zygomycetes. Mycoses. 2008; 51(2): 147–154. PubMed Abstract \| Publisher Full Text\n\nSipsas NV, Gamaletsou MN, Anastasopoulou A, et al.: Therapy of mucormycosis. J. Fungi. 2018; 4(3): 90. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSivagnanam S, Sengupta DJ, Hoogestraat D, et al.: Seasonal clustering of sinopulmonary mucormycosis in patients with hematologic malignancies at a large comprehensive cancer center. Antimicrob. Resist. Infect. Control. 2017; 6: 1–11. Publisher Full Text\n\nSkiada A, Lass-Floerl C, Klimko N, et al.: Challenges in the diagnosis and treatment of mucormycosis. Med. Mycol. 2018; 56(suppl_1): S93–S101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSkiada A, Pagano L, Groll A, et al.: Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) Working Group on Zygomycosis between 2005 and 2007. Clin. Microbiol. Infect. 2011; 17(12): 1859–1867. PubMed Abstract \| Publisher Full Text\n\nSmith C, Lee SC: Current treatments against mucormycosis and future directions. PLoS Pathog. 2022; 18(10): e1010858. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSmith JA, Kauffman CA: Pulmonary fungal infections. Respirology. 2012; 17(6): 913–926. Publisher Full Text\n\nSpellberg B, Edwards J Jr, Ibrahim A: Novel perspectives on mucormycosis: pathophysiology, presentation, and management. Clin. Microbiol. Rev. 2005; 18(3): 556–569. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpellberg B, Ibrahim AS: Recent Advances in the Treatment of Mucormycosis. Curr. Infect. Dis. Rep. 2010; 12(6): 423–429. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpellberg B, Ibrahim AS, Chin-Hong PV, et al.: The Deferasirox-AmBisome Therapy for Mucormycosis (DEFEAT Mucor) study: a randomized, double-blinded, placebo-controlled trial. J. Antimicrob. Chemother. 2012; 67(3): 715–722. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpellberg B, Walsh TJ, Kontoyiannis DP, et al.: Recent advances in the management of mucormycosis: from bench to bedside. Clin. Infect. Dis. 2009; 48(12): 1743–1751. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpringer J, Lackner M, Ensinger C, et al.: Clinical evaluation of a Mucorales-specific real-time PCR assay in tissue and serum samples. J. Med. Microbiol. 2016; 65(12): 1414–1421. PubMed Abstract \| Publisher Full Text\n\nStearman R, Yuan DS, Yamaguchi-Iwai Y, et al.: A Permease-Oxidase Complex Involved in High-Affinity Iron Uptake in Yeast. Science. 1996; 271(5255): 1552–1557. PubMed Abstract \| Publisher Full Text\n\nSucharew H, Macaluso M: Methods for research evidence synthesis: The scoping review approach. J. Hosp. Med. 2019; 14(7): 416–418. Publisher Full Text\n\nSugar A: Agents of mucormycosis and related species. Agents of mucormycosis and related species. 3rd ed.1990; 1962–1972.\n\nSun QN, Fothergill AW, McCarthy DI, et al.: In vitro activities of posaconazole, itraconazole, voriconazole, amphotericin B, and fluconazole against 37 clinical isolates of zygomycetes. Antimicrob. Agents Chemother. 2002; 46(5): 1581–1582. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSyed-Abdul S, Babu AS, Bellamkonda RS, et al.: Using artificial intelligence-based models to predict the risk of mucormycosis among COVID-19 survivors: An experience from a public hospital in India. J. Infect. 2022; 84(3): 351–354. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSymeonidis AS: The role of iron and iron chelators in zygomycosis. Clin. Microbiol. Infect. 2009; 15: 26–32. PubMed Abstract \| Publisher Full Text\n\nTahiri G, Lax C, Cánovas-Márquez JT, et al.: Mucorales and Mucormycosis: Recent Insights and Future Prospects. J. Fungi. 2023; 9(3). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTedder M, Spratt JA, Anstadt MP, et al.: Pulmonary mucormycosis: results of medical and surgical therapy. Ann. Thorac. Surg. 1994; 57(4): 1044–1050. Publisher Full Text\n\nTober M: PubMed, ScienceDirect, Scopus or Google Scholar–Which is the best search engine for an effective literature research in laser medicine? Med. Laser Appl. 2011; 26(3): 139–144. Publisher Full Text\n\nTorres-Narbona M, Guinea J, Martínez-Alarcón J, et al.: Impact of zygomycosis on microbiology workload: a survey study in Spain. J. Clin. Microbiol. 2007; 45(6): 2051–2053. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTrifilio SM, Bennett CL, Yarnold PR, et al.: Breakthrough zygomycosis after voriconazole administration among patients with hematologic malignancies who receive hematopoietic stem-cell transplants or intensive chemotherapy. Bone Marrow Transplant. 2007; 39(7): 425–429. Publisher Full Text\n\nvan Burik J-AH , Hare RS, Solomon HF, et al.: Posaconazole is effective as salvage therapy in zygomycosis: a retrospective summary of 91 cases. Clin. Infect. Dis. 2006; 42(7): e61–e65. PubMed Abstract \| Publisher Full Text\n\nvan Rhijn N , Bromley M: The consequences of our changing environment on life threatening and debilitating fungal diseases in humans. J. Fungi. 2021; 7(5): 367. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWatts WJ: Bronchopleural fistula followed by massive fatal hemoptysis in a patient with pulmonary mucormycosis: a case report. Arch. Intern. Med. 1983; 143(5): 1029–1030. PubMed Abstract \| Publisher Full Text\n\nWu H-Y, Chang P-H, Huang Y-S, et al.: Recommendations and guidelines for the diagnosis and management of Coronavirus Disease-19 (COVID-19) associated bacterial and fungal infections in Taiwan. J. Microbiol. Immunol. Infect. 2023; 56(2): 207–235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang N, Zhang L, Feng S: Clinical Features and Treatment Progress of Invasive Mucormycosis in Patients with Hematological Malignancies. J. Fungi. 2023; 9(5): 592. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYuan F, Chen J, Liu F, et al.: Successful treatment of pulmonary mucormycosis caused by Rhizopus microsporus with posaconazole. Eur. J. Med. Res. 2021; 26: 1–4. Publisher Full Text" }	[ { "id": "334224", "date": "19 Nov 2024", "name": "Eric Dannaoui", "expertise": [ "Reviewer Expertise Medical mycology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, the authors present a systematic review of pulmonary mucormycosis. They start with an extended introduction that encompasses general information of all forms of mucormycosis. The methods section outlines the article selection process and specifies the main review question. The results show that 28 articles were analyzed, with key findings briefly summarized. Finally, the authors discuss the main points in relation to existing literature\nThe \"Background\" section covers various clinical forms of mucormycosis, which could benefit from a sharper focus on pulmonary mucormycosis (PM) as it is the primary topic of this review. Some references cited are not fully up-to-date. The inclusion of multiple mucormycosis forms sometimes makes the statements unclear; for example, the mortality rate is noted as around 50%, but it’s unclear if this figure applies to all mucormycosis types or is specific to PM\nEpidemiology: Including information on other forms of mucormycosis in this section introduces confusion. To improve clarity, it would be more effective to concentrate exclusively on PM.\nMolecular Diagnosis: The role of qPCR in diagnosing mucormycosis is not emphasized enough. This technique has transformed mucormycosis diagnosis and warrants a more detailed discussion. Additionally, it’s important to note that qPCR is versatile and can be applied to a variety of samples beyond blood, including respiratory specimens and tissue biopsies\nIron Chelating Agents: The information on iron-chelating agents as an adjunctive therapy appears disproportionately detailed relative to other sections. Reducing this section or balancing it with more information on alternative therapies could improve the overall focus and coherence of the manuscript.\nReview Question: The review question would benefit from clarification. The current phrasing suggests an aim to establish treatment guidelines based on the literature. However, comprehensive, recent guidelines by international experts already address this topic. It would be helpful to specify how this review adds unique value or complements existing guidelines.\nKey Results: The presentation of key results could be improved for clarity. The distinction between studies that “recommend” versus those that “mention” a therapy is unclear and should be specified. For instance, of the 28 articles included, it is noted that two explicitly recommend against voriconazole use. Clarification is needed on for the remaining 26 articles, whether they support, oppose, or simply discuss its usage without recommendation.\nDiscussion Primary Therapies: Please clarify whether posaconazole is suggested as a possible first-line treatment for PM. The text also mentions that 11 articles support combination therapy, yet no specific results are provided in the results section to demonstrate that combination therapy is more effective than monotherapy. Including relevant data or further explanation would enhance clarity.\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? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "334217", "date": "28 Nov 2024", "name": "Maria Drogari-Apiranthitou", "expertise": [ "Reviewer Expertise Clinical Mycology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the submitted manuscript titled “Management of Pulmonary Mucormycosis: A Systematic Review,” the authors state their objective as identifying and mapping the management of PM through a systematic review approach. While the study tackles an important subject, it exhibits several shortcomings.\nMajor points\nBackground.\nThe introduction is overly lengthy, whereas it should rather focus on the main subject which is PM and the challenges associated with its treatment. The authors claim that “this systematic review aims to shed light on recent treatment protocols for PM”, and that “a systematic review is appropriate because many of these treatments are new or emerging”. It would be helpful to provide more specificity on how their systematic review will contribute to advancing current knowledge in this field.\nMethodology and Results\nWhile the PRISMA-ScR method used (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) is a valid guideline designed to ensure transparency and comprehensiveness in the reporting of scoping reviews, it seems that the authors did not take full advantage of it. Rather than merely presenting numerical summaries (e.g., the number of papers reporting specific comorbidities or the use of L-AmB), it would be of more value to group patients by key underlying conditions (e.g., hematologic malignancies, diabetes) and tabulate these alongside the therapies they received and their outcomes. This would allow for a more insightful analysis of potential associations between treatments and outcomes.\nResult presentation.\nTable 1 appears redundant, as the search methodology could be more effectively described in the text. Fig. 2 seems to inaccurately represent the data. For instance, it suggests that L-AmB and surgery were used in equal numbers of studies, whereas in most cases, these interventions were applied simultaneously. A tabular format would better represent this information. Fig. 3 is not informative in its current form. Presenting patient numbers and their characteristics in a table would be more effective for conveying meaningful insights.\nDiscussion and Conclusions\nThe Discussion section is overly generic, which may be attributed to the absence of patient-specific results. For instance, conclusions such as “The results indicate that early diagnosis and early and aggressive surgery may hold the key to effective management” and “The control of co-morbidities such as diabetes continues to be a crucial aspect of effective management” do not appear to be directly supported by the data presented. Additionally, the study lacks detailed results regarding novel or adjunctive therapies, along with patient-specific data such as underlying diseases, risk factors, species of Mucorales involved, demographics, country of origin, etc, which would provide deeper insights.\nOther Points of Concern There are several inaccuracies, or outdated literature has been occasionally used. Some examples:\nIn the Background, the statement that malignancies (63.4%), diabetes mellitus (17.1%), and solid organ transplantation (9.8%) are the most common underlying conditions is misleading. Globally, diabetes is the leading cause of mucormycosis, with hematologic malignancies ranking first only in Europe. There is more recent literature that reflects this trend and should be cited.\nFurthermore, under Epidemiology, some contradictory data are presented. The most common clinical presentations of mucormycosis are rhino-orbito-cerebral (ROC), pulmonary, cutaneous, and disseminated. Jeong et al. report corresponding rates of 34%, 21%, 20%, and 14%, while in the European study of the Working Group on Zygomycosis the corresponding numbers were 27%, 30%, 26%, and 15%. The data from Pana et al. (2016) specifically pertain to children, but this distinction is not made. It should be also mentioned that in India, during the COVID-19 pandemic, PM cases indeed increased, but the predominant form of mucormycosis was ROC [refer 1].\nTo summarize, the current study appears incomplete and does not achieve its objectives. It would be more valuable to include a detailed analysis of all patients from the retrieved articles, potentially using statistical methods to draw conclusions about the effectiveness of different treatment modalities and their association with patient outcomes.\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? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-1165
https://f1000research.com/articles/13-841/v1	26 Jul 24	{ "type": "Systematic Review", "title": "A scoping review of health models for the community mental health needs of the United Arab Emirates: Nurturing the social determinants of mental health through social prescribing in the Middle East", "authors": [ "Richard Mottershead", "Sadeq AL-Fayyadh", "Nabeel Al-Yateem", "Muhammad Arsyad Subu", "Wegdan Bani-Issa", "Mohamed Hassan Taha", "Fatma Refaat Ahmed", "Jacqueline Maria Dias", "Shukri Adams", "Adil Farooq Wali", "Ghada Shahrour", "Abbas Al Mutair", "Conrad Murendo", "Nafi Alonaizi", "Ali Alhaiti", "Majed Mowanes Alruwaili", "Abeer Nuwayfi Alruwaili", "Jim McManus", "Sadeq AL-Fayyadh", "Nabeel Al-Yateem", "Muhammad Arsyad Subu", "Wegdan Bani-Issa", "Mohamed Hassan Taha", "Fatma Refaat Ahmed", "Jacqueline Maria Dias", "Shukri Adams", "Adil Farooq Wali", "Ghada Shahrour", "Abbas Al Mutair", "Conrad Murendo", "Nafi Alonaizi", "Ali Alhaiti", "Majed Mowanes Alruwaili", "Abeer Nuwayfi Alruwaili", "Jim McManus" ], "abstract": "Despite the growing interest in social prescribing the diversification of health and social care strategies to support the well-being of patients has remained entrenched with a focus on the hospital setting within the Middle East. The United Arab Emirates has commenced progressing community mental health care to lead changes in how care and treatment are delivered within the United Arab Emirates. The authors adopted the use of the framework of Arksey and O’Malley (2005) to provide a systematic approach to searching the literature and creating a comprehensive foundation to guide the review. This scoping review provides a better understanding of the compatibility, content and outcomes of a selection of health models. The scoping review findings will inform the proposed use of social prescribing as an actionable approach to create a focus on the need to include and empower the social determinants of mental health. This article proposes an evidence-based health strategy that supports and enhances recent additions to national legislation on the inclusion of the Mental Health Law within the United Arab Emirates to meditate and prevent inequities in addressing the mental health needs of citizens and residents within the nation’s diverse communities.", "keywords": [ "mental illness", "community mental health", "health models", "scoping review", "social prescribing", "social determinants of mental health", "United Arab Emirates", "Middle East." ], "content": "Introduction\n\nIndividuals with mental health needs encounter challenges in their abilities to handle everyday tasks throughout the course of their illness. The authors explain that mental health care delivery within the United Arab Emirates (UAE), continues to be predominantly delivered via a traditional in-patient model with opportunities for the development of community mental health services. This view is shared by The World Health Organisation (WHO, 2017) explains that this overreliance of hospital-based care has the potential to create barriers for allowing families to be involved in the care and treatment which subsequently may affect recovery from mental illness. Dattani (2021) provides great insight in explaining that although the prevalence rates of mental health conditions in the Middle East have remained relatively consistent over the past two decades, mental health conditions are increasing as a share of the total disease burden. Al Habeeb et al. (2023) states that collectively, the Middle East and North Africa (MENA) region forms the global concentration for the proportion of mental health disorders as a share of the total disease burden. Dattani (2021) in agreement, highlights that in Qatar, Kuwait, Oman, and Jordan the share of mental health conditions as a share of the total disease burden is over double the global average of 5%. The study’s authors urge caution in that the post-COVID-19 era has created an imperative for healthcare providers to continue to explore new innovative strategies to address the mental health needs of a population having experienced a global humanitarian crisis. This correlates with Al Habeeb et al. (2023) that the young population may be at further risk of mental illness and a higher burden of noncommunicable diseases. Far from a want of being the harbingers of doom, the authors highlight hope in that there is indeed, an increased focus regionally on mental health by policymakers and there are clear signs of progress across the Middle East.\n\nGlobally, there has been a progression away from long-term mental health hospitals, due in part to isolation and limited and ineffective treatments that did not address the full range of SDMH. The WHO (Singh, 2021) identifies that there was a progression for best practice towards integrated health systems oriented towards health and social care arrangements in the community setting. The noted sociologist Erving Goffman (1963) noted the historical negative impact of institutionalization within the seminal work on mental health institutions, referred to as Asylums. Since that time period there has been an agenda to replace full reliance on the mental institutions and instead include community centres, outpatient facilities and mental health provision in general hospitals. This initiative is on-going and preserves is with international agenda’s such as the WHO comprehensive mental health action plan 2013-2030: We must rise to the challenge (Singh, 2021). Within the MENA region there has still been a lingering reliance on in-patient care, and this has been self-reported in Saudi Arabia and Jordan where there are noted opportunities to progress community care. The WHO (2020) reports that in Jordan 49% of patients in mental hospitals remain for five years or more and a further 17% for between one and five years. Al-Diyab (WHO, 2020) Saudi Arabia’s director general of mental health reported his concern that, of the then 4,000 beds available in mental hospitals, 1,000 were blocked by patients who could not leave as their families would not accept them back. Whilst, hard to digest within a region that is admired for its strong family support and compassion, it is to be understood when paralleled to Goffman’s work (1961) and regional literature on the presence of stigma towards those suffering with mental illness (Zolezzi et al., 2018). Goffman widened the understanding of deprivation approaches by describing the progression away from institutionalisation as a series of ‘degradations’ and a process of ‘mortification’, in which an individual’s identity and personal characteristics are eroded over time due in part to a lack of access to their community and family (1961). Recognizing this need for an expansive approach to community care the Emirates Health Services (EHS) has launched an initiative to develop a network of primary mental health clinics in the community, strengthening community mental health services across the UAE (WAM, 2020).\n\nThe author’s purpose is to review health models from different countries as found within the literature with correlation to the best practices towards community care. This paper highlights social prescribing as an alternative treatment strategy to the traditional biomedical models embedded within the over reliance of the mental health hospitals. Social prescribing is advised to assist individuals to connect and thrive within their communities and to support improved health and well-being as linked to the social determinants of mental health. The authors highlight possible challenges towards the dissemination and implementation of the identified health models before concluding the paper.\n\n\nObjective and review question\n\nThe author’s rationale for conducting a scoping review was to provide a methodology for determining the state of the evidence on the selected topic, this is especially useful when issues require clarification before empirical studies are undertaken. Therefore, the purpose of this study is to adopt Arskey and O’Malley’s scoping review methodology to determine the following with respect to identifying appropriate health models to support SDMH and the adoption of social prescribing:\n\n1. What is the extent and nature of published scientific literature on health models including the research designs used, areas of clinical practice, and compatibility for use of social prescribing to address SDMH?\n\n2. To what extent do the identified models address the core components of community care needs in the UAE and support the adoption of the proposed community focused treatment strategy of social prescribing to provide a holistic review of SDMH?\n\nA secondary purpose of this study was to reflect on the depth and breadth of evidence surrounding challenges of establishing new care strategies for community care by charting the published systematic reviews on historical hurdles to paradigm shifts in care provision. This review was conducted as a secondary procession to identify evidence for policy makers to consider when seeking to enhance client-centered frameworks by adopting new health models since effective care is the most definable and consistent component of care in the community.\n\n\nMethods: Scoping review\n\nThis study undertakes a scoping review of the relevant literature on models of health and selects those that have an evidence base to address clients and societal needs of SDMH. The models, if adopted could enable the use of social prescribing within community settings to support the healthcare systems within the UAE. Where possible the authors will seek to highlight modifications to identified health models to illustrate how these models can be modified to meet the study’s aim.\n\nThe use of scoping reviews is advocated by Arksey and O’Malley (2005). They explain that the use of a scoping review can highlight if there is a need to address broader topics where many different study designs might be applicable and whether there is a challenge in identifying a clear question. Arksey and O’Malley (2005) further explain that whereas literature and systematic reviews are predominantly concerned with providing answers to questions from a relatively narrow range of quality assessed studies, scoping reviews are less inclined to seek to address a specific research question nor, consequently, to assess the quality of included studies. This was of particular interest for this study as the establishment of the UAE’s first community mental health services as the authors interest to create a treatment strategy that address SDMH inclusive of medical strategies needed a review strategy that was broad, evidence based and yet, capable to identify capable and effective health models.\n\nThe study adhered to the suggested framework of Arksey and O’Malley (2005). This framework provided a systematic approach to searching the literature and also aided in establishing a comprehensive foundation to guide the review. There was a need by the authors to determine the extent of research previously conducted on the identified models and to highlight any grey literature, theory or perspectives that may have relevance to the understanding of the selected topic a sit applied to the culture and the people of the Emirates. Table 1 provides a tabular format for the study’s adherence to this framework. The authors needed to adapt the model proposed by Arksey and O’Malley but this has some similarities to the experiences of Colquhoun et al. (2014). These authors emphasised that a scoping review is not a linear process but rather describes a cyclical process of the researcher (authors) going back-and-forth between early findings and new emerging insights. Therefore, the authors made changes in the search terms and even the questions. Hence, the sections not being sequential with the identified six stages of the Arksey and O’Malley (2005) framework.\n\n\n\n1. Identify the Research Questions\n\n2. Identify the Relevant Studies\n\n3. Study Selection\n\n4. Charting the Data\n\n5. Collating, Summarising and Reporting\n\n6. Consult Stakeholders and Policy Makers – Aim: To obtain more references, provide insights on what the literature fails to highlight (Optional).\n\nThe scoping review within this study incorporated the 2 identified questions to explore the aim of this study: What evidence is there of appropriate health models that can be adopted to use social prescribing to treat mental illness and address SDMH within the community care setting. The search determined that there had been regional interest in social prescribing within the United Kingdom (UK), Europe and the United States (US) and that this had created a wide-ranging source of research and literature on social prescribing (Morse et al., 2022). What was less evident was a review of health models to implement this strategy in community mental health care settings within the Middle East. This necessitated a need for the authors to undertake a broader and wider focus with a flexible hierarchy of evidence to identity relevant literature. The scoping review extrapolated the evidence from published literature and identified the profile and key themes aligned to the needs assigned to a proposed health model. The health models were analysed and identified in conjunction with the relevance of and success of their implementation on community settings, alongside information gained from an evidence base for their application to the ethos of social prescribing as an empowering and alternative as a non-pharmaceutical focused treatment scheme that could be implemented within UAE society and culture.\n\nKey databases searched were: CINAHL, MEDLINE, Cochrane Library, ASSIA, Web of Science and Scopus. The database search was also supplemented by hand searches of relevant publications/policy documents located within the University of Sharjah libraries. All considered literature was considered key to underpinning and providing an evidence base for this review article. No time restriction was set initially, as the authors wanted to seek relevant literature that may be seminal and illuminated the historical significance of the evidence base presented. However, for specific studies relating to health models and social prescribing, a secondary literature search was undertaken from the time periods 1940’s to 2024 to capture the most current research. A wide range of studies were sought that focused on policy objectives and initiatives influenced by international and national health agenda, through to independent and statutory studies exploring relevant health models, social prescribing and SDMH. A wide variety of search terms were used independently or in different combinations which were directly pertinent to the research questions or were slightly tangential to the research questions, this was to ensure that any emergent sources that may be linked to seminal literature might be found, and their relevance explored to identify innovative new healthcare strategies and or approaches.\n\nThe study has conducted a scoping review of existing relevant studies and will not recruit any participants directly; thus, ethical approval was not required.\n\n\nResults\n\nThe concept behind self-management as mentioned previously is self-efficacy (Liu et al., 2023). It is accepted that individuals experiencing mental ill-health may have different symptoms that directly affect their cognitive ability to engage in society. Therefore, managing the symptoms of mental health is extremely important. In coping with such conditions, healthcare providers within the community must empower clients and let them be positively involved in addressing their SDMH through an individualized plan of care. Williams et al. (2007) highlights that self-management education programs are significant for empowering clients to acquire new skills in order to enhance the self-care of their conditions. In reviewing the literature of the evidence base of health models the authors ensured that self-management and self-efficacy were adopted conceptually as gatekeepers for the inclusion of any identified models. Four noteworthy types of models identified by the authors are the Health Belief Model, Motivational Interviewing Health Promotion Model and finally the Crescent of Care Nursing Model. These four models can be utilised with minimal involvement of the traditional bio-medical model practices arguably entrenched within the region’s healthcare practices. These suggested models of care align with a social prescribing framework and could be applied to health policy directives within the region.\n\nHealth Belief Model\n\nThe Health Belief Model (HBL) was developed by Hockbaum, Leventhal Kegeles and Rosenstock in the 1960’s. The model was identified within the scoping review as it has relevance as it creates a focus for the client to be able to make choices on their own health care needs (Rosenstock, 1966). This active decision-making approach was based on the seminal psychological theories first identified and explored by Lewin (1944), who proposed that individuals assign value to the potential outcome, this therefore influences the selection of health behaviours based on their belief of the results of the desired outcome.\n\nLater studies by Wallston (1992) and Schenkman et al. (2008) demonstrated the benefits of this framework for health promotion for those with heath needs. Their research has relevance for this study in that their findings indicate that the HBM, as a socio-cognitive approach that could support the mental health needs of individuals. In applying this model to social prescribing, the authors propose that individuals might be likely engage in the selected psychosocial interventions prescribed if they have the mindfulness that the given health-related treatment has a positive impact on their activities of daily living, when they believe the intervention will be effective, and when they perceive few limitations to participating and taking empowering action. The authors believe that the HBM could provide a structure to developing and evaluating social prescribing in the UAE when applied to community mental health schemes as there is an enhanced emphasis on improving mental health awareness as applied to the causalities of the social determinants of mental health and associated well-being of people in the UAE.\n\nFirst devised by Millar (1983) and then expanded by Millar and Rollnick (1995) motivational interviewing (MI) has been recognized as highly effective in the treatment of mental illness. MI was first devised for the treatment of addictions and alcohol misuse as a directive counselling approach. From its conception there have been encouraging results demonstrating its effectiveness in promoting change in health behaviour and client led lifestyle changes. A key concept of MI is that it seeks to delve into the individual’s ambivalence not to promote healthy change and seeks to alter these maladaptive responses (Levensky et al., 2007). When exploring this model for the use of social prescribing within community mental health settings, there is strong evidence for this client-centered approach but does rely on the client’s intrinsic motivation to change and so there would be a holistic effort from all multi-disciplinary teams to have a familiarity and confidence in applying MI within the community setting. This model follows four key counseling principles (Rollnick, Miller, Butler, 2023; Levensky et al., 2007) which the authors have reviewed and adapted to the focus of this study:\n\nThe adapted model of Rollnick, Miller, Butler (2023) and Levensky et al. (2007) by this study’s authors provides a proposed framework for the use of social prescribing in the community mental health setting that focuses on and seeks to impact the social determinants of mental health. The framework relies on the practitioner’s interpersonal style ability to engage in reflective listening, asking open-ended questions, affirming, and summarizing their engagement with their client. This approach could instill motivation to change in the client by creating alternative cognitive realities of their life post engagement with MI (Table 2).\n\nHistorical conceptions on health promotion were predominantly focused on supporting the individual with healthcare needs to help themselves make lifestyle changes (Minkler, 1989). However, as discussed by Whitehead (2004) there has since been an evolving dominance of socio-political emphasis in health promotion which has overtaken a former emphasis on individualistic and behaviour focused care. The authors highlight the ability of the health promotion model to assist with the transformative process of developing community mental health services in the UAE as the model has an evidence base within the socio-political of health promotion activities. Therefore, the model has an evidence base to develop and reform social structures through developing participation with social prescribing with representative stakeholders from multiple agencies and disciplines. However, caution should be taken as the model has historically incurred criticism that with the focus on individual responsibility for health can contribute to victim blaming (Hancock, 1986). Early studies by Robertson and Minkler (1994) acknowledged that health promotion recognized the social, economic and political determinants of health with a later inclusion of social justice as noted by Carlisle (2000).\n\nThe authors determine that the health promotion model could create a workable framework by which the ecologically driven socio-political-economic determinants of health are addressed as they impact on community mental health. However, the authors acknowledge that this model does not have a specific focus on religion and spirituality. As emphasized by Lovering (2008) there is a need to create an emphasis on the importance on Muslim faith as it applies to health in countries in the Middle East. Therefore, the authors expanded the parameters of the scoping review and identified the following model for inclusion in this study.\n\nThe Crescent of Care nursing model is derived from an ethnographic study of the health beliefs and care meanings of Arab Muslim nurses caring for Arab Muslim patients in the Middle East region by Lovering (2008). The model is a culturally sensitive and holistic approach to the spiritual, cultural, psychosocial, interpersonal, and clinical caring needs of Arab Muslims within the UAE and the wider MENA region. Lovering (2008) demonstrates the linkage of professional nursing values and combines them to creation of this model. The model creates a central organizing point with the client and their family as the focal point. Shared meanings on spirituality between the nurse, patient and family nurture meaningfulness and enhance care. The authors remonstrate that this model links into the SDMH as it is set within a context of psychosocial, cultural, interpersonal, clinical, and spiritual elements of care by respectfully acknowledging that an Arab conceptualization of health is derived from the religion of Islam. The wisdom of including this model within this scoping review is the presence and relevance of the concept of tawhid. Kounsar (2016) describes tawhid as a oneness with Allah and requires that a Muslim lives in a way that demonstrates a unity of the body and mind with Allah. Lovering (2008) writes that Tawhid implies therefore that there is no separation of the body from the spiritual dimension of health. Kounsar (2016) highlights central beliefs to Islam that Muslims also believe. This ethos can be applied to seeking to address the SDMH via social prescribing as illustrated within the following model (Figure 1) used by Al-Fayyadh et al. (2022) to illustrate Lovering’s Cresent of Care Nursing Model:\n\nThis model is based on Al-Fayyadh et al. (2022) interpretations of Lovering’s Crescent Care Model which supports clients to understand and appreciate the link between short and long-term goals. This paper suggests that this approach is driven by religious and cultural sensitivity that may enhance motivation for the client and so support them adhering to the psychosocial interventions identified as part of social prescribing. The authors suggest that the inclusion of a focus on the ethos of tawhid may promote continued involvement in goal setting, active participation, and enhanced responsivity in that the clients take responsibility for their own health and empowered care through social prescribing. The interplay via shared belief can foster and promote effective and culturally and religiously nuances psychosocial intervention that the client wholeheartedly embraces through tawhid. As in all changes, there are inherent challenges to progress which will be discussed now.\n\nThe World Health Organisation (2022) estimates that the majority of individuals with mental illness do not seek treatment, citing reasons as concerns a perceived damaging of their family’s reputation, standing within the community, opportunities for marriage, encountering discrimination, exclusion from society, and stigma. Consequently, these individuals experience diminished self-esteem (Stuart et al., 2019) and poor academic achievement (Bruffaerts et al., 2018).\n\nGoffman (1963, p. 3) describes stigma as “an attribute that is deeply discrediting. It diminishes the social status of an individual by reducing them in the eyes of others from being whole and usual to tainted and discounted”. Stigmatization has the potential to diminish an individual’s self-esteem, cause friction within familial units, and have an impact on their prospects by negatively affecting their employability (Picco et al., 2019). Within a previous study by Mottershead and Ghisoni (2021) it was proposed that social prescribing is an empowering strategy to assist individuals to connect and thrive within their communities and supports improvements in their health. This has also been observed within the Middle East within a study by Mottershead and Alonaizi (2022) and Mottershead (2022) in exploring social prescribing use with addiction and substance misuse treatment strategies. Whilst further research is required, it may be theorized that there is an associated stigma towards mental illness that still creates challenges for treatment within a public and community setting. Again, noted by Mottershead and Alonaizi (2022) was that whilst, social prescribing schemes have demonstrated a reassuring evidence base and continue to gain popularity, there has been little evidence of its use within the Middle East. A question, must there be contemplated – why?\n\nThis article argues that stigma alone is not the causality but rather that healthcare systems have these become transfixed on hospital-based care for mental illness due decision making predominantly focusing on the foundation of medical services since the conception of the UAE in 1971. This is in no way a criticism, few countries have achieved the success of the UAE in healthcare, but a realization might acknowledge a concept that Weber, Husserl and later Bourdieu (1990) identified as ‘Habitus’. It has been seen in other areas of research as argued by Professor Loader at the University of Oxford (Loader, 2007) that society can directly impact the formation of services. It is feasible that a symbiotic relationship may be experienced to a general public’s sensitivities (stigma) towards mental illness and the ability of a health services to create new strategies and treatments. Habitus, entails competence and know-how, it demonstrates great skill and awareness of how to achieve success through a pre-determined set of strategies, policies and procedures almost effortlessly through reflexivity (Bourdieu, 1990).\n\nAs the reference to ‘dexterity’ suggests, entails competence and know-how. It captures the skilled activity of the expert player rather than the conditioned response of the lab rat. The footballer who moves instinctively into the right position on the pitch, arriving just as the ball does and at exactly the right angle to it to put it in the back of the net, all without having to think reflectively about doing so, exemplifies this, as Bourdieu’s (1990). However, as was seen during the Covid pandemic, preexisting systems either failed or had to be modified, innovation became the lifeblood of a healthcare ability to become resilient and to adapt. The authors argue that this same process should be followed as a wider contemplation of the SDMH, and social prescribing will support the evolvement of current practices that utilize treatments pre-dominantly focused on pharmaceutical interventions for mental illness.\n\n\nConclusion\n\nIdentified challenges exist in developing workforces capable of mental health within communities setting and independent from the current institutional arrangements that do not meet all SDMH. Caution must be taken not to replicate errors and delays away from institutionalized care which can isolate clients away from families and their communities, making reiteration all the more difficult. Lack of mental health awareness due to engrained practices (habitus) are further compromised with the presence of stigma within health systems not utilizing health models that seek to enhance the quantity and quality of care. Such issues have existed in much of the world and should not be seen as solely regional concerns. Opportunities exist for shifts in treatment provision as suggested by the inclusion of social prescribing to aid services to meet the full range of SDMH. The inclusion of mental health strategies and laws herald improvements with a recognition of the likely benefits of integrating mental healthcare delivery with community care and the management of common mental health conditions indicating encouraging changes to current practices.\n\nWith 21st century life impacting on well-being there is an imperative to adopt health models with an ethos of self-management as enshrined within social prescribing. The article has presented for consideration, four self-management models with a theoretical evidence-base that could be applied to care for those experiencing mental illness within the community setting in the UAE and wider Middle East region. The focus on the SDMH via social prescribing links into the agenda of the UAE Centennial 2071 (2018). The author’s present these four models emphasizing their benefits; however, a challenge is identified in the need to ensure that health insurance recognizes the importance of social prescribing and empowers clients to select this as a health delivery option. Although, challenges are present, the study demonstrates that if there is to be a provoking of new healthcare strategies, then a focus on SDMH will create a sustainable community mental healthcare strategy, empowering clients, and acknowledging the significant importance of the inclusion of families within the recovery and care of mental illness.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\n\nReferences\n\nAl-Fayyadh S, Diener E, Wright V: Spirituality as a core concept in the theoretical literature of nursing: A comparative overview between Watson & Lovering’s perspectives. Nurs. Forum. 2022; 57(4): 717–723. PubMed Abstract \| Publisher Full Text\n\nAl Habeeb, et al.: Mental health in the Middle East Measuring progress towards integrated, accessible and equitable mental health. Economist Impact. 2023. Reference Source\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\nBourdieu P: The Logic of Practice. Polity Press; 1990.\n\nBruffaerts R, Mortier P, Kiekens G, et al.: Mental health problems in college freshmen: Prevalence and academic functioning. J. Affect. Disord. 2018; 225: 97–103. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarlisle S: Health promotion, advocacy and health inequalities: a conceptual framework. Health Promot. Int. December 2000; 15(4): 369–376. Publisher Full Text\n\nColquhoun HL, Levac D, O’Brien KK, et al.: Literature reviews: time for clarity in definition, methods, and reporting. J. Clin. Epidemiol. 2014; 67(12): 1291–1294. PubMed Abstract \| Publisher Full Text\n\nDattani S: Mental health Our World in Data.2021. Reference Source\n\nGoffman E: Asylums: Essays on the social situation of mental patients and other inmates. London: Penguin Books; 1961.\n\nGoffman E: Stigma. Englewood Cliffs, NJ: Prentice Hall; 1963.\n\nHancock T: Lalonde and beyond: Looking back at “A New Perspective on the Health of Canadians”. Health Promot. Int. May 1986; 1(1): 93–100. Publisher Full Text\n\nKounsar A: The concept of tawhid in islam: in the light of perspectives of prominent Muslim scholars. J. Islam. Thought Civiliz. 2016 Fall; 06(2): 95–110. Publisher Full Text Reference Source\n\nLevensky ER, Forcehimes A, O’Donohue WT, et al.: Motivational interviewing: an evidence-based approach to counseling helps patients follow treatment recommendations. Am. J. Nurs. 2007; 107(10): 50–58. Publisher Full Text\n\nLewin K: A Research approach to leadership problems. J. Educ. Sociol. 1944 Mar 1; 17(7): 392–399. Publisher Full Text\n\nLiu Q, Jin Y, Wang Y, et al.: Association between self-efficacy and self-management behaviours among individuals at high risk for stroke: Social support acting as a mediator. J. Clin. Nurs. 2023; 32: 71–82. PubMed Abstract \| Publisher Full Text\n\nLoader I: The principles and limits of the penal system: initiating a conversation. Commission of English Prisons; 2007.\n\nLovering S: Arab Muslim nurses’ experiences of the meaning of caring. The University of Sydney; 2008. Doctoral thesis. Reference Source\n\nMillar WR: Motivational interviewing with problem drinkers. Behav. Psychother. 1983; 11: 147–172. Publisher Full Text\n\nMillar WR, Rollnick S: What is motivational interviewing? Behav. Cogn. Psychother. 1995; 23: 325–334. Publisher Full Text\n\nMinkler M: Health education, health promotion and the open society: an historical perspective. Health Educ. Q. 1989; 16(1): 17–30. PubMed Abstract \| Publisher Full Text\n\nMorse DF, Sandhu S, Mulligan K, et al.: Global developments in social prescribing. BMJ Glob. Health. 2022; 7(5): e008524. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMottershead R: The social prescribing of psychosocial interventions in the treatment of addictions and substance use disorders with military veterans: a reclamation of identity and belonging. F1000Res. 2022; 11(944): 944. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMottershead R, Alonaizi N: Empowering social prescribing and peer support: A proposed therapeutic alliance against addictions and substance misuse within the middle east. J. Drug Alcohol Res. 2022; 11. Publisher Full Text\n\nMottershead R, Ghisoni M: Horticultural therapy, nutrition and post-traumatic stress disorder in post-military veterans: developing nonpharmaceutical interventions to complement existing therapeutic approaches. F1000Res. 2021; 10: 885. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPicco L, Chang S, Abdin E, et al.: Associative stigma among mental health professionals in Singapore: a cross-sectional study. BMJ Open. 2019; 9: e028179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobertson A, Minkler M: New health promotion movement: a critical examination. Health Educ. Q. 1994; 21(3): 295–312. Publisher Full Text\n\nRollnick S, Miller WR, Butler CC: Motivational interviewing in health care: Helping patients change behaviour. 2nd ed. The Guilford Press; 2023.\n\nRosenstock IM: Why people use health services. Millbank Memorial Fund Quarterly. 1966; 44: 94–127. Publisher Full Text\n\nSchenkman M, Hall D, Kumar R, et al.: Endurance exercise training to improve economy of movement of people with Parkinson disease: three case reports. Phys. Ther. 2008; 88(1): 63–76. PubMed Abstract \| Publisher Full Text\n\nSingh OP: Comprehensive Mental Health Action Plan 2013-2030: We must rise to the challenge. Indian J. Psychiatry. 2021 Sep-Oct; 63(5): 415–417. Epub 2021 Oct 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStuart H, Sartorius N, Thornicroft G: Fighting Mental Illness-Related Stigma: What We Have Learned.Javed A, Fountoulakis K, editors. Advances in Psychiatry. Cham: Springer; 2019. Publisher Full Text\n\nWhitehead D: Health promotion and health education: advancing the concepts. J. Adv. Nurs. 2004; 47: 311–320. Publisher Full Text\n\nWorld Health Organization: Dementia fact sheet.September 2017. Reference Source\n\nThe World Health Organisation: World mental health report: Transforming mental health for all.2022. Reference Source\n\nWAM: UAE marks World Mental Health Day.2020. Reference Source\n\nWHO: Jordan WHO Special Initiative for Mental Health Situational Assessment. Ministry of Health: Hashemite Kingdom of Jordan; 2020.\n\nWallston KA: Hocus-pocus, the focus isn’t strictly on locus: Rotter’s social learning theory modified for health. Cogn. Ther. Res. 1992; 16(2): 183–199. Publisher Full Text\n\nWilliams JW Jr, Gerrity M, Holsinger T, et al.: Systematic review of multifaceted interventions to improve depression care. Gen. Hosp. Psychiatry. 2007; 29(2): 91–116. Publisher Full Text\n\nVISION 2071 UAE Centennial 2071: The World’s Leading Nation (Arabic): 2018. Reference Source\n\nZolezzi M, Alamri M, Shaar S, et al.: Stigma associated with mental illness and its treatment in the Arab culture: A systematic review. Int. J. Soc. Psychiatry. 2018; 64(6): 597–609. PubMed Abstract \| Publisher Full Text" }	[ { "id": "313321", "date": "14 Aug 2024", "name": "Mohamad Musa", "expertise": [ "Reviewer Expertise Mental health", "mental illness", "the Middle East region", "migrant and refugee health." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article presents a scoping review examining health models that could support the implementation of social prescribing and address the social determinants of mental health (SDMH) in community mental health care settings in the United Arab Emirates (UAE). The authors argue there is a need to move away from hospital-based mental health care toward more community-based approaches in the UAE and wider Middle East region. They review four health models - the Health Belief Model, Motivational Interviewing, Health Promotion Model, and Crescent of Care Nursing Model - and discuss how these could provide frameworks for implementing social prescribing to address SDMH in community sett\nThe scoping review methodology is described, but more details could be provided on the specific search strategy, inclusion/exclusion criteria, and how articles were selected and analyzed. The authors mention using the Arksey and O'Malley framework but do not fully detail how each step was implemented.\nThe authors provide a reasonable argument for how the reviewed health models could support implementation of social prescribing and address SDMH in community settings. However, the conclusions could be strengthened by more clearly linking the specific components of each model to social prescribing approaches and SDMH. Additionally, more discussion of potential limitations of the models or challenges in implementation would provide a more balanced assessment.\nGood work overall and the paper may be approved after the multiple revisions above.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? 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": [] } ]	1	https://f1000research.com/articles/13-841
https://f1000research.com/articles/12-781/v1	05 Jul 23	{ "type": "Research Article", "title": "Effects of steeping duration and concentration of metabolites from rhizosphere bacteria on germinability of cowpea (Vigna unguiculata), soybean (Glycine max), sesame (Sesamum indicum) and okra (Abelmoschus esculentus)", "authors": [ "Oghenerobor Akpor", "Ayotunde Ajinde", "Tolulope Ogunnusi", "Ayotunde Ajinde", "Tolulope Ogunnusi" ], "abstract": "Vigorous germination and growth are linked to crop yield. This study was carried out to assess the effect of steeping duration and metabolite concentration on priming of 5 different crops, using the metabolites of five (5) bacterial isolates that were also characterized through Gas Chromatography-Mass Spectrometry (GC-MS). The crop seeds were steeped in cold-extracted metabolites of the 5 isolates for a known period (1, 2, 3, 4, and 5 h) and then also in different metabolites concentrations for a known duration determined as optimal in the first experiment. Characterization of cold-extracted metabolites was also carried out using GCMS. The results of this study revealed that steeping cowpea and soybean for longer durations (< 3 h) could be inhibitory to growth and development. For concentration it was either a case of lower concentration being optimal or there was no detectable pattern with concentration. The metabolites of the different isolates revealed the present of some common molecules, and some of the GCMS-identified metabolites (e.g., Hexadecanoic acid) have been shown to possess growth promotion properties in other studies. This study highlights that large endosperm seeds such as cowpea and soybean are more prone to the negative effects of steeping for longer durations, and further experiments should be carried out to isolate and purify the bioactive moieties for further studies and onward application.", "keywords": [ "Germinability", "rhizobacteria", "germinability", "seed vigor" ], "content": "Introduction\n\nSeeds are critical inputs in agricultural production. However, poor crop stand, a major production constraint in the developing world1 can result from low-quality seeds and unfavorable edaphic and abiotic factors. This indicates that effort must be made to ensure that seeds are properly prepared, so that their germination and growth and crop yield are not negatively impacted. To this end, seed priming has been proposed and used. The beneficial effects of seed priming on a variety of crops have been confirmed.2–5 Although, priming, as a plant growth enhancement technique, can be applied at numerous stages in the developmental cycle of a plant, it is typically utilized on seeds for reasons of practicality and simplicity.\n\nPriming usually involves soaking seeds in a solution to kickstart various pre-germinative activities,6,7 and it typically involves re-drying the seed before plant.8 Several methods of priming that have been shown to enhance the agro-morphic parameters of various crops exist. Hydropriming involves steeping the seeds in water9; osmopriming involves the use of an osmoticum10; halopriming involves soaking in salt solutions11; solid-matrix priming involves priming on a solid material12; and hormonal priming, which involves the use of plant growth regulators such as abscisic acid (ABA),13,14 gibberellic acids (GAs),6 or salicylic acid (SA).15–17 Biopriming involving the use of microbial products is a relatively new priming strategy that comes with the advantage of environmental friendliness and may be also be less expensive than most of the priming methods available.\n\nSeed priming has been shown to enhance germination, reduce germination time, and improve seedling vigor.18 Priming also increase the resistance of seeds to environmental stress.19 Positive priming effects have been reported for many crops.20–25\n\nAlthough, the exact mechanism of priming is not well-understood, it is generally understood to involve specific physiological and biochemical reactions.26,27 The synchronous germination and high germination rate seen as a result of seed priming is attributable to metabolic repair that occur during the priming process,28 increase in the concentration of germination-promoting metabolites,26 and osmotic fine-tuning.29 Also, seed priming leads to an increase in the concentration of α-amylase, an enzyme that play huge role in starch metabolism, in order to meet the energy demand of the growing embryo.28\n\nOptimal priming duration is plant-specific due to seed structures that are unique morphologically and physiologically. Since bacteria secret substances that can promote the growth of plants,30 the determination of effective concentration is also key towards the development of the wholesome application of these substances. Optimal concentrations of chemicals used in priming have been determined.31,32\n\nHowever, while there is ample amount of research works existing on other priming methods, microbial priming is less-well research and the optimization of priming parameters is even less so. Hence, we set out to understand the impact of steeping duration and metabolite concentration on the growth promotion activity of secondary metabolites on selected crops (cowpea, soybean, sesame, and okra) vis-a-vis some agro-morphic parameters by sowing seeds soaked in metabolites of some previously-isolated bacteria immediately without drying. The crops used for priming in this study are of huge economic importance in the tropical region where they are a vital source of dietary requirements. Therefore, there is the need to boost their production and seed priming is a veritable tool to achieving this end.\n\n\nMethods\n\nThe metabolites used for the study were extracted from cultures of Serratia liquefaciens, (OP830504), S. liquefaciens (OP830503), Providencia rettgeri (OP830491), P. rettgeri (OP830498), and Bacillus cereus (OP830501). The bacterial strains were isolated from rhizospheres within Afe Babalola University environment.\n\nThe bacterial strains were isolated using the standard pour-plating procedure. After isolation, distinct colonies were streaked on nutrient agar plates to obtain pure cultures, after which they were stored on agar slants at 4 °C±2 °C until when needed.\n\nFor metabolite extraction, the cold extraction method as reported by Ref. 33 was adopted. The respective extracts were put in clean sterile universal bottles and stored 4 °C±2 °C until when needed.\n\nCharacterization of the metabolites was carried using gas chromatography mass-spectroscopy procedure. The equipment (Varian 3800/4000) was equipped with an Agilent splitter split/splitless BP5 (30 m × 0.25 mm × 0.25 microns) capillary column with nitrogen used as a gas carrier.\n\nThe seeds used for the study were cowpea (Vigna unguiculata), soy-bean (Glycine max), sorghum (Sorghum bicolor), sesame (Sesamum indicum), and okra (Abelmoschus esculentus). All the seeds were sourced from local markets in Ado-Ekiti, Ekiti State, Nigeria.\n\nPrior to use, the respective seeds were subjected to viability tests. Preliminary viability testing was carried out by soaking approximately 100 seeds from a lot in 200 mL of sterile distilled in a 400 mL beaker and allowed to stand for 2 min. Seeds that floated were discarded and considered non-viable while those that settled at the bottom of the beaker were subjected to further viability testing. Further viability testing of the seeds was carried out by planting approximately seven seeds in transparent plastic containers that contained absorbent cotton wool as blotters in triplicates and incubating under fluorescent light for 7 d. Seed lots that showed average percent germination of at least 65% were considered as viable and used for germinability studies.\n\nGerminability experiments were carried out by investigating the effects of steeping duration and metabolite concentration on the seeds.\n\nThe effect of steeping duration of seeds in the respective metabolites on germinability was carried out under 1, 2, 3, 4, and 5 h. The respective seeds from the viable lots were steeped in a known concentration of metabolite and allowed to stand for 5 h duration. Every one hour, for a 5 h duration, approximately seven seeds were withdrawn and planted in transparent plastic cups and incubated for 7 d. At the expiration of incubation, final percent germination, mean germination time, germination index and vigor index were estimated as follows:\n\n• Final germination%FGP=total number of germinated seedstotal number of seeds sown×100%34\n\n• Mean germination timeMGT=∑fxf35\n\nWhere f is the number of seeds germinated on day x\n\n• Germination indexGIX=8×N1+7×N2+6×N3+…+1×N836\n\nWhere N1, N2,N3…N8 represent the number of seeds that germinated on the first, second, and third until the 8th day, and 8, 9, 7 … 1 are the weights given to the number of germinated seeds on the first, second, and third day up to the 8th day.\n\n• Vigor indexVIX=FGP×average plant height37\n\nWith respect to effect of metabolite concentration, 200 mg/L, 400 mg/L, 600 mg/L, 800 mg/L and 1000 mg/L were used for the study. The seeds were steeped in the respective metabolite concentrations and allowed to stand for the optimal steeping time obtained in the first experiment before planting and incubation. At the expiration of the 7 day incubation period, final percent germination, mean germination time, germination index and vigor index were estimated were estimated.\n\nThe study did not involve humans or animals, hence ethical approval was not obtained from any ethics committee. The study proposal was however approved by the Board of the College of Postgraduate Studies, Afe Babalola University, Ado-Ekiti, Nigeria.\n\n\nResults\n\nGenerally, final percent germination of the cowpea seeds showed significantly highest and lowest values in setups steeped for 2 and 5 h, 1 and 5 h, 1, 2, and 3 and 4 h in metabolites from Isolates K, L and M, respectively. There was no significantly difference between final percent germination at the different steeping durations for seeds treated in metabolite from Isolate N. In addition, seeds treated with metabolite from Isolate O showed significantly lowest final percent germination at 3 and 5 h. With respect to mean germination time, significantly lowest values were recorded for seeds steeped for 1 h (metabolites from Isolates K and M), 4 and 5 h (metabolite from isolate L), 1, 4, and 5 h (metabolites from Isolate N), and 1, 2, and 4 (metabolite from Isolate O). Germination index showed significantly lowest values at 3 h (metabolite from Isolate L), 4 and 5 h (metabolite from Isolate M), 1-3 h (metabolite from Isolate N), and 3 and 5 h (metabolite from Isolate O). For vigor index, significantly lowest values were observed at 2, 4 and 5 h (metabolite from Isolate M), 1, 3, and 5 h (metabolite from Isolate N), and 4 and 5 h (metabolite from Isolate O). Also, germination and vigor indices of the seeds showed significantly lowest values in setups treated for 5 h (metabolites K and L) (Table 1).\n\nIn the case of the soybean seeds, final percent germination of seeds showed the highest values at 2 h steeping duration when treated in the respective metabolites, apart from those treated in Isolate O, where 1 h steeping duration was observed to show highest values. Furthermore, significantly lowest mean germination times were recorded in seeds steeped for 1, 2, and 3 h, 1 and 2 h, 1, 4, and 5 h in metabolites from isolates L, M and N, respectively, and 2 h in metabolites from isolate K and 1, 3, and 4 h in metabolites from isolate O. However, significantly highest germination index was observed in seeds treated for 1 and 2 h in metabolite K, 2 h in metabolite L, 1-3 h in metabolite M, 2 and 3 h in metabolite N, and 1 h in metabolite O. Also, for seedling vigor index, significantly highest values were observed at 2 h (metabolites K and L), 1, 3, 4, and 5 h (metabolite M), 2 and 3 h (metabolite N), and 1 h (metabolite O) (Table 2).\n\nFor the sesame seeds, remarkably high final percent germination values (>78%) were observed in the respective treatments, irrespective of the steeping duration. However, significantly lowest mean germination time was observed for seeds steeped for 1 h (metabolites from isolate O), 2 h (metabolites from isolates L and M) and 1, 2, 3, and 5 h (metabolites from isolate K). Also, significantly highest germination index was observed for seeds steeped for 2 and 4 h (metabolite from isolate K), 2 h (metabolites from isolates L and M) and 1 h (metabolites from isolates N and O). In the case of seedling vigor index, seeds steeped for 2 and 3 h (metabolites from isolates K and O), 1 h (metabolite from isolates L and M) and 3 h (metabolite from isolate N) showed significantly highest values (Table 3).\n\nWhen okra seeds were steeped in the metabolites for varying durations, final percent germination of the okra seeds showed significantly highest values in seeds treated for 3 h (metabolite K), 4 h (metabolite L) and 1 and 5 h (metabolite N). There was no significant difference between final germination of the seeds treated with metabolite from isolate M at the different steeping durations. Also, mean germination time showed no significant difference at the different steeping durations for seeds treated with metabolites from isolates K, M and O. However, significantly lowest mean germination times were observed for seeds steeped for 2 and 5 h and 3-5 h, when treated with metabolites from isolates L and N, respectively. Furthermore, seeds steeped for 3 h showed significantly highest germination and vigor indices when treated with metabolites from isolates K respectively. Significantly highest germination index values were observed for seeds steeped for 3 h (Metabolite K), 2-4 h (metabolite L), 1, 3, and 4 h (metabolite M), 1, 3, 4, and 5 h (Isolate N), and 1-4 h (Isolate O). Finally, for seedling vigor index, significantly highest values were observed at 3 h (metabolite K), 3 and 4 h (metabolite L), 3 and 4 h (metabolite M), 1, 4, and 5 (metabolite N), and 3 and 4 h (metabolite O) (Table 4).\n\nAt the different concentrations of the respective metabolites, significantly lowest final precent germination values were observed for cowpea seeds treated with 800 mg/L of metabolites from isolates K, L, and N. Final percent germination of cowpea seeds treated with metabolites from isolates M and O did not differ significantly between the respective concentrations. Also, significantly lowest mean germination time was observed for seeds treated with metabolite concentrations of 200, 600, and 800 mg/L (metabolite from isolate K), 400 and 800 mg/L (metabolite from isolate L), and 400 mg/L (metabolite from isolates M), 200 – 800 mg/L (metabolite N), and 200-600 mg/L (metabolite O). Significantly highest germination index values were observed in seeds treated with metabolite concentrations of 200 and 600 mg/L (metabolite K), 600 mg/L (metabolite L), 200, 400, 600, and 1000 mg/L (metabolite N), and 200, 600, and 800 mg/L (metabolite O) (Table 5). In the case of seedling vigor index, significantly highest values were observed at concentrations of 600 mg/L (metabolite K), 200, 600, and 1000 mg/L (metabolite L), 600 and 1000 mg/L (metabolite M), 400, 600, and 1000 mg/L (metabolite N), and 200-600 mg/L (metabolite O) (Table 5).\n\nFor the soybean seeds, significantly lowest final percent germination values were observed in treatments with metabolite concentrations of 200, 600, 800, and 1000 mg/L (metabolite from isolate K), 800 mg/L (metabolite from isolate M), and 600 mg/L (metabolite from isolate from N), and 1000 mg/L (metabolite from isolate O). In the case of mean germination time, significantly lowest values were recorded in seeds that were treated with 200, 400, and 800 mg/L (metabolite from isolate K), 200, 400, 600, and 1000 mg/L (metabolite from isolate L), 200, 600, and 1000 mg/L (metabolite from isolate M), 200, 400, and 800 mg/L (metabolite from isolate N), 200, 400, and 600 mg/L (metabolite from isolate M). Generally, highest germination index values were observed in seeds that were treated with 400 mg/L, 600 and 1000 mg/L, 400 and 800 mg/L, and 400 and 800 mg/L of metabolites from isolates K, M, N, and O, respectively.\n\nFor seeds treated with metabolites from isolates K, M, N, and O, significantly highest seedling vigor index values were observed in seeds treated with 400 mg/L, 600 mg/L, 400 mg/L, and 600 mg/L, respectively (Table 6).\n\nIn the case of the sesame seeds, remarkably high final germination (> 90 %) was observed at all steeping duration for all steeping durations. Significantly lowest mean germination time was recorded for seeds treated with 600 mg/L (metabolites from isolates K and L), 1000 mg/L (metabolites from isolates M and O) and 200, 400, and 600 mg/L (metabolite from isolate N). Generally, significantly highest germination index was observed in seeds treated with 600 mg/L of metabolite from isolate K, 600 mg/L, 800 mg/L, and 1000 mg/L of metabolites from isolate L, 1000 mg/L of metabolites from isolate M, 200-600 mg/L of metabolites from isolate N, and 1000 mg/L of metabolites from isolate O. For seedling vigor index, significantly highest values were observed at 400 and 600 mg/L for metabolite K, 600 and 800 mg/L for metabolite L, 200 and 1000 mg/L for metabolite M, 200 mg/L for metabolite N, and 1000 mg/L for metabolite O (Table 7).\n\nFurthermore, final percent germination of the okra seeds showed significantly lowest values in setups that were treated with 800 mg/L of metabolites from isolates K and N, 200, 800, and 1000 mg/L of metabolite from isolate L, 800 and 1000 mg/L of metabolite from isolate M, and 200 mg/L of metabolite from isolate O. In the case of mean germination time, seeds treated with metabolites from isolates M and N showed no significance difference at the different concentrations, while 800 mg/L and 200, 400, and 1000 mg/L of metabolites from isolates K and O showed significantly highest values, respectively. With respect to germination index, significantly highest values were recorded in seeds treated with 400, 600, and 1000 mg/L (metabolite from isolate K), 600 mg/L (metabolite from isolate L), 200-800 mg/L (metabolite from isolate M), and 800 and 1000 mg/L (metabolites from isolates N and O). For vigor index, seeds treated in metabolites at 400, 600, and 1000 mg/L (metabolite K), 600 mg/L (metabolite L), 200-600 mg/L (metabolites M and N), and 800-1000 mg/L (metabolite K) (Table 8).\n\nIn the metabolite from S. liquefaciens (OP830504), the major compounds that were detected included Methyl lactate (10.40%), 9,12-Octadecadienoic acid (Z,Z)- (17.50%), n-Hexadecanoic acid (13.38%), Phytol (5.96%), Oleic acid (11.48%) and 9,12-Octadecadienoic acid (Z,Z)- (17.01%). Also, for the metabolite from P. rettgeri (OP830491), n-Hexadecanoic acid (14.13%), Octadecane (7.90%), Phytol (9.31%), 11,14,17-Eicosatrienoic acid, methyl ester (5.96%), Lupeol (7.74%), Stigmasterol (15.00%) and β-Sitosterol (12.19%) were the most dominant compounds (Table 9).\n\nIn addition, the metabolites from S. liquefaciens (OP830503) revealed the presence of Tetradecanoic acid (8.85%), Phytol (29.23%) and 11,14,17-Eicosatrienoic acid, methyl ester (25.17%) as the most dominant. In the case of the metabolite from P. rettgeri (OP830498), Cyclohexanol, 5-methyl-2-(1-methylethyl)- (5.73%), 9,12-Octadecadienoic acid (Z,Z)- (6.05%), Tetradecanoic acid (6.26%), 3,7,11,15-tetramethyl-2-hexadecen-1-ol (17.54%), n-Hexadecanoic acid (21.96%) and 9,12-Octadecadienoic acid (Z,Z)- (12.45%) were the most dominant (Table 9).\n\nThe metabolites from B. cereus (OP830501) were Tetradecanoic acid (15.00%), Oleic acid (26.69%) and 11,14,17-Eicosatrienoic acid, methyl ester (19.22%) as the most dominant compounds (Table 9).\n\n\nDiscussion\n\nSeeds that germinate vigorously offers better crop yield.38 For cowpea, generally, final percent germination reached a significantly highest value at shorter steeping duration, then decreased afterwards. However, for Isolate N and O, all values were statistically the same or nearly so. With soybean, it increased with increasing steeping duration until 1, 2, or 3 h, then decreasing afterward, even though this decrease was sometimes insignificant. Although, microbial metabolites are known to promote germination,39–41 this pattern of result for cowpea and soybean could be ascribed to nutrient and electrolyte leakage at prolonged steeping duration.42 The risk of bacterial and fungal proliferation which can lead to seed decay and spoilage is increased when large endosperm seeds such as soybean and cowpea are primed at longer steeping periods and sown immediately as in this study.\n\nPriming for a shorter period may not allow enough water and bioactive metabolites to enter the seeds and too long a priming period may cause seeds not to germinate.43 The results of this study shows that steeping soybean and cowpea for shorter periods is sufficient for maximal germination values. Steeping duration did not seem to have an impact on final germination pattern on sesame, as high values were distributed throughout without order. There was also no order to the distribution of FPG values for okra, indicating that duration of steeping in the metabolites did not significantly influence germination. This uneven germination pattern could be linked to the hard seed coat of okra,44 which perhaps limited imbibition. This hard seed coat resulted in very high maximal steeping durations of 12 h45 and 48 h46 for okra. Insufficient imbibition can lead to germination delay,47 a situation that could have happened with a hardy seed such as okra in this study, since the highest steeping duration in this study was 5 h and low final germination values were recorded for it.\n\nThe effect of steeping duration on mean germination time was negligible for all the crops, as no patterns were observed. All the values obtained “congregated’ around 5. It therefore makes no agronomic sense to attach any importance to significant results here. However, other researchers have reported better mean germination times.48,49\n\nA higher germination index shows that germinated seeds appeared faster. In the case of cowpea, there was a general decrease in values with increasing steeping time for all isolates and this decline was significant for some isolates. There was also a general but insignificant decline from lower to higher steeping durations with soybean. However, for sesame and okra, steeping time was not significantly affecting the values. Okra required a 48-hour of steeping duration for maximal germination index.46\n\nVigor index reached its statistical highest at a lower steeping duration for all the isolates in the case of cowpea, then decreased afterwards, and this same pattern was also observed for soybean and sesame. The highest value for okra was not limited to lower steeping periods. In fact, the significantly highest value was obtained at either 3 or 4 h for virtually all isolates. A high steeping duration of 48 hours produced the best vigor index in okra.46 The seed coat of okra limit ample imbibition at short steeping periods.\n\nThere was generally no observable pattern for cowpea, soybean, and sesame, and abrupt drop in values were observed for okra with regards to concentration. This may have a lot to do with the erratic emergence of okra seeds50 than any other thing. Similarly, germination was also found to be concentration-independent in the biopriming of canola seeds with varying concentrations of bacterial cell-free supernatants of Devosia sp. (SL43).51 While increasing concentration did not impact germination negatively, it is usually not the case with chemical or hormonal priming where the impact of priming on germination and seedling parameters seems to always be concentration-dependent, with negative and drastic effects at higher concentrations.52,53\n\nConcentration was not effective in producing an impact of significant agronomic proportion on mean germination time in all the crops, as values clustered around 5. With respect to germination index, there was no clear pattern for cowpea, and generally for soybean and okra, too. For metabolites from isolates L, M, and O used in the priming of sesame seeds, there was a rare increase in GIX with increasing concentration, that was also significant.\n\nFor cowpea, seedling vigor index gradually peaked at lower concentration for all isolates, then decreased with increasing concentration, although the decreased was statistically insignificant at times. Similarly, for soybean it peaked at a lower concentration, then a significant decline was observed. Sesame recorded no clear pattern with increasing concentration, however, in the case of isolate K, it peaked at a lower concentration, then decreased steadily afterwards, and for isolate L, it rose steadily and peaked significantly at the highest concentration. Mostly, there was no directional change with concentration for seedling vigor index of okra seeds steeped in these metabolites. The hard seed coat of okra is responsible for the ambiguous response of okra to priming at different concentrations.\n\nThe GC-MS analysis of the extracts detected the presence of a number metabolites in the metabolome of each of them, some of which were common to all isolates. The compounds detected belong to categories such as alkanes, alcohols, carboxylic acids, esters, and terpenes. The ability of alcohols such as 2,3-butanediol produced by various species of Bacillus to promote the growth of Arabidopsis thaliana has been reported.54–56 Tetrahydrofuran-3-ol and 2-heptanone 2-ethyl-1-hexanol from Bacillus species as well have also been reported to improve the growth of A. thaliana and tomato.57\n\nOleic acid has been commonly detected in the metabolomes of some rhizobacteria.58 It was detected in all five strains in this study. n-Hexadecanoic acid, a metabolite detected in the metabolome of two of the isolates in this study, and hexadecane, have been shown to possess the ability to improve the growth of Vigna radiata.59\n\n\nConclusion\n\nThis study enables us to understand the dynamics surrounding the effectiveness of microbial metabolites, something that is not possible with typical screening assays that employs a constant concentration. However, the function of the various metabolites in the isolates sampled needs to be properly investigated to identify the bioactive metabolites responsible for growth promotion. The organisms themselves will have to be further studied to better understand the production of the bioactive metabolites.", "appendix": "Data availability\n\nFigshare. Raw data on germinability parameters at different metabolite concentrations and steeping duration in microbial metabolite. DOI: https://doi.org/10.6084/m9.figshare.23284865.v1. 60\n\n\nAcknowledgements\n\nThe authors are grateful to Afe Babalola University for providing the facilities for the study\n\n\nReferences\n\nHarris D, Joshi A, Khan PA, et al.: On-farm seed priming in semi-arid agriculture: development and evaluation in maize, rice and chickpea in India using participatory methods. Exp. Agric. 1999; 35(1): 15–29. Publisher Full Text\n\nArif M, Jan MT, Khan NU, et al.: Effect of seed priming on growth parameters of soybean. Pak. J. Bot. 2010; 42(4): 2803–2812.\n\nZulfiqar F: Effect of seed priming on horticultural crops. Sci. Hortic. 2021; 286: 110197. Publisher Full Text\n\nGuo Y, Li D, Liu L, et al.: Seed priming with melatonin promotes seed germination and seedling growth of Triticale hexaploide L. under PEG-6000 induced drought stress. Front. Plant Sci. 2022; 13: 13. Publisher Full Text\n\nNeha T, Mohapatra S, Sirhindi G, et al.: Seed priming with brassinolides improves growth and reinforces antioxidative defenses under normal and heat stress conditions in seedlings of Brassica juncea. Physiol. Plant. 2022; 174(6): e13814. PubMed Abstract \| Publisher Full Text\n\nChunthaburee S, Sanitchon J, Pattanagul W, et al.: Alleviation of salt stress in seedlings of black glutinous rice by seed priming with spermidine and gibberellic acid. Notulae Botanicae Horti Agrobotanici Cluj-Napoca. 2014; 42(2): 405–413. Publisher Full Text\n\nIbrahim EA: Seed priming to alleviate salinity stress in germinating seeds. J. Plant Physiol. 2016; 192: 38–46. Publisher Full Text\n\nSher A, Sarwar T, Nawaz A, et al.: Methods of seed priming. Priming and pretreatment of seeds and seedlings: implication in plant stress tolerance and enhancing productivity in crop plants.2019; 1.\n\nAfzal I, Basra SM, Ahmad NA, et al.: Effect of priming and growth regulator treatments on emergence and seedling growth of hybrid maize (Zea mays L.). Int. J. Agric. Biol. 2002; 4(2): 303–306.\n\nRouhi HR, Aboutalebian MA, Sharif-Zadeh F: Effects of hydro and osmopriming on drought stress tolerance during germination in four grass species. Int. J. AgriScience. 2011; 1(2): 107–114.\n\nNawaz A, Amjad M, Pervez MA, et al.: Effect of halopriming on germination and seedling vigor of tomato. Afr. J. Agric. Res. 2011; 6(15): 3551–3559.\n\nKhan AA, Maguire JD, Abawi GS, et al.: Matriconditioning of vegetable seeds to improve stand establishment in early field plantings. J. Am. Soc. Hortic. Sci. 1992; 117(1): 41–47. Publisher Full Text\n\nAli HM, Siddiqui MH, Al-Whaibi MH, et al.: Effect of proline and abscisic acid on the growth and physiological performance of Faba bean under water stress. Pak. J. Bot. 2013; 45(3): 933–940.\n\nWei LX, Lv BS, Li XW, et al.: Priming of rice (Oryza sativa L.) seedlings with abscisic acid enhances seedling survival, plant growth, and grain yield in saline-alkaline paddy fields. Field Crop. Res. 2017; 203: 86–93. Publisher Full Text\n\nFarahmandfar E, Shirvan MB, Sooran SA, et al.: Effect of seed priming on morphological and physiological parameters of fenugreek seedlings under salt stress. Int. J. Agric. Crop Sci. 2013; 5(8): 811.\n\nUlfat AN, Majid SA, Hameed A: Hormonal seed priming improves wheat (Triticum aestivum L.) field performance under drought and non-stress conditions. Pak. J. Bot. 2017; 49(4): 1239–1253.\n\nDotto L, Silva VN: Beet seed priming with growth regulators. Semina: Ciências Agrárias. 2017; 38(4): 1785–1798. Publisher Full Text\n\nHeydariyan M, Basirani N, Sharifi-Rad M, et al.: Effect of seed priming on germination and seedling growth of the caper (Capparis Spinosa) under drought stress. Int. J. Adv. Biol. Biomed. Res. 2014; 2(8): 2381–2389.\n\nAfzal I, Rehman HU, Naveed M, et al.: Recent advances in seed enhancements. New challenges in seed biology-basic and translational research driving seed technology.2016; 47–74. Publisher Full Text\n\nDell’Aquila A, Tritto V: Germination and biochemical activities in wheat seeds following delayed harvesting, ageing and osmotic priming. Proceedings of the International Seed Testing Association. 1991.\n\nArif M, Jan MT, Marwat KB, et al.: Seed priming improves emergence and yield of soybean. Pak. J. Bot. 2008; 40(3): 1169–1177.\n\nBajehbaj AA: The effects of NaCl priming on salt tolerance in sunflower germination and seedling grown under salinity conditions. Afr. J. Biotechnol. 2010; 9(12): 1764–1770. Publisher Full Text\n\nGhassemi-Golezani K, Dastborhan S, Zehtab-Salmasi S: Seed priming and field performance of borage (Borago officinalis L.) under different irrigation treatments. Int. J. Agron. Plant Prod. 2013; 4(1): 82–87.\n\nHameed A, Sheikh MA, Jamil A, et al.: Seed priming with sodium silicate enhances seed germination and seedling growth in wheat (Triticum aestivum L.) under water deficit stress induced by polyethylene glycol. Pak. J. Life Soc. Sci. 2013; 11(1): 19–24.\n\nArif M, Jan MT, Mian IA, et al.: Evaluating the impact of osmopriming varying with polyethylene glycol concentrations and durations on soybean. Int. J. Agric. Biol. 2014; 16(2).\n\nBasra SM, Farooq M, Tabassam R, et al.: Physiological and biochemical aspects of pre-sowing seed treatments in fine rice (Oryza sativa L.). Seed Sci. Technol. 2005; 33(3): 623–628. Publisher Full Text\n\nHu J, Xie XJ, Wang ZF, et al.: Sand priming improves alfalfa germination under high-salt concentration stress. Seed Sci. Technol. 2006; 34(1): 199–204. Publisher Full Text\n\nFarooq MS, Basra SM, Ahmad N: Improving the performance of transplanted rice by seed priming. Plant Growth Regul. 2007; 51: 129–137. Publisher Full Text\n\nBradford KJ: Manipulation of seed water relations via osmotic priming to improve germination under stress conditions. HortSci. 1986; 21(5): 1105–1112. Publisher Full Text\n\nTejera B, Heydrich M, Rojas MM: Antagonism of Bacillus spp. against phytopathogenic fungi of rice cultivation (Oryza sativa L.). Plant Protection Magazine. 2012; 27(2): 117–122.\n\nGhiyasi M, Myandoab MP, Tajbakhsh M, et al.: Influence of different osmopriming treatments on emergency and yield of maize (Zea mays L.). Research. J. Biol. Sci. 2008; 3(12): 1452–1455.\n\nRuttanaruangboworn A, Chanprasert W, Tobunluepop P, et al.: Effect of seed priming with different concentrations of potassium nitrate on the pattern of seed imbibition and germination of rice (Oryza sativa L.). J. Integr. Agric. 2017; 16(3): 605–613. Publisher Full Text\n\nAkpor OB, Okonkwo MA, Ogunnusi TA, et al.: Production, characterization and growth inhibitory potential of metabolites produced by Pseudomonas and Bacillus species. Sci. Afr. 2022; 15: e01085. Publisher Full Text\n\nLeggatt CW, Justice OL, Hay WD, et al.: Rules for testing seeds: association of official seed analysts. Proceedings of the Association of Official Seed Analysts. The Association of Official Seed Analysts; 1949 Jan 1; pp. 23–59.\n\nEllis RH, Covell S, Roberts EH, et al.: The influence of temperature on seed germination rate in grain legumes: II. Intraspecific variation in chickpea (Cicer arietinum L.) at constant temperatures. J. Exp. Bot. 1986; 37(10): 1503–1515. Publisher Full Text\n\nSalehzade H, Shishvan MI, Ghiyasi M, et al.: Effect of seed priming on germination and seedling growth of wheat (Triticum aestivum L.). Research. J. Biol. Sci. 2009; 4(5): 629–631.\n\nAbdul-Baki AA, Anderson JD: Vigor determination in soybean seed by multiple criteria 1. Crop Sci. 1973; 13(6): 630–633. Publisher Full Text\n\nPedrini S, Merritt DJ, Stevens J, et al.: Seed coating: science or marketing spin? Trends Plant Sci. 2017; 22(2): 106–116. Publisher Full Text\n\nHung R, Lee S, Rodriguez-Saona C, et al.: Common gas phase molecules from fungi affect seed germination and plant health in Arabidopsis thaliana. AMB Express. 2014; 4(1): 1–7. Publisher Full Text\n\nGfeller V, Huber M, Förster C, et al.: Root volatiles in plant–plant interactions I: High root sesquiterpene release is associated with increased germination and growth of plant neighbours. Plant Cell Environ. 2019; 42(6): 1950–1963. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFincheira P, Parada M, Quiroz A: Volatile organic compounds stimulate plant growing and seed germination of Lactuca sativa. J. Soil Sci. Plant Nutr. 2017; 17(4): 8538–8567.\n\nPallaoro DS, Camili EC, Guimarães SC, et al.: Methods for priming maize seeds. J. Seed Sci. 2016; 38: 148–154. Publisher Full Text\n\nDekkers BJ, Costa MC, Maia J, et al.: Acquisition and loss of desiccation tolerance in seeds: from experimental model to biological relevance. Planta. 2015; 241: 563–577. PubMed Abstract \| Publisher Full Text\n\nBarupal S, Sharma R, Kumar M, et al.: Seed priming: A effective method for enhancing seed quality and plant stand establishment in okra (Abelmoschus esculentus L.). J. Pharm. Innov. 2022; 11(2): 1359–1364.\n\nKaur H, Chawla N, Pathak M: Effect of different seed priming treatments and priming duration on biochemical parameters and agronomic characters of okra (Abelmoschus esculentus L.). Int. J. Plant Physiol. Biochem. 2015; 7(1): 1–1.\n\nKujur AB, Lal GM: Effect of hydropriming and osmopriming on germination behaviour and vigor of soybean (Glycine max L.) seeds. Agric. Sci. Dig. 2015; 35(3): 207–210. Publisher Full Text\n\nGill PK, Sharma AD, Singh P, et al.: Changes in germination, growth and soluble sugar contents of Sorghum bicolor (L.) Moench seeds under various abiotic stresses. Plant Growth Regul. 2003; 40: 157–162. Publisher Full Text\n\nAl-Mudaris MA, Jutzi SC: The influence of fertilizer-based seed priming treatments on emergence and seedling growth of Sorghum bicolor and Pennisetum glaucum in pot trials under greenhouse conditions. J. Agron. Crop Sci. 1999; 182(2): 135–142. Publisher Full Text\n\nKaurivi JZ, Shilulu I: Priming sorghum seeds with water at different time rates. 8th African Crop Science Society Conference, El-Minia, Egypt, 27-31 October 2007. African Crop Science Society; 2007; pp. 1689–1691.\n\nRahman I, Ali S, Adnan M, et al.: Effect of seed priming on growth parameters of Okra (Abelmoschus esculentus L.). Pure Appl. Biol. 2016; 5(1): 165–171. Publisher Full Text\n\nShah A, Subramanian S, Smith DL: Seed priming with Devosia sp. cell-free supernatant (CFS) and citrus bioflavonoids enhance canola and soybean seed germination. Molecules. 2022; 27(11): 3410. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDhakal P, Subedi R: Influence of mannitol priming on maize seeds under induced water stress. J. Agric. Crops. 2020; 6(3): 27–31. Publisher Full Text\n\nEbrahimi N, Kaboli SH: Effect of different times and KNO3 concentrations on Silybum marianum seedling enhancement. Journal of Medicinal plants and By-product. 2020; 9(1): 51–58.\n\nRyu CM, Farag MA, Paré PW, et al.: Invisible signals from the underground: bacterial volatiles elicit plant growth promotion and induce systemic resistance. Plant Pathol. J. 2005; 21(1): 7–12. Publisher Full Text\n\nAsari S, Matzén S, Petersen MA, et al.: Multiple effects of Bacillus amyloliquefaciens volatile compounds: plant growth promotion and growth inhibition of phytopathogens. FEMS Microbiol. Ecol. 2016; 92(6): fiw070. PubMed Abstract \| Publisher Full Text\n\nRath M, Mitchell TR, Gold SE: Volatiles produced by Bacillus mojavensis RRC101 act as plant growth modulators and are strongly culture-dependent. Microbiol. Res. 2018; 208: 76–84. PubMed Abstract \| Publisher Full Text\n\nJiang CH, Xie YS, Zhu K, et al.: Volatile organic compounds emitted by Bacillus sp. JC03 promote plant growth through the action of auxin and strigolactone. Plant Growth Regul. 2019; 87(2): 317–328. Publisher Full Text\n\nLiu WW, Wei MU, Zhu BY, et al.: Antagonistic activities of volatiles from four strains of Bacillus spp. and Paenibacillus spp. against soil-borne plant pathogens. Agric. Sci. China. 2008; 7(9): 1104–1114. Publisher Full Text\n\nJishma P, Hussain N, Chellappan R, et al.: Strain-specific variation in plant growth promoting volatile organic compounds production by five different Pseudomonas spp. as confirmed by response of Vigna radiata seedlings. J. Appl. Microbiol. 2017; 123(1): 204–216. PubMed Abstract \| Publisher Full Text\n\nAkpor O: Raw data on germinability parameters at different metabolite concentrations and steeping duration in microbial metabolite. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "193085", "date": "04 Sep 2023", "name": "Debasis Mitra", "expertise": [ "Reviewer Expertise Plant Microbe Interactions", "Soil Microbiology", "Arbuscular Mycorrhizal Fungi", "Biocontrol", "Environmental Microbiology", "Strigolactone" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 \"Effects of steeping duration and concentration of metabolites from rhizosphere bacteria on germinability of cowpea (Vigna unguiculata), soybean (Glycine max), sesame (Sesamum indicum) and okra (Abelmoschus esculentus)\" investigated a compelling topic to evaluate the impact of steeping duration and metabolite concentration on seed priming of five distinct crops, utilizing the metabolites of five bacterial isolates that were also characterized via Gas Chromatography-Mass Spectrometry (GC-MS). The results indicated that longer steeping duration may have a negative effect on larger endosperm seeds, such as cowpea and soybean, and further research is needed to isolate and purify the active compounds for additional studies and practical applications. Despite the fact that this study has many positive aspects and is suitable for this journal's scope, however, the manuscript needs to be revised critically and some important details need to be addressed.\nMinor Comments:\nCorrect all grammatical mistakes. Verify that every citation in the text is linked to an appropriate reference in the reference section. Ensure that every reference has a textual citation that corresponds to it.\nMajor Comments:\nRevise the title, remove the crops scientific name from the title, and add all in abstract.\n\nThe abstract is a too general statement that does not convey the objective of your study and highlights the major flaws in your discussion of findings.\n\nAdd Gas Chromatography-Mass Spectrometry (GC-MS) in Keywords\n\n“The bacterial strains were isolated from rhizospheres within Afe Babalola University environment.” rewrite it and give proper isolation and identification details.\n\nMetabolite extraction protocol must be explained in detail alone with GC-MS procedure.\n\n“Ethical approval” put it in end.\n\nNCBI accession numbers show in one place only, no need to write in every place. It's recommended to use it with the strain name or code.\nExample. OP830504 - Serratia liquefaciens AYO-O or AYO-O; OP830503 - Serratia liquefaciens AYO-N or AYO-N; OP830491 - Providencia rettgeri AYO-B /AYO-B....\n\nThe conclusion is poorly written and lacks properly investigated findings and discussion regarding the role of metabolites in crop growth and development.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "10798", "date": "17 Jan 2024", "name": "Oghenerobor B. Akpor", "role": "Author Response", "response": "Dear Reviewer, Please find enclosed within this document our response to your comments. Minor comments: Correct all grammatical mistakes. Verify that every citation in the text is linked to an appropriate reference in the reference section. Ensure that every reference has a textual citation that corresponds to it. Response: Adequate attention has been paid to the grammar, citation, and referencing. Major Comments: Revise the title, remove the crops scientific name from the title, and add all in abstract. Response: This has been attended to. The abstract is a too general statement that does not convey the objective of your study and highlights the major flaws in your discussion of findings. Response: Rectified Add Gas Chromatography-Mass Spectrometry (GC-MS) in Keywords Response: Rectified “The bacterial strains were isolated from rhizospheres within Afe Babalola University environment.” rewrite it and give proper isolation and identification details. Response: Corrected Metabolite extraction protocol must be explained in detail alone with GC-MS procedure. Response: Revised “Ethical approval” put it in end. Response: The stipulated correction has been made NCBI accession numbers show in one place only, no need to write in every place. It's recommended to use it with the strain name or code. Example. OP830504 - Serratia liquefaciens AYO-O or AYO-O; OP830503 - Serratia liquefaciens AYO-N or AYO-N; OP830491 - Providencia rettgeri AYO-B /AYO-B.... Response: Corrections have been made The conclusion is poorly written and lacks properly investigated findings and discussion regarding the role of metabolites in crop growth and development. Response: It has been reworked" } ] }, { "id": "201475", "date": "06 Oct 2023", "name": "Hillary Righini", "expertise": [ "Reviewer Expertise Agriculture" ], "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\nAbstract\nFirst, why did the authors choose bacteria agents of human-infection for extraction of metabolite?? Could they represent risk also in agriculture for the environment and for the workers(in a view for future application)? This is an important issue that must be well argued and explained.\nThe work consists of only a test on seed germination, so I think that materials and methods should be more and better explained.\nThen, the authors must pay attention to the language. The text is difficult to read and it does not flow well. In particular, the abstract is very difficult to read because of English language.\nA careful checking for spelling and grammatical is required throughout the text and often the sentences have no sense.\nMaterials and methods lack of many important details.\nHere, I reported some suggestions, but MORE are needed.\nABSTRACT\n‘Vigorous germination and growth are linked to crop yield.’ This sentence should introduce better the scope of this work. In this way it doesn’t mean anything.\n‘For concentration it was either a case of lower concentration being optimal or there was no detectable pattern with concentration.’ It is difficult to read and understand. Through out the manuscript, there are several sentence like this, very difficult to understand.\nI would like to underline that ‘a seed can be treated, not steeped’. So, seeds were treated by immersion/dipping/soaking for a period.\nMATERIALS AND METHODS\n‘.. until when needed.’, it better ‘until use’.\n‘The bacterial strains were isolated using the standard pour-plating procedure’, it needs a reference.\n‘After isolation, distinct colonies were streaked on nutrient agar plates to obtain pure cultures,’. How was carried out the isolation? How did you identified the bacteria?\nIt is not clear the temporal succession of the methodological steps.\nHave you isolated the bacteria? And then identified? Or they were already isolated, identified and stored in your university??\n‘Prior to use, the respective seeds were subjected to viability tests.’ Change with ‘First, a test was carried out on seeds in order to assess their viability’.\n‘Preliminary viability testing was carried out by soaking approximately 100 seeds from a lot in 200 mL of sterile distilled in a 400 mL beaker and allowed to stand for 2 min. ‘ I suggest to change with ‘Preliminary viability testing was carried out by soaking 100 seeds in 200 mL of sterile distilled in a beaker for 2 min’.\n‘approximately’ is not a scientific term.\n‘sterile distilled’ what? Water, compounds?\nIt is only one ‘viability test’ that includes two steps: first step for excluding those seeds that floated, the second step for testing the germination percentage. This part should be explained better.\n‘cotton wool’ was sterilized?\nHas the cotton been moistened? Which were the environmental conditions during the incubation for 7 days? Temperature (day/night), humidity.\n‘known concentration’, which ones?\n‘respective’ which ones?\n‘under 1, 2, 3, 4, and 5 h’. Not correct. The right way is ‘FOR 1,2,3,4 or 5 hours.’ (For example, seeds were treated by immersion for 4 hours).\nEach formula needs a reference.\nIt is not clear how the authors have weight the compounds to obtain 200 mg/L, 400 mg/L, 600 mg/L, 800 mg/L and 1000 mg/L. In materials and methods, there is no a statical paragraph. It is not clear how many repetitions. Where is the control?\nK, L, M, N, O: it is not clear their meaning. Moreover, in the results sometimes 'K, L, M, N, O' are reporte, sometimes the name of bacterial species. It is a confused way.\n‘The bacterial strains were isolated using the standard pour-plating procedure’ explain the procedure and insert a reference for it.’\n‘from rhizospheres within Afe Babalola University environment’: rhizosphere of which plant? How was this environment managed? Was there any crop, are still any crops? Is it a resting soil?\n‘Afe Babalola University’ change with ‘Afe Babalola University (Ekiti, Nigeria)’\n‘All the seeds were sourced from local markets in Ado Ekiti, Ekiti State, Nigeria’. You must indicate the producer, the city, an the production and purchase date.\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? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "10799", "date": "17 Jan 2024", "name": "Oghenerobor B. Akpor", "role": "Author Response", "response": "Dear Reviewer, Please find enclosed our responses to your comments. First, why did the authors choose bacteria agents of human-infection for extraction of metabolite?? Could they represent risk also in agriculture for the environment and for the workers (in a view for future application)? This is an important issue that must be well argued and explained. Answer: Serratia is a genus of opportunistic pathogens of immunocompromised patients. The main pathogen in this genus is Serratia marcescens and Serratia liquefaciens are rarely implicated in infectious diseases. Providencia rettgeri is also a rare pathogen of humans and Bacillus cereus is a minor pathogen of foodborne illnesses. Moreover, strains of these organisms are common constituents of commercial preparations for plant growth promotion. This informed our decision to include them in this study. Nevertheless, the investigation of their pathogenicity will be carried out down the line in view of possible future application. Only then can their biosafety be ascertained. The work consists of only a test on seed germination, so I think that materials and methods should be more and better explained. Answer: The authors have gone to great lengths to expound the Material and Methods section. Then, the authors must pay attention to the language. The text is difficult to read and it does not flow well. In particular, the abstract is very difficult to read because of English language. Answer: The errors have been corrected. Significant improvements have been made to the composition and flow of the text. A careful checking for spelling and grammatical is required throughout the text and often the sentences have no sense. Answer: The authors have gone to great lengths to improve the grammar, style, and spelling in the text Materials and methods lack of many important details. Answer: Significant and important changes have been made. Here, I reported some suggestions, but MORE are needed. ABSTRACT ‘Vigorous germination and growth are linked to crop yield.’ This sentence should introduce better the scope of this work. In this way it doesn’t mean anything. Answer: Rectified. ‘For concentration it was either a case of lower concentration being optimal or there was no detectable pattern with concentration.’ It is difficult to read and understand. Through out the manuscript, there are several sentences like this, very difficult to understand. Answer: Corrected. I would like to underline that ‘a seed can be treated, not steeped’. So, seeds were treated by immersion/dipping/soaking for a period. Answer: The necessary has been made. MATERIALS AND METHODS ‘.. until when needed.’, it better ‘until use’. Answer: Corrected. ‘The bacterial strains were isolated using the standard pour-plating procedure’, it needs a reference. Answer: Corrected. ‘After isolation, distinct colonies were streaked on nutrient agar plates to obtain pure cultures,’. How was carried out the isolation? How did you identified the bacteria? Answer: The requisite changes have been made. It is not clear the temporal succession of the methodological steps. Answer: Changes have been made. It now follows a logical succession. Have you isolated the bacteria? And then identified? Or they were already isolated, identified and stored in your university? Answer: They were isolated from a previous experiment separate from this study and stored on agar slants. They were identified through 16S rRNA. ‘Prior to use, the respective seeds were subjected to viability tests.’ Change with ‘First, a test was carried out on seeds in order to assess their viability’. Answer: The suggested correction has been made ‘Preliminary viability testing was carried out by soaking approximately 100 seeds from a lot in 200 mL of sterile distilled in a 400 mL beaker and allowed to stand for 2 min. ‘ I suggest to change with ‘Preliminary viability testing was carried out by soaking 100 seeds in 200 mL of sterile distilled in a beaker for 2 min’. Answer: The suggested correction has been made ‘approximately’ is not a scientific term. Answer: The suggested correction has been made ‘sterile distilled’ what? Water, compounds? Answer: Water. The necessary correction has been made It is only one ‘viability test’ that includes two steps: first step for excluding those seeds that floated, the second step for testing the germination percentage. This part should be explained better. Answer: The suggested correction has been made ‘cotton wool’ was sterilized? Answer: No. Has the cotton been moistened? Which were the environmental conditions during the incubation for 7 days? Temperature (day/night), humidity. Answer: Those were not measured. ‘known concentration’, which ones? Answer: This has been corrected ‘respective’ which ones? Answer: The 4 different seeds. It has been recast ‘under 1, 2, 3, 4, and 5 h’. Not correct. The right way is ‘FOR 1,2,3,4 or 5 hours.’ (For example, seeds were treated by immersion for 4 hours). Answer: The suggested correction has been made Each formula needs a reference. Answer: They were actually included in the original manuscript submitted. It is not clear how the authors have weight the compounds to obtain 200 mg/L, 400 mg/L, 600 mg/L, 800 mg/L and 1000 mg/L. Answer: Corrections made. In materials and methods, there is no a statical paragraph. It is not clear how many repetitions. Answer: The suggested correction has been made. Where is the control? Answer: No control because water is water, no concentration gradient. K, L, M, N, O: it is not clear their meaning. Moreover, in the results sometimes 'K, L, M, N, O' are reported, sometimes the name of bacterial species. It is a confused way. Answer: The full names were only used in the presentation of the results of metabolite characterization to ensure brevity, elsewhere in the Result section the letters were used. ‘The bacterial strains were isolated using the standard pour-plating procedure’ explain the procedure and insert a reference for it.’ Answer: Rectified ‘from rhizospheres within Afe Babalola University environment’: rhizosphere of which plant? How was this environment managed? Was there any crop, are still any crops? Is it a resting soil? Answer: 1. It’s a resting soil with various grasses. 2. The rhizospheres were not noted. 3. It was a managed grassland. ‘Afe Babalola University’ change with ‘Afe Babalola University (Ekiti, Nigeria)’ Answer: The suggested correction has been made ‘All the seeds were sourced from local markets in Ado Ekiti, Ekiti State, Nigeria’. You must indicate the producer, the city, an the production and purchase date. Answer: Unfortunately, the seeds were not labelled. But they were procured from a seed dealer who supplies farmers with fresh seeds. Nonetheless, in order to ascertain their viability, the germination test was carried out" } ] } ]	1	https://f1000research.com/articles/12-781
https://f1000research.com/articles/11-472/v1	28 Apr 22	{ "type": "Research Article", "title": "Plasma glucose, HbA1c, insulin and lipid profile in Sudanese type 2 diabetic patients with cardiovascular disease: a case control study", "authors": [ "Salsabbil Idris Abdallah", "Nuha Eljailli Abubaker", "Mariam Abbas Ibrahim", "Ahmed Abd Alla", "Rami Adam Humaida", "Salsabbil Idris Abdallah", "Nuha Eljailli Abubaker", "Mariam Abbas Ibrahim", "Rami Adam Humaida" ], "abstract": "Background: Type 2 diabetes mellitus (T2DM) and its consequences are a serious global public health issue. By 2030, the number of people with type 2 diabetes is predicted to reach 439 million. The purpose of this study is to evaluate the plasma levels of glucose, HbA1c, insulin, and lipid profile in Sudanese T2DM patients. Methods: This case control study included 165 Sudanese patients with diabetic type 2 and a cardiovascular condition as cases and 165 diabetic type 2 volunteers without a cardiovascular disorder as controls. The concentrations of plasma glucose, HbA1c, and lipid profile were assessed using a Mindray BS-480 auto-chemistry analyzer, and insulin was analyzed using a Cobase 411 auto analyzer. The collected data were analyzed using statistical tools for social science computer programs (SPSS version 21). Results: According to the findings, (59.4 %) of patients between the ages of (50-69). Females made up 50.9 %. (38.2 %) of patients had an illness duration of between (8-15 years). (41.8%) of individuals did not have hypertension. There was a substantial rise in BMI, FBG, HbA1c, HDL-C, and insulin among diabetics with cardiovascular disease compared to diabetics without cardiovascular disease (p-value = 0.001, 0.000, 0.018, and 0.000). Females had significantly higher blood TC, LDL-C, HDL-C, and BMI than males (p-values = 0.000, 0,001, and 0.000, respectively). There were significant positive correlation between FBS, HBA1c, insulin and duration of disease (r=0.155, p, value=0.005) (r=0.160, p, value=0.004)(r=0.103, p. value=0.061)respectively, while there were significant negative correlation between TC, TG,LDL-C, HDL-C and duration of disease (r=-0.152, p, value= 0.006)(r=-0.023, p, value=0.678)(r=-0.113, p, value= 0.040)(r=-0.145, p, value=0.008)respectively. Conclusion: When comparing diabetics with cardiovascular disease to diabetics without cardiovascular disease, there was a substantial rise in BMI, FBG, HbA1c, HDL-C, and insulin. FBS, HBA1c, insulin, and illness duration all had a strong positive connection.", "keywords": [ "FBS", "HBA1c", "T2DM", "HDL-C", "and HDL-C" ], "content": "Introduction\n\nT2DM has no established cause, however it is known to be caused by physiological, genetic, and environmental variables such as obesity, family history, and pollution (Yang et al., 2018). T2DM and its consequences are a major global public health issue, and cardiovascular disease (CVD) represents a significant health burden in Sub-Saharan Africa, including Sudan (Almobarak et al., 2018).\n\nIn fact, T2DM and CVD share several risk factors, such as obesity, hypertension, hyperglycemia, insulin resistance, serum lipid and lipoprotein abnormalities, which are defined mostly by high serum triglycerides and low levels of high-density lipoprotein (HDL) cholesterol (Rosa et al., 2018; Vepsäläinen, 2013) Hypertension in people with diabetes increases the risk of peripheral arterial disease, as well as dyslipidaemia, which is a significant risk factor for developing macrovascular complications in diabetic patients and contributes to an increased risk of coronary heart disease (World Health Organization, 2006; Chokshi et al., 2013). Diabetes, hypertension, and obesity or being overweight all raise the risk of cardiovascular problems and other morbidities (Brown et al., 2000). Insulin resistance, on the other hand, has been linked to a two to five-fold increase in CVD mortality and is a mixture of multiple cardiometabolic risk factors such as obesity, poor glucose metabolism, hypertension, and dyslipidemia. It is also a risk factor for type 2 diabetes (Vepsäläinen, 2013). A recent study in Sudan found that low HDL is a common trait in two-thirds of diabetics, whereas high cholesterol and triglycerides were found in more than a quarter (Awadalla et al., 2018).\n\nThe evaluation of these lipid pathways and insulin resistance in Sudanese diabetes, in addition to the recurrent lipid profile study, may be an important cooperative step in the prediction of CVD since these atherogenic impacts may be mitigated by lifestyle changes. As a result, the purpose of this study was to evaluate the plasma levels of glucose, HbA1c, insulin, and lipid profile in Sudanese patients with T2DM.\n\n\nMethods\n\nThis analytical case control study was approved by the Clinical Chemistry Department and the Research Committee of the College of Medical Laboratory Science at Sudan University of Science and Technology, ethical approval No (DSR – IEC – 02 – 1 – 2020), a written informed consent was taken from all participants in the study for data collection and publication. Between March 2020 and August 2021, the research was conducted in the Zenam Diabetic Center and Sudan Cardic Center at Khartoum Siate. The case group consisted of 165 Sudanese patients with diabetes type 2 and a cardiovascular condition who were diagnosed by physicians, whereas the control group consisted of 165 diabetic type 2 volunteers who did not have a cardiovascular problem (the sample size was calculated by using sample size Formula n = p = the proportion to the target population. q = 1-p z = the standard normal deviation, usually set at 1.96, which correspond to the level 95% confidence level, d = degree of accuracy desired, set at 0.05). Patients with renal, liver, or thyroid disease, as well as those who smoked, drank, or had hepatitis A, B, or C, were excluded from the study as all that conditions may affect the levels of tested parameters. The case and control groups were age matched, ranging from 30 to 100 years old. The demographic data was acquired via a questionnaire after all participants gave their informed permission. The heights and weights of all the participants were measured. The BMI was computed by dividing the weight (kg) by the square of the height (m2) as proposed by Romero et al. (2012). Only one sample was obtained from each participant by using conventional vein puncture procedure, accordingly; 3 ml of blood was collected into a heparin container, spun at 3000 rpm for 3 minutes, and plasma was recovered and kept at -20°C until evaluated.\n\nThe concentrations of plasma glucose, HbA1c, and lipid profiles were determined using a Mindray BS-480 auto-chemistry analyzer, whereas insulin levels were determined using a Cobase 411 auto analyzer as proposed by Annani-Akollor et al. (2019). To ensure the accuracy and precision of the results, a level of control and calibrator given by the manufacturer in the reagent kit was evaluated using a sample run on a Mindary BS 480 auto analyzer.\n\nThe information gathered was analyzed with the use of a computer application called statistical packages for social science (SPSS version 21). The results were reported as percentages with a mean and standard deviation; No data were missed. To compare means in groups and subgroups; the ANOVA test was employed, and Pearson's correlation test was utilized to establish the relationship between study variables. Statistical significance was defined as a p-value of less than 0.05.\n\n\nResults\n\nIn this study, 330 people were included, with 165 diabetes type 2 patients with cardiovascular disease as the case group and 165 diabetic type 2 patients without cardiovascular disease as the control group. The findings revealed that 11.5% aged 30 to 49 years, 59.4% of patients aged 50 to 69 years, and 29.1% of patients aged 70 to 100 years were in the 30 to 49 age group, 59.4% of patients aged 50 to 69 years, and 29.1% of patients aged 70 to 100 years. Females accounted for 50.9% of the total, while men accounted for 49.1%. Duration of DM (33.3%) ranges from one month to seven years, (38.2%) from eight to fifteen years, and (28.5%) from sixteen to twenty-five years (More than 15 years). HTN lasted 24.2% (from 1 month to 7 years), 17.6% of the time (8-15 years), 16.4% of the time (more than 15 years), and 41.8% of the time there was no HTN. When comparing diabetics with cardiovascular disease to diabetics without cardiovascular disease, there was a substantial rise in BMI (29.4 5.3 kg/m2, p value = 0.001) as in Table 1.\n\nThe biochemical differences between people with and without cardiovascular disease shown in Table 2, there were significant increases in FBG, HBA1c, TG, HDL-c, and insulin between the two groups with p values 0.05, but no significant statistical difference in TC and LDL-c with p values > 0.05. (2).\n\nAs shown in Table 3, females had a significantly higher BMI, TC, LDL-C, and HDL-C than males, but FBG, HBA1c, TG, and insulin levels were not significantly different.\n\nThe results indicated that HBA1candinsulin had a significant positive association with age, whereas LDL-c had a significant negative correlation with age. FBS, TC, TG, and HDL-c had no correlation with age. FBS, HBA1c, TC, TG, HDL-c, LDL-c, insulin, and BMI had no link, but there was a substantial positive correlation between FBS, HBA1c, and insulin and diabetes duration. As shown in Table 4, there was a strong negative association between TC, HDL-c, and LDL-c and diabetes duration, but no link between TG, insulin, and diabetes length.\n\n\nDiscussion\n\nThe overall features of research participants revealed that patients aged 50-69 years old had the largest proportion of diabetics with cardiovascular disease. This finding was also obtained by Wu et al. (2015) who stated that the prevalence was greater among people aged 50 and older, as well as Teo and Dokainish (2017) reported that, the prevalence of CVD increased with age. Females had a larger prevalence of diabetic patients with cardiovascular complications (50.9%) than men (49.1 percent), this conclusion is similar to that of Teo and Dokainish (2017), which revealed a greater frequency of CVD in females.\n\nThe frequency of diabetic complications was much greater in individuals who had diabetes for a longer period of time. These findings are consistent with the findings of the Alam et al. (2021), which stated that long-term exposure to diabetes causes several diabetic problems. Furthermore, Rana et al. (2016) stated that patients with diabetes for more than ten years should be regarded to have a higher risk of cardiovascular disease.\n\nThis study found a significant difference in mean BMI, FBG, HBA1c, triglycerides, and insulin hormones between the two groups (P values 0.000, 0.001, 0.000, 0.015, and 0.000, respectively), as well as a significant decrease in mean HDL-C (P value 0.018), while there was no significant statistical difference in total cholesterol and LDL-C (P value > 0.05). Patients with T2DM at the LDL-C goal are nevertheless at a considerable risk of CVD events, according to a research by Timón et al. (2014) reported that, this residual risk is linked to a number of variables, including an increase in TG-rich proteins, a drop in HDL-C, and generalized obesity as measured by the body mass index (BMI), which is linked to a number of CVD risk factors and cardiovascular risk in T2DM patients.\n\nThis study found a significant increase in mean BMI, total cholesterol, HDL-C, and LDL-C in diabetic females when compared to diabetic males with a p value of 0.000. This finding is in line with another study that found: The prevalence of overweight in men and women varies depending on the country's level of development; higher BMI is more prevalent in men than women in high-income countries, whereas in low and middle-income countries, particularly in Arab countries, found a significant increase in mean BMI, total cholesterol, HDL-C, and LDL-C in women than men (Aderibigbe et al., 2018).\n\nWith a p value of > 0.05, there is no statistically significant difference in FBG, HBA1c, triglycerides, or insulin hormones. This finding is comparable to that of Moor et al. (2017) who found that mean total cholesterol and LDL-C levels were greater in women than in men, with a statistically significant difference, whereas HDL-C and triglycerides were not. This finding is also in line with that of Bertoluci and Rocha (2017) who found that women with diabetes had a greater chance of dying from cardiovascular causes than men.\n\nOur research found a substantial positive link between HBA1c, insulin hormone levels, and diabetes patients' age (r = 0.115, p-value = 0.037, r = 0.122, p-value = 0.027). This result was verified by Huang et al. (2021) who found that there was a positive association between HBA1c level and age (Huang et al., 2021).\n\nAlthough there was a significant negative association between LDL-C and age (r = -0.123, p = 0.026), there was no correlation between study parameters and BMI in this research. A significant positive correlation was also found between FBs, HBA1c level, and Duration of DM (r = 0.155, p-value = 0.005, r = 0.160, p-value = 0.004), as well as a significant negative correlation between total cholesterol, HDL-C, LDL-C, and Duration of DM (r = -0.152, p-value = 0.006, r = - 0.145, p-value = 0.040, r = -0.113, p = 0.040. This result is similar to another result from a study carried out by Priya and Begum (2020), which found a substantial positive link between HBA1c, total cholesterol, LDL-C, and duration of diabetes, but a significant negative correlation between HDL-C and duration of diabetes (Priya and Begum, 2020).\n\nThe samples were collected from two centers in Khartoum state.\n\n\nData availability\n\nFigshare. Salsabil. DOI: https://doi.org/10.6084/m9.figshare.19375664.v2 (AbdAlla et al., 2022)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).", "appendix": "References\n\nAbdAlla A, Abdallah SI: Salsabil data. figshare. Dataset. 2022. Publisher Full Text\n\nAderibigbe MA, Obafemi TO, Olaleye MT, et al.: Affects of Genser, Age and Treatment Duration on Lipid Profile and Renal Function Indices in Diabetic Pateins Attending a Teaching Hospital in South Westren Nigeria. Afri. Health Sci. 2018; 18(4): 900–908. PubMed Abstract \| Publisher Full Text\n\nAlam S, Hasan MK, Neaz S, et al.: Diabetes Mellitus: Insights from Epidemiology, Biochemistry, Rish Factors, Diagnosis, Complications and Comprehensive Management. Diabetology. 2021; 2: 36–50. Publisher Full Text\n\nAlmobarak A, Awadalla H, Osman M, et al.: Prevelance and Predictive Factors for Heart Failure among Sudanese Individuals with Diabetes: Population Based Survey. J. Public. Health Emerg. 2018; 2(5). Publisher Full Text\n\nAnnani-Akollor ME, Laing EF, Osei H, et al.: Prevalence of metabolic syndrome and the comparison of fasting plasma glucose and HbA1c as the glycemic criterion for MetS definition in non-diabetic population in Ghana. Diabetol. Metab. Syndr. 2019; 11: 26. Publisher Full Text\n\nAnon: Sex difference in cardiovascular risk factors and disease prevention.2015; 241(1): 211–218. Publisher Full Text\n\nAwadalla H, Noor SK, Elmadhoun WM, et al.: Comparison of serum lipid profile in type 2 diabetes with and without adequate diabetes control in Sudanese population in north of Sudan. Diabetes Metab. Syndrome. 2018; 12(6): 961–964. PubMed Abstract \| Publisher Full Text\n\nBertoluci M, Rocha V: Cardiovascular risk assessment in patients with diabetes. Diabetol. Metab. Syndr 2017; 9(25): 25. PubMed Abstract \| Publisher Full Text\n\nBrown CD, Higgins D, Donato KA, et al.: Body mass index and the prevakence of hypertension and dyslipidemia. Obes. Res. 2000; 8(9): 605–619.\n\nChen Y, Zhao X, Wu H: Metabolic Stress and Cardiovasculer Diease in Diabetes Mellitus; American Heart Associaition. Arterioscler. Thromb. Vasc. Biol. 2019; 39: 1911–1924. Publisher Full Text\n\nChokshi NP, Grossman E, Messerli FH: Blood pressure and diabetes: vicious twins. Heart. 2013 Apr; 99(8): 577–585.\n\nHuang S, Huang P, Li J, et al.: Hemoglobin A1c Levels Associated with Age and Gender in Taiwanese Adults without Prior Diagnosis with Diabetes. Int. J. Environs. Res. Public Health 2021. 2021; 18: 3390. PubMed Abstract \| Publisher Full Text\n\nMoor V, Amougou S, Ombotto S, et al.: Dyslipidemia in Patients with a Cardiovascular Risk and Disease at the University Teaching Hospital of Yaoundé, Cameroon. J. Vasc. Med. 2017; 2017: 1–5. PubMed Abstract \| Publisher Full Text\n\nPriya S, Begum N: Correlation of Lipid Profile with Duration of Diabetes and HBA1c Levels in Type 2 Diabetes Mellitus Patients: A Descriptive Cross-sectional Study. SBVJ journal of Basic, Clinical and Applied Health Science. 2020; 3: 19–22. Publisher Full Text\n\nRana JS, Liu JY, Moffet HH, et al.: Diabetes and prior coronary heart disease are not necessarily risk equivalent for future coronary heart disease events. J. Gen. Internal Med. 2016; 31(4): 387–393. PubMed Abstract \| Publisher Full Text\n\nRomero M, Flores R, Molina R, et al.: The body mass index (BMI) as a public health tool to predict metabolic syndrome. Open J. Prev. Med. 2012; 2(1): 59–66. Publisher Full Text\n\nRosas S, Arcidianon B, Chiefari E, et al.: Type 2 Diabetes Mellitus and Cardiovascular Disease: Genetic and Epigenetic Links. Front. Endocrinol. 2018; Publisher Full Text\n\nShi Y, Hu FB: The global implications of diabetes and cancer. Lancet. 2014; 383: 1947–1948. Publisher Full Text\n\nShi Y, Vanhoutte PM: Macro- and microvascular endothelial dysfunction in diabetes. J. Diabetes. 2017; 9: 434–449. Publisher Full Text\n\nTeo K, Dokainish H: The Emerging Epidemic of Cardiovasculer Risk Factor and Atherosclerotic Disease in Developing Countries. Can. J. Cardiol. 2017; 33: 358–365. PubMed Abstract \| Publisher Full Text\n\nTimón I, Collantes C, Galindo A, et al.: Type 2 diabetes and cardiovascular disease: Have all risk factors the same strength: World. J. Diabetes. 2014; 5(4): 444–470. PubMed Abstract \| Publisher Full Text\n\nVepsäläinen T: Factors Predicting Mortality in Type 2 Diabetes; TurunYliopistonJulkaisujaAnnalesUniversitatisTurkuensisSarjaser. DOSATOM. 2013; 1086. MEDICA ODONTOLOGICA.\n\nWorld Health Organisation: Preventing chronic diseases, a vital investment. A WHO Global Report.Geneva: 2006.\n\nWu F, Guo Y, Chatterji S, et al.: Common risk Factor for Chronic non communicable Diseases among Older adult in China, Ghana, Mexico, India, Russia and South Africa. The study on global Ageing and adult health (SAGE) Wave 1BMC public Health; 2015. Publisher Full Text\n\nYang C, Kelaini S, Caines R, et al.: RBPs Play Important Roles in Vascular Endothelial Dysfunction Under Diabetic Conditions, article. Front. Physiol. 2018; 9: 20 September 2018. PubMed Abstract \| Publisher Full Text" }	[ { "id": "172786", "date": "23 May 2023", "name": "Diarmuid Smith", "expertise": [ "Reviewer Expertise Clinical diabetes 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\nThank you for asking me to review this article on cardiovascular disease in Sudanese patients with Type 2 diabetes.\nThe article was interesting and describes CV risk in a Sudanese population with T2DM which I think would be interesting for your readers.\nHowever there are a number of issues with the paper.\nMajor Issues\n\nThe writing needs to be improved throughout the paper and there were a few paragraphs in which I could not understand what the author was trying to say for example page 3 paragraph 3 needs to be rewritten; page 3 the first paragraph of the results section needs to be rewritten as the results are not clear in this paragraph.\n\nThroughout the manuscript the term diabetic with cardiovascular disease or diabetic needs to be changed to Type 2 diabetes with cardiovascular disease or Type 2 diabetes without cardiovascular disease\n\nThe paper would have been strengthened by having a non-diabetic control group with cardiovascular disease to see what the differences were in relation to BMI. lipids etc in those with and without diabetes\n\nThe data was collected in 2 centres in Khartoum. Were the lab tests done in the one lab or 2 separate labs and what was CV for the Aic assay and other assays? please comment\n\nThe authors ethical approval for the study was not obtained, please explain.\n\nHow was cardiovascular disease defined?\n\nWhy was smoking excluded?\n\nWas there a difference in medication type between with and without cardiovascular disease particularly in relation to statin therapy and hypoglycaemic agents\n\nCould the authors comment in the discussion section on why they thought the A1c was higher in those with CV disease compared to those without?\n\nThe term insulin hormone levels should be replaced with the term serum insulin levels.\nI would be grateful if there manuscript could be rewritten to improve the content, understanding, results and discussion section of the paper.\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": "179450", "date": "20 Jun 2023", "name": "Jalal Taneera", "expertise": [ "Reviewer Expertise Diabetes 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\nIn this study, the authors assessed the plasma levels of glucose, HbA1c, insulin, and lipid profile in Sudanese T2DM patients. A case-control design was used, including 165 T2DM patients with cardiovascular conditions as cases and 165 T2DM patients without cardiovascular disorders as controls. Results showed a notable increase in BMI, fasting blood glucose (FBG), HbA1c, HDL cholesterol (HDL-C), and insulin in people with diabetes with cardiovascular disease. Females had higher TC, LDL-C, HDL-C, and BMI levels than males. Positive correlations were observed between FBS, HbA1c, insulin, and illness duration. These findings provide valuable insights into metabolic profiles and cardiovascular implications in Sudanese T2DM patients. The study is a straightforward investigation that can be improved by adding extra data (see comments below).\nMajor Issues:\nThe study will benefit from some English improvement.\nIt was unclear in the study what was the criteria for cardiovascular complications .. author is requested to define such important issues.\nFamily history of cardiovascular complications should be addressed in the T2DM patients with cardiovascular conditions group.\nIt would be great if the authors showed the types of drugs described for these patients and subsequently dragged some data (if possible) if certain anti-diabetic drugs protect against cardiovascular complications compared to others. What are the clinical implications for the data? I failed to see any implications in the discussion.\nPlease expand more on the study limitations.\nOther issues:\nHBA1c should be HbA1c.\nDefine what is HTN.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/11-472
https://f1000research.com/articles/13-1148/v1	07 Oct 24	{ "type": "Case Report", "title": "Case Report: A rare case of septic pulmonary embolism from a focus of soft tissue infection: A case report", "authors": [ "Abenezer Dagnachew Abebe", "Atiklet Zerihun Zewdie", "Mihret Kebede Adugna", "Henok Bahru Wodajeneh", "Muluken Alemayehu Workiye", "Eyerusalem Yalew Talemma", "Eyosias Lemma Teshome", "Ashenafi Tesfaye Bedada", "Ayanaw Guadie Mamo", "Frewoyni Gedey Gebregziahber", "Mihret Kebede Adugna", "Henok Bahru Wodajeneh", "Muluken Alemayehu Workiye", "Eyerusalem Yalew Talemma", "Eyosias Lemma Teshome", "Ashenafi Tesfaye Bedada", "Ayanaw Guadie Mamo", "Frewoyni Gedey Gebregziahber" ], "abstract": "This is a case of septic pulmonary embolism in a patient presented with a right foot ulcer as foci of infection. A Septic Pulmonary embolism is a thromboembolic event in which case an infected thrombus from an infectious focus; distal to the lung vasculature travels through the lung and results in occlusive, inflammatory and infectious insult to the lung. Clinically it may present as mild respiratory symptoms such as cough, fever or more severe symptoms such as shortness of breath (SOB), hemoptysis, pleuritic chest pain or difficulty breathing1; on computed tomography (CT) imaging, cavitary or non-cavitary peripheral nodules with or without feeding vessel, consolidation and Pleural effusion are prominent findings.2 In this case report, we present a rare case of septic pulmonary emboli from a foci of soft tissue infection.", "keywords": [ "Septic pulmonary embolism (SPE)", "Infectious foci", "Computed Tomography (CT)", "Soft tissue infection" ], "content": "Introduction\n\nSeptic Pulmonary embolism (SPE) is characterized by a thromboembolic event wherein an infected thrombus originating from an infectious focus distal to the lung vasculature migrates through the lung, leading to occlusive, inflammatory, and infectious damage to the lung. The clinical manifestation of this condition can range from a gradual onset of symptoms such as fever and respiratory manifestations including cough, dyspnea, hemoptysis, and pleuritic chest pain to a sudden sepsis syndrome.1 Previously, SPE was linked to right-sided infective endocarditis in intravenous drug users,2 postpartum septic thrombophlebitis, and Lemierre’s syndrome.3,4 However, in recent years, there has been a shift in the epidemiology, highlighting the significance of infected vascular catheters, implantable devices,5 and more recently, septic thrombophlebitis due to contiguous deep soft tissue or bone infection of the extremities.6 The diagnostic challenge of pulmonary embolism arises from the non-specific nature of clinical and laboratory data. Presently, computed tomography stands out as the most dependable imaging modality for characterizing chest findings in patients with SPE.7,8 Therefore, clinicians should maintain a high level of suspicion when encountering a patient with an extrapulmonary site of infection who presents with respiratory symptoms. Early clinical identification and prompt administration of broad-spectrum antibiotics significantly enhance the patient’s prognosis.1 Here, we describe a case of septic pulmonary emboli in a patient with a right foot ulcer serving as the focal point of infection.\n\n\nCase presentation\n\nA female patient aged 55 years presented at Sheno primary hospital, Oromia, Ethiopia, exhibiting symptoms such as high-grade persistent fever, shortness of breath, productive cough with blood-tinged sputum, and right-sided pleuritic chest pain lasting for 2 weeks. She had previously visited a private hospital nearby where she received unspecified oral antibiotics without experiencing any relief from her symptoms. Additional information revealed that she was also dealing with swelling and ulceration on her right foot, accompanied by purulent discharge from the big toe for the past 3 weeks, a condition for which she had not sought medical attention. Her medical history did not indicate any presence of diabetes or hypertension, nor did it include any contact with individuals suffering from chronic cough or tuberculosis. Upon physical examination, the patient displayed signs of respiratory distress, with a respiratory rate of 32 breaths/min, a pulse rate of 104/min, an axillary temperature of 38.9°C, and an oxygen saturation of 82% with room air. Furthermore, edema was observed in her right foot (non-pitting edema) along with an ulcer on the big toe oozing purulent discharge. Laboratory tests conducted on the same day of presentation showed a total white blood cell count of 24,220/μL with 93.8% granulocytes, a platelet count of 487,000 μL, and normal values for other complete blood count (CBC) parameters. Elevated levels of acute inflammatory markers were also detected, with a C-reactive protein (CRP) level of 179.6 mg/L, Highly-sensitive CRP (HsCRP) greater than 5mg/L, and an Erythrocyte Sedimentation Rate (ESR) of 70 mm/hr. Comprehensive metabolic panel and Organ function tests yielded normal results, ruling out the presence of tuberculosis. Additionally, tests for VDRL, hepatitis B and C viral markers, as well as HIV, all returned negative results. The coagulation profile showed no abnormalities, with values of 12.4 sec for PT, 1.02 sec for INR, and 36.7 sec for APTT. Urinalysis results were also normal, indicating no signs of urinary tract infection.\n\nImaging revealed an unremarkable ultrasound of the abdomen and pelvis, except for right lower lobe consolidation on the lung. Both arterial and venous doppler study of the right extremity exhibited normal findings, with the exception of right leg subcutaneous edema. The Trans-thoracic Echocardiography demonstrated normal results, showing no structural abnormalities or vegetations on the valves. A Chest CT scan with contrast identified multiple peripheral irregular nodules, some with cavitation and a typical feeding vessel sign. Additionally, right-sided pleural effusion and right basal consolidation were observed. Following the comprehensive clinical, laboratory, and imaging assessments, the patient was diagnosed with Septic pulmonary emboli secondary to soft tissue infection. The treatment regimen included Ceftriaxone 1 gm IV BID, Vancomycin 1 gm IV BID, as well as supportive oxygen therapy with 1L of INO2 via nasal prong. Furthermore, wound debridement and twice daily wound care initiation took place, leading to the patient’s admission to the Inpatient department for close monitoring. Subsequent follow-ups indicated a favorable progression in the patient’s condition, ultimately resulting in complete recovery. The patient was discharged from the hospital on the 14th day of admission without any relapses during the follow-up period.\n\n\nDiscussion\n\nIn previous times, Septic Pulmonary emboli were predominantly linked with Lemierre’s syndrome,4 post-partum septic pelvic thrombophlebitis,3and right-sided infective endocarditis in IV drug users.2 However, in the recent decade, there has been a shift in focus towards changes in the epidemiology, notably the significance of infected vascular catheters and implantable devices9 and more recently septic thrombophlebitis arising from contiguous deep soft tissue or bone infection of the extremities.6 Consequently, an escalating number of patients are exhibiting symptoms stemming from an extrapulmonary origin of infection, diverging from the traditional presentation documented in earlier literature. In our case study, we also describe a patient with soft tissue infection of the right foot as the focal point of infection as illustrated in Figure 1A with Sonographic features of cellulitis in Figure 1B indicating the rising occurrence of soft tissue as a primary site of infection.\n\nIn a retrospective study conducted from January 2000 to January 2013 at Hennepin County Medical and an urban teaching hospital in Minneapolis, Minnesota, USA, 40 patients were studied with septic pulmonary embolism. The median age of the patients was 46 years, with common presenting symptoms including febrile illness (85%) and pulmonary complaints (66%), such as pleuritic chest pain (22%), cough (19%), and dyspnea (15%). The sources of infection varied, with skin and soft tissue infection accounting for 44%, infective endocarditis for 27%, and infected peripheral deep venous thrombosis for 17%. A majority of cases (85%) were bacteremic with Staphylococcus aureus.1 This study featured a 55-year-old female patient who exhibited high-grade fever, productive cough with blood-tinged sputum, dyspnea, right-sided pleuritic chest pain, and a focus of infection in the right foot and big toe ulcer. As observed by Umesh Goswami et al., skin and soft tissue infection was the most common source of infection (44%), consistent with this case report. While Staphylococcus aureus was the causative organism in the referenced study, blood culture was not performed in the current case due to prior antibiotic exposure and test unavailability. However, many studies identify Staphylococcus aureus as an etiological agent.\n\nIn a retrospective analysis of patients with septic pulmonary emboli admitted between January 2007 and June 2018 at the Department of Respiratory and Critical Care Medicine, Hospital of Guangxi Medical University, China, Staphylococcus aureus was the predominant pathogen found in blood cultures (30.3%).10 Similarly, in a recent retrospective study conducted from January 1, 2018 to December 22, 2020 at Mogadishu Somali Turkey Education and Research Hospital, Somalia, Staphylococcus aureus was the most prevalent pathogen, accounting for approximately 52.6% of cases.11\n\nThe pathogenesis of septic pulmonary emboli arising from soft tissue infections involves the extravasation or translocation of bacteria from the extrapulmonary site into the systemic venous circulation.9 Subsequently, these bacteria can directly cause damage through toxins12 and indirectly through inflammatory mediators,13 occasionally leading to local thrombosis14 that facilitates bacterial growth. The embolization of these bacteria-containing thrombi to the pulmonary circulation can result in metastatic parenchymal lung infections, characterized by radiologic changes typical of septic pulmonary embolism, including cavitary and non-cavitary nodules, micro lung abscesses, consolidation, and pleural effusion. The diagnosis of septic pulmonary emboli presents challenges to clinicians due to nonspecific clinical and laboratory findings. Suspicions of SPE should arise in febrile bacteremic patients with an identified extrapulmonary source of infection who develop secondary pulmonary symptoms like pleuritic chest pain, dyspnea, and cough.1 With an elevated leukocyte count and increased acute inflammatory markers along with supportive chest findings on physical examination, it is advisable for the patient to undergo chest CT with contrast, which is often the preferred imaging modality in various research studies. Although not pathognomonic, the presence of bilateral wedge-shaped opacity, bilateral cavitary or non-cavitary nodules with a feeding vessel sign is highly indicative of septic pulmonary emboli. A retrospective analysis carried out at Surat Government Medical College in Gujarat, India, between 2018 and 2019 involved the study of chest CT scans from 10 patients. The findings revealed that 9 patients (90%) exhibited the classical feeding vessel sign, 8 patients (80%) displayed bilateral involvement, 7 patients (70%) presented with nodular cavitary and non-cavitary lesions, 2 patients (20%) showed pleural effusion, and 3 patients exhibited wedge opacities, while 6 patients (60%) displayed patchy ground glass opacity and consolidation.8 Another retrospective study conducted at Mogadishu, Somali Turkey Education and Research Hospital in Somalia involved chest CT scans of 19 patients. The results indicated that bilateral opacities were the most prevalent radiographic lesion type, observed in all patients (100%), followed by nodular (73.9%), cavitation (57.9%), consolidation (47.4%), non-nodular (26.3%), pleural effusion (26.3%), and feeding vessel sign (15.8%).11 In our case, the chest CT findings revealed multiple irregular peripheral nodules, some of which exhibited cavitations and demonstrated the typical feeding vessel sign, in addition to right-sided pleural effusion and right basal consolidation, as depicted in Figure 2A to D aligning with findings from numerous studies.\n\nTreatment of septic pulmonary embolism should be commenced promptly in the early stages of the disease course and ought to encompass cause-specific interventions like wound debridement, abscess drainage, valve and catheter replacement, and other similar procedures. Identification of the microbiologic origin through blood, sputum, and pleural fluid cultures, along with deep soft tissue, bone, and explanted device cultures15 when applicable, is crucial for tailoring culture-specific antibiotic therapy. The initiation of empiric antibiotic treatment early on may constrain the microbiologic diagnosis.16 Staphylococcus aureus, notably Methicillin Susceptible Staphylococcus Aureus, remains the predominant pathogen in various research findings, aligning with the frequent occurrence of skin and soft tissue infections as the initial extrapulmonary source. Immediate commencement of empiric antibiotic therapy, starting with Staphylococcus aureus coverage and broad-spectrum antibiotics supplementation, is recommended. Subsequent adjustments to the antibiotic regimen based on culture outcomes should be made, continuing treatment for a minimum duration of 2-6 weeks. Treatment duration should be guided by clinical progress, follow-up culture results, inflammatory markers, and imaging studies. In our case report, blood culture was forgone due to the patient’s prior exposure to antibiotics and the unavailability of the test in our facility. Therapy was initiated with vancomycin 1gm IV BID and Ceftriaxone 1gm IV BID, considering coverage for Staphylococcus and broad-spectrum antibiotic inclusion. This approach yielded favorable outcomes in our patient, as evidenced by clinical amelioration, reduction in white blood cell count and acute inflammatory markers, and resolution of chest abnormalities in subsequent follow-up assessments.\n\n\nConclusion\n\nSeptic pulmonary embolism is an infrequent clinical entity with a serious prognosis if not promptly identified and managed. A heightened level of suspicion in individuals with infections outside the lungs who present with respiratory symptoms aids in the recognition of this condition. Utilization of chest CT is widely endorsed for imaging in septic pulmonary embolism, revealing distinct features like the feeding vessel sign. The primary treatment involves early administration of intravenous antibiotics and targeted therapies tailored to the specific cause, including procedures like abscess drainage, wound cleansing, and removal of infected medical devices. While it is preferable to tailor antibiotic therapy based on culture results, initiation of empirical antibiotic treatment should not be delayed as numerous studies have identified the predominance of staphylococcus aureus isolation. Therefore, selecting the appropriate antibiotics in light of this particular pathogen is crucial for effectively managing these patients.\n\n\nEthical approval\n\nAccording to the review board policy of our institution, ethical approval was obtained from the hospital ethics review committee for this case report and the images that go with it, the Patient’s written informed consent was also obtained for publishing this case as well as on usage of the images that go with it.", "appendix": "Acknowledgment\n\nWe express our gratitude to the patient and her family for supplying all pertinent details, and also to the healthcare providers involved in the management of this patient.\n\n\nReferences\n\nGoswami U, Brenes JA, Punjabi GV, et al.: Associations and Outcomes of Septic Pulmonary Embolism. Open Respir. Med. J. 2014; 8(1): 28–33. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMacMillan JC, Milstein SH, Samson PC: Clinical spectrum of septic pulmonary embolism and infarction. J. Thorac. Cardiovasc. Surg. 1978; 75(5): 670–678. PubMed Abstract \| Publisher Full Text\n\nGorenstein A, Gross E, Houri S, et al.: The pivotal role of deep vein thrombophlebitis in the development of acute disseminated staphylococcal disease in children. Pediatrics. 2000; 106(6): E87. PubMed Abstract \| Publisher Full Text\n\nGoldenberg NA, Knapp-Clevenger R, Hays T, et al.: Lemierre’s and Lemierre’s-like syndromes in children: survival and thromboembolic outcomes. Pediatrics. 2005; 116(4): e543–e548. PubMed Abstract \| Publisher Full Text\n\nCook RJ, Ashton RW, Aughenbaugh GL, et al.: Septic pulmonary embolism: presenting features and clinical course of 14 patients. Chest. 2005; 128(1): 162–166. Publisher Full Text\n\nBrenes JA, Goswami U, Williams DN: The association of septic thrombophlebitis with septic pulmonary embolism in adults. Open Respir. Med. J. 2012; 6: 14–19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNaidich DP, Lubatt Roger Schinella E, Garay SM: Septic Pulmonary Emboli: CT-Radiographic Correlation L: Dorothy I. McCaule?\n\nShah T, Priyanka H, Desai P: A Study of Radiological Appearances of Septic Pulmonary Embolism in Contrast Enhanced Computed Tomography Thorax. Int. J. Contemp. Med. Res [IJCMR]. 2020; 7(2): 1–4. Publisher Full Text\n\nNaber CK: Staphylococcus aureus bacteremia: epidemiology, pathophysiology, and management strategies. Clin. Infect. Dis. 2009; 48 Suppl 4: S231–S237. PubMed Abstract \| Publisher Full Text\n\nJiang J, Li LQ, Hua LL, et al.: Septic pulmonary embolism in China: Clinical features and analysis of prognostic factors for mortality in 98 cases. BMC Infect. Dis. 2019; 19(1): 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMohamud MFY, Mukhtar MS: Presenting Clinicoradiological Features, Microbiological Spectrum and Outcomes Among Patients with Septic Pulmonary Embolism: A Three-Year Retrospective Observational Study. Int. J. Gen. Med. 2022; 15: 5223–5235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoyle-Vavra S, Daum RS: Community-acquired methicillin-resistant Staphylococcus aureus: the role of Panton-Valentine leukocidin. Lab. Investig. 2007; 87(1): 3–9. Publisher Full Text\n\nHolm K, Frick IM, Björck L, et al.: Activation of the contact system at the surface of Fusobacterium necrophorum represents a possible virulence mechanism in Lemièrre’s syndrome. Infect. Immun. 2011; 79(8): 3284–3290. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGonzalez BE, Teruya J, Mahoney DHJ, et al.: Venous thrombosis associated with staphylococcal osteomyelitis in children. Pediatrics. 2006; 117(5): 1673–1679. Publisher Full Text\n\nRomano L, Spanu T, Calista F, et al.: Tsukamurella tyrosinosolvens and Rhizobium radiobacter sepsis presenting with septic pulmonary emboli. Clin. Microbiol. Infect. 2011; 17(7): 1049–1052. PubMed Abstract \| Publisher Full Text\n\nGrace CJ, Lieberman J, Pierce K, et al.: Usefulness of blood culture for hospitalized patients who are receiving antibiotic therapy. Clin. Infect. Dis. 2001; 32(11): 1651–1655. Publisher Full Text" }	[ { "id": "331978", "date": "25 Oct 2024", "name": "Ahmet Cemal Pazarlı", "expertise": [ "Reviewer Expertise Pulmonary infections", "İntertisiel Lung Diseases", "Sleep Apnea" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 article presents a rare case of septic pulmonary embolism (SPE) in a 55-year-old female patient with a soft tissue infection in her right foot. The patient exhibited typical symptoms of septic embolism, including chest pain, cough, hemoptysis, and fever. Diagnosis was confirmed by contrast-enhanced chest CT, which revealed peripheral nodules and cavitary lesions. The patient was treated with broad-spectrum antibiotics and wound care, leading to a full recovery.\n-The article adequately supports its clinical findings, and the diagnostic methods, particularly the imaging techniques, are applied appropriately. Although septic pulmonary embolism is a challenging diagnosis, the clinical findings, imaging results, and laboratory data are well-documented. The use of CT imaging to confirm the diagnosis is consistent with the literature.\nHowever, the absence of blood culture results is a notable limitation. The article explains that the patient had prior antibiotic exposure, which prevented the test, but this weakens the diagnostic confirmation. Suggestion: The authors could provide more explanation on how the lack of blood culture affects the diagnostic certainty and discuss potential alternatives.\n- The methods section is clear and provides a detailed description of the diagnostic and treatment process. The diagnostic approach, including the use of imaging and laboratory testing, is well-explained and replicable. Suggestion: It would be helpful to add a discussion on alternative diagnostic methods, especially in cases where blood culture cannot be performed.\n- The article is well-supported by clinical data, including imaging and laboratory findings. The provided CT scan images and laboratory results are consistent with the case presentation. The article adheres to F1000Research’s Open Data policy by making the relevant data available.\n\nDiagnostic Process: The absence of blood culture is a significant limitation, and the article would benefit from a discussion of how this impacts the overall diagnostic certainty. While the explanation provided (previous antibiotic exposure) is valid, more consideration of other diagnostic options is warranted Treatment Approach: The antibiotic treatment aligns with the literature and appears appropriate. However, additional information about how the antibiotic regimen was adjusted over time, as well as the criteria for treatment duration, would enhance the article.\n\nThis case report contributes to the literature by describing a rare case of septic pulmonary embolism secondary to soft tissue infection. The article is well-written, scientifically valid, and provides valuable insights for clinical practice. However, the lack of blood culture data and the absence of alternative diagnostic strategies should be addressed.\n\nThe article has academic merit, but some minor revisions are necessary to address the limitations mentioned above.\nI suggest a citation (Güleç M, et al., 2024 [Ref - 1]) Septic pulmonary embolism (SPE) can arise from various sources of infection, leading to diverse clinical presentations. While soft tissue infections are a rare cause of SPE, catheter-related infections are more commonly reported. In a case described (Ref - 1), a septic pulmonary embolism resulted from an infected hemodialysis catheter, highlighting the significant role that indwelling catheters and medical devices play as sources of infection in SPE cases\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "331977", "date": "31 Oct 2024", "name": "Luca Valerio", "expertise": [ "Reviewer Expertise Venous thromboembolism", "Pulmonary embolism", "Deep vein thrombosis", "Thrombophlebitis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Authors present a case of septic pulmonary embolism in a patient with a site of infection unusually associated with this pulmonary condition. The insidious presentation with mild respiratory symptoms, the important differential diagnosis of tuberculosis, and the finding of the unusual association of septic pulmonary emboli with an infection in the foot are reported. The Authors clearly emphasize as take-home message the need of a high index of suspicions of physicians treating patients with a specific pulmonary symptoms in the presence of soft tissue infections far from the lungs, and also put correctly the finding of the association with a non-pulmonary infection in the context of recent literature describing a possible epidemiologic shift in the association between non-pulmonary infectious foci and septic pulmonary emboli.\nThe article is generally well-written in all aspects: structure (the required section are in the required order and include the information necessary in each section), interpretation/conclusions (the peculiarities of the case and the learning point for clinicians are clearly identified), and quality/clarity of written English. I commend the Authors for clearly describing the timing of diagnostic tests, often unclear in case reports, and in particular the duration of symptoms and previous medication received in another institution, details that are often forgotten in case reports in the field of septic thrombophlebitis (most patients will have presented to either primary care or to an emergency department before the hospitalisation in which the diagnosis is made and where the case report originates). However, I have a number of suggestions to improve clarity, especially regarding the structure and conciseness of the Discussion and some information (namely, figures) that belong to the Case presentation, as well as recommendations to provide the reader with updated literature on the topic.\n\n1. Abstract: Rather than \"We describe a case of septic pulmonary embolism in a patient who presented with a right foot ulcer primary infection focus.\" 2. Abstract: In \"A Septic Pulmonary Embolism\", neither the article \"A\" nor the capital letters are necessary. Please also remove the capital \"P\" in \"Pleural effusion\" toward the end of the Abstract. 3. Abstract: I suggest correcting the sentence \"in which case an infected thrombus from an infectious focus; distal to the lung vasculature travels through the lung and results in occlusive, inflammatory and infectious insult to the lung\" into \"in which a septic thrombus from an infectious focus distal to the lung vasculature travels to the lung and results in occlusive and inflammatory pulmonary damage.\" 4. Abstract: \"such as cough, fever\" works better as \"cough with fever\", as the two symptoms usually co-exist in mild cases, and a comma is in appropriate for a list of only two elements. 5. Abstract: Acronyms should not be present. Please remove \"(SOB)\" and \"(CT)\". They should be introduced upon first occurrence in the main text of the article itself, not in the Abstract. 6. Abstract: I suggest that the Authors replace \"cavitary or non-cavitary\" with \"often cavitary\". \"Cavitary or non-cavitary\" is not informative, as it means that whether the nodule is cavitary is irrelevant. In contrast, what is known about the radiological appearance of SPEs is that they are often cavitary - meaning that the finding may be specific enough to support the diagnosis if it is present, but not sensitive enough as to rule out the diagnosis if it is absent. 7. Abstract: Please replace the last sentence, \"In this case report, we present a rare case of septic pulmonary emboli from a foci of soft tissue infection.\", which is an unnecessary repetition of the first sentence, with a conclusion specific to this case such as \"This case suggests that septic pulmonary embolism should be suspected even in patients with infections far from the pulmonary vasculature\". 8. Abstract: The Abstract should not include any references. Please remove references (1) and (2). References and abbreviations should only be included in the main text. 9. Introduction: \"migrates to the lung\" whould be correct, as \"migrates through the lung\" suggests that the thrombus may completely pass the lungs without affecting them. 10. Introduction and Discussion: Please write “Lemierre syndrome” without the genitive \"'s\" (possessive form). \"Lemierre syndrome\" is the most common name of the condition, the recommended standard for medical eponyms (see for instance [Ayesu K et al. 2018 (Ref - 3) doi: 10.5195/jmla.2018.284] and [Jana N et al. 2009 (Ref - 4) doi: 10.1186/1471-2288-9-18], and the main MeSH entry in the National Library of Medicine (https://www.ncbi.nlm.nih.gov/mesh/?term=Lemierre). 11. Introduction/Discussion: References (5), (6) and (9) are not recent (one is 20 years old, the other 13 years old, the last 15 years old) and all can be replaced, in the sentences in the Introduction and Discussion in which they are used, by the more recent review on the topic: [Valerio L et al. 2023 (Ref - 1) doi: 10.1055/s-0043-1760843]. The review provides a comprehensive reference for the sentence \"However, in recent years, there has been a shift in the epidemiology, highlighting the significance of infected vascular catheters, implantable devices, and more recently, septic thrombophlebitis due to contiguous deep soft tissue or bone infection of the extremities.\" 12. Case presentation: The AMA Manual of Style, 11th Edition, recommends that \"woman\" is used rather than \"female patient\" or \"female individual\" (with the exception of studies with sample sizes including both children and adults); AMA Manual of Style, paragraph 11.7, \"Whenever possible, a patient should be referred to as a man, woman, boy, girl, or infant.\". Therefore, please write \"A woman aged 55 years\" rather than \"A female patient aged 55 years\". 13. Case presentation: \"exhibiting symptoms such as\" can be written more concisely, and it wrongly suggests that the list of symptoms is non-exhaustive (it should be exhaustive: all relevant symptoms should be listed). Therefore, I suggest that it is replaced with simply \"with\". 14. Case presentation: the sentence \"Additional information revealed that\" is unclear. Who provided the additional information? The previous hospital? Maybe the Authors mean \"Upon repeated history taking, it emerged that...\" or simply \"In addition, ...\".\n\n15. Case presentation: the medical term for \"big toe\" is \"hallux\". Please correct upon all occurrences throughout the article. 16. Case presentation: More concise than \"Her medical history did not indicate any presence of diabetes or hypertension, nor did it include any contact with individuals suffering from chronic cough or tuberculosis.\" would be \"Her medical history did not include diabetes, hypertension, or any contact with individuals sufferings from chronic cough or tuberculosis\". 17. Case presentation: rather than writing \"edema was observed in her right foot (non-pitting edema)\" you could simply write \"non-pitting edema was observed in her right foot\". 18. Case presentation: it does not make sense to provide acronyms for terms that do not recur any longer in the rest of the article. For instance, there does not seem to be any reason for the acronyms \"CBC\", \"CRP\", \"hsCRP\", and \"ESR\" to be provided and they can be removed completely. 18. Case presentation: the sentence \"Comprehensive metabolic panel and Organ function tests yielded normal results, ruling out the presence of tuberculosis.\" should be clarified: it should be specified which tests exactly were conducted, as \"organ function tests\" is not a standard label for specific medical tests worldwide (in contrast with CBC, which means quite the same everywhere in the world). In addition, I do not believe that any organ function test is so sensitive for tuberculosis that it can rule out tuberculosis: one can have tuberculosis with perfectly normal \"organ functions\". I believe TB skin tests, sputum smear, adn culture are necessary (even though not perfectly sensitive). 19. Case presentation: please write out the meaning of \"VDRL\" rather than writing the abbreviation only. 20. Case presentation: \"Urinalysis results were also normal\" can be written more simply as \"Urinanalysis was also normal\". 21. Case presentation: \"Imaging revealed an unremarkable ultrasound of the abdomen and pelvis, except for right lower lobe consolidation on the lung.\" can be more succinctly written as \"Abdomen and pelvis ultrasound showed a pulmonary consolidation in the right lower lobe and was otherwise unremarkable\". 22. Case presentation: \"The Trans-thoracic Echocardiography\" could better be written as \"A transthoracic echocardiography\". 23. Case presentation: the finding of the transthoracic echoocardiography can be written more succinctly as \"A transthoracic echocardiography showed no structural abnormalities or valvular vegetations.\". 24. Case presentation: The findings of blood, sputum and wound cultures should be reported in very thorough details, and the choice of the antibiotics in the treatment regimen (Ceftriaxone, Vancomycin) should be chosen with care. Was it an empiric treatment? Was it recommended by microbiologists/infectious disease specialists, based on the coverage of which agents? In particular, specify whether, when, and with what results blood cultures and wound cultures of the right foot ulcers were conducted. This is extremely important in a case of infection. I read later that the discussion of blood cultures is contained in the Discussion in the sentence \"blood culture was not performed in the current case due to prior antibiotic exposure and test unavailability\", but this should be moved to the case presentation! 25. Case presentation: the sentence \"Furthermore, wound debridement and twice daily wound care initiation took place, \" could be better written as \"Furthermore, wound debridement was performed and wound care took place twice daily.\". 26. Case presentation: I believe that \"patient's admission to the Inpatient department\" simply means \"patient's admission into hospital\". By definition, an admission is always to an inpatient department (and an inpatient department or ward only includes patients that were admitted). 27. Case presentation: The sentence \"The patient was discharged from the hospital on the 14th day of admission without any relapses during the follow-up period.\" could probably be simply written as \"The patient was discharged from the hospital on the 14th day of admission.\". The second part, \"without any relapses during the follow-up period.\", is unclear: if it refers to the inpatient follow-up, then the sentence is unnecessary, because the previous sentence had already stated that the patient had complete recovery until discharge. If it refers to post-discharge follow-up, then this should be stated clearly, including when exactly and how many times the patient was seen after discharge. 28. Discussion: \"In previous times\" should be amended to \"Until recently\" or \"In the past\" or other similar expression. 29. Discussion: The reference currently numbered as (4), Goldenberg 2005 et al., is quite old and it only refers to children, while the case described here is an adult. The Authors may better replace it with a more recent sources on the topic, such as [Valerio L et al. 2020 (Ref - 2) doi: 10.1055/a-1177-5127]. 30. Discussion: rather than \"Consequently, an escalating number of patients are exhibiting symptoms stemming from an extrapulmonary origin of infection, diverging from the traditional presentation documented in earlier literature.\", I suggest \"Consequently, septic pulmonary emboli are increasingly found in patients with an extrapulmonary primary infection focus, diverging from the traditional presentation\". 31. Discussion: The figures 1A and 1B should be moved to the Case Presentation, and not shown first in the Discussion. 32. Discussion: There are some issues with the order of the information, the logics of the literature reviews, and the quantity of information. I suggest that the Discussion is reordered as follows: first, the pathogenesis and the diagnosis of SPE in general should be discussed, so that the discussion should start with the section from \"The pathogenesis of septic pulmonary emboli...\" up to \"aligning with findings from numerous studies\". However, this section should be adapted: the CT figures should be presented and mentioned first in the case presentation, and not in the Discussion for the first time.\n\nThen, the specific issue of the extrapulmonary sources of infection should be discussed. Now, the section from \"In previous times...\" to \"52.6% of cases\" should be included. However, this section should be amended as follows. In this section (again, from \"In a retrospective study...\" to \"52.6% of cases\"), several narrative reviews of previous studies are shown. However, in the Discussion of a case report, this should be done with a specific goal, which here is not clear. I assume the main idea is to show the distribution of primary infectious foci in other studies. If this is correct, please simplify \"pulmonary complaints (66%), such as pleuritic chest pain (22%), cough (19%), and dyspnea (15%).\" into \"diverse symptoms consistent with lower respiratory infection (66%)\". In the mention of the previous literature, please simplify the way the previous study is referenced: \"In a retrospective study conducted from January 2000 to January 2013 at Hennepin County Medical and an urban teaching hospital in Minneapolis, Minnesota, USA, \" can be simplified into \"In a retrospective study conducted from 2000 to 2013 in a teaching hospital in Minnesota, USA,\". Instead, the phrase \"As observed by Umesh Gswami et al.\" does not provide enough information - it is a retrospective study, a review, a meta-analysis? Please include this detail and the country rather than the name of the first Author.\nPlease simplify \"In a retrospective analysis of patients with septic pulmonary emboli admitted between January 2007 and June 2018 at the Department of Respiratory and Critical Care Medicine, Hospital of Guangxi Medical University, China,\" into \"In a single-center retrospective analysis of China including patients with septic pulmonary emboli admitted between 2007 and 2018,\", and \"Similarly, in a recent retrospective study conducted from January 1, 2018 to December 22, 2020 at Mogadishu Somali Turkey Education and Research Hospital, Somalia\" into \"Similarly, in a recent retrospective study conducted in Somalia on patients admitted from 2018 to 2020\". Please also discuss the recent review [Valerio L et al. 2023 (Ref - 1) doi: 10.1055/s-0043-1760843].\nFinally, the section on treatment, starting from \"Treatment of septic pulmonary embolism\" to \"subsequent follow-up assessment\" can remain as last, where it is now. This section is well-written and I only recommend one amendment: the Discussion should not repeat points already reported in the Case presentation. Therefore, the final sentences \"In our case report, blood culture was forgone due to the patient’s prior exposure to antibiotics and the unavailability of the test in our facility. Therapy was initiated with vancomycin 1gm IV BID and Ceftriaxone 1gm IV BID, considering coverage for Staphylococcus and broad-spectrum antibiotic inclusion. This approach yielded favorable outcomes in our patient, as evidenced by clinical amelioration, reduction in white blood cell count and acute inflammatory markers, and resolution of chest abnormalities in subsequent follow-up assessments.\" can be shortened into \"In our case, blood culture was forgone due to the patient’s prior exposure to antibiotics and the unavailability of the test in our facility. Empiric intravenous antibiotic therapy with ceftriaxone and vancomycin was followed by clinical improvement, reduction of the acute inflammatory markers, and resolution of chest abnormalities.\". 33. Conclusion: well-written, no strong recommendation here.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1148
https://f1000research.com/articles/13-1145/v1	07 Oct 24	{ "type": "Research Article", "title": "Justice-centered best practices for accessibility to public buildings in a tier II city: Insights from a Delphi expert consensus", "authors": [ "Sidhiprada Mohapatra", "G Arun Maiya", "Ullas U Nayak", "Rashmi Sheelvant", "Vennila J", "Joanne Watson", "Rama Devi Nandineni", "Sidhiprada Mohapatra", "G Arun Maiya", "Ullas U Nayak", "Rashmi Sheelvant", "Vennila J", "Joanne Watson" ], "abstract": "Background Despite beneficial progress in policies, awareness and advocacy, accessibility gaps exist in public buildings in India. Challenges achieving full inclusivity still exist, due to a lack of clear guidance for implementing accessible solutions. Retrofitting older buildings, particularly in developing tier II cities is a major challenge. The authors of this paper aimed to address this issue using a four-round Delphi method to generate a Justice-Centered Best Practices (JCBPs) for accessibility provisions for individuals with mobility disabilities.\n\nMethods Conducted in Udupi, the study involved experts including administrators, policy implementers, auditors, advocates, healthcare professionals, individuals with disabilities and their caregivers. In the first round, a 117-item list was generated through triangulation of three methods. In subsequent rounds, experts rated each item using a 5-point Likert scale on feasibility, affordability and priority. Responses were considered valid if the agreement reached ≥80% on the total score. The prioritised list of JCBPs was finalised at a consensus meeting.\n\nResults Out of forty-eight experts who began the study, 16 participated in the final meeting. The Wilcoxon signed rank test (p value>0.05) of expert ranking indicated that the scoring of items remained consistent between the two rounds. A machine learning decision tree analysis identified items securing ≥ 80% agreement as the most reliable decision with an accuracy=71.43%. The McNemar’s Test p value=0.79 confirmed consistency of expert scoring on the items with high agreement rates.\n\nConclusion Finally, 33 built and non-built environment items scored highest rank. Stakeholder engagement, use of low-cost technology solutions, coordination between public administrations, funding, good governance practice, awareness, and advocacy were few of the solutions that can help ensure accessibility is in place for individuals with mobility disabilities. The study methodology and findings create a robust foundation for evidence-based JCBPs for accessibility provisions for individuals with mobility disabilities.", "keywords": [ "administration", "decision tree", "expert", "inclusion", "municipality", "machine learning", "public spaces" ], "content": "Introduction\n\nGlobally, the number of individuals living with disabilities is rising. The causes and consequences of disabilities vary across different stages of life and among different nations.1,2 For instance, in the United States, over 24.6% of individuals with disabilities are in the labor force,3 while in India, individuals with disabilities continue to be marginalised and underrepresented in the workforce.4 The lack of accessible infrastructure and unequal opportunities for education and skill development prevent individuals with disabilities from participating equitably in paid employment.2\n\nInternational protocols such as the Standard Rules on the Equalization of Opportunities for Persons with Disabilities, the United Nations, and the Universal Declaration of Human Rights (UDHR) acknowledge the necessity of promoting and protecting the rights of individuals with disabilities, with the duty resting on governments and governing bodies.5 Globally, efforts are being undertaken towards the development of inclusive nations. The Sustainable Development Goals (SDG), encourages all states to eliminate poverty and enhance living conditions by providing equal opportunities, and equitable environment for all. SDG 11, in particular, promotes inclusive, safe, sustainable, and resilient cities.6 With 60% of the world’s population residing in cities, fostering inclusive cities are likely to have a positive impact on both health and quality of life.7 This emphasizes the need to recognize the opportunity divide and economic costs associated with the exclusion of individuals with disabilities from mainstream society.6,7\n\nDespite inclusive practices gaining global momentum, most developing nations, including India, have yet to establish such practices as mainstream. Consequently, individuals with disabilities remain a minority group in education and the workforce, leading to dependency, poverty and exclusion, further limiting access to services.4,8,9 In India, 40-42% of individuals with disabilities face poverty, affecting their social participation in leisure, political, cultural and religious spheres.4,10,11 This creates a cascading effect of disability, marginalisation and lack of social participation.12 Accessible public buildings are crucial for promotion of equal opportunities and prevention of discrimination against individuals with disabilities.10 Public buildings serve as providers of services to all, and aid in mitigating the symbiotic relationship between poverty, exclusion and disability.4,10 Research from developed and developing countries have identified challenges experienced by individuals with disabilities due to inaccessible public buildings and facilities.13 However, there is a significant gap in knowledge transfer and implementation in long-neglected tier II cities.14 These cities are characterized by diverse settlements, governance systems, multiple infrastructural developments, differing cultural and social constructs, and varied economic opportunities.14–16 These features necessitate a multidisciplinary approach to address their unique accessibility challenges.\n\nBuilding developers and industries, are often reluctant to implement accessibility provisions, due to perceived costs, lack of user demand, insufficient understanding of user needs and aesthetic concerns.17–20 They frequently prioritize immediate profits over the long-term value of the building.17,21 Therefore, it is imperative to utilize collaborative research techniques like Delphi methods that can effectively involve a multidisciplinary team with diverse views, including architects, urban planners, builders, evaluators, and accreditors of civic structures.22,23\n\nThus, to address the intricate challenges and engage meaningfully with the end-users we employed the Delphi method. This systematic and structured research method is used in complex situations to elicit anonymous responses from experts. Involving multidisciplinary stakeholders, will aid in building consensus and proposing strategic solutions for accessibility challenges.24 Local authorities can utilize these insights to create inclusive cities by understanding the needs of all stakeholders and allocating resources effectively.\n\nAim: Thus, we used a Delphi consensus process to develop a list of justice-centered best practices to enhance accessibility to public buildings by persons with motor disabilities in Udupi city.\n\nThis study is underpinned by two theoretical paradigms, Spatial Justice and the Person-Environment-Occupation-Performance (PEOP) paradigms. An integration of the two frameworks allowed an examination of accessibility to public buildings from a justice-centered perspective. A spatial justice paradigm promotes equitable distribution of resources, advocating for inclusive design and community involvement.25 While, the PEOP framework, enables an examination of the dynamic interaction between individuals with disabilities, their environments, and their activities, focusing on enhancing performance and participation.26 Combining these frameworks provides multidisciplinary practitioners an understanding of spatial inequalities and injustices enabling them to design and manage public buildings that promote inclusivity, accessibility, fairness and enhance performance. Figure 1 illustrates the theoretical frameworks of the research process. This approach provides a framework for considering public buildings in terms of their accommodation of diverse needs, promotion of full participation and equitable access for individuals with mobility disabilities.\n\n\nMethods\n\nThis study is conducted and reported as per the Recommendations for the Conducting and REporting of DElphi Studies (CREDES)27 as given under reporting guidelines.28\n\nUdupi, a tier II city situated in the southwestern state of Karnataka, India, is renowned for its beaches, temples, and cuisine. The city is known for its extensive history and cultural heritage, which is evident in its architectural style, artwork, and festivities. Furthermore, Udupi is a center of excellence for education and healthcare. The town houses several hospitals with state-of-the-art medical facilities, making it a popular choice for medical tourism. Udupi’s unique blend of tradition and modernity, coupled with its exceptional cultural and natural beauty, make it one of India’s most visited destinations.\n\nThe Census of 2011 has classified the urban settlement of Udupi as a Statutory Town.29 The city is governed by the Udupi City Municipal Council, which is entrusted with the provision of fundamental civic amenities to the inhabitants.30 These include water supply, sanitation, waste management, and road maintenance. The Udupi City Municipal Council is further organized into several administrative departments, including the engineering department, which oversees infrastructure development. Organizational structure of stakeholders involved in accessibility provisions for public buildings is shown in Figure 2.\n\nA four-round Delphi method was used in the study. The Delphi process is a useful methodology for proposing solutions for future scenarios. It facilitates the contribution of experts’ opinions anonymously, leading to consensus on a phenomenon. The Delphi methodology was chosen for its ability to achieve consensus in domains characterized by uncertainty.24\n\nA sampling frame was generated to list out all experts as per the organogram given in Figure 2. Participants were identified using convenience sampling. Stakeholders involved in city development were invited to participate in the study. This included those managing public facilities and buildings, overseeing public projects, making policy decisions, planning and executing accessibility policies, working in public administration in the city Municipal Council and advocating for disability rights. Further, using a snowball sampling technique, individuals were prompted to suggest other pertinent stakeholders who were involved in matters of accessibility or disability. Additionally, the network that was established through the Centre for Comprehensive Rehabilitation at the academic institution was employed to reach out to all potential stakeholders. Upon confirmation, the purpose of the study, time, and the process of the Delphi technique was explained. Forty-eight experts expressed a willingness to participate. Extended file 1 gives the network of experts.31\n\nTo ensure diverse involvement, the researchers approached experts who are engaged in financing, policy-making, administration, standardization, and legal compliance of public buildings, as well as individuals with mobility impairments who utilize these structures. To be considered as an expert, they should understand the needs of individuals with mobility disabilities, and/or should have experience in advocating for disability rights. Table 1 shows the criteria for selection of experts.\n\nThe four rounds of Delphi were conducted in person. All the instructions were given in both English and Kannada. The study was carried out between November 2021 to November 2023. The Delphi rounds are described below.\n\nRound-1: Delphi Questionnaire Development\n\nThe first round of the Delphi study included three methods to generate an exhaustive list of needs for individuals with mobility disabilities while accessing public buildings. The list also consists of practices to improve accessibility to public buildings.:\n\nLiterature review\n\nThe researchers undertook a literature search in PubMed, Scopus, Web of Science, and Cochrane using the terms “mobility disability”, “accessibility”, “experiences”, “built environment” and “public buildings”. We utilized the PEOP model to explore the factors that influence accessibility and task performance in public buildings by persons with motor disabilities. Two authors (SM and UN) reviewed challenges and opportunities to enhance accessibility to public buildings from the literature. All practices including the built environment and non-built environment were included. Extended file 2 gives the search strategies used for the databases.32\n\nOnsite observation\n\nSix public buildings were selected through purposive sampling ensuring a heterogeneous user, substantial pedestrian traffic, and security concerns are met. Unobtrusive observations helped to identify real-time challenges faced by individuals with mobility disabilities, offering insights into problems in a realistic setting.33\n\nExpert inputs\n\nFollowing this, the experts were requested to enumerate all requisite amenities and arrangements imperative to render public buildings in the city of Udupi entirely accessible to individuals with mobility disabilities. The instructions given were, “Kindly list all requisite amenities and arrangements imperative to render public buildings in the city of Udupi entirely accessible to individuals with mobility disabilities.” Content analysis of the responses was done to develop items for the subsequent rounds using the software Open Coding System 4.0 (ITS and Epidemiology, University of Umea).34 The responses were listed and analysed to identify duplicate responses. Items with similar meanings were also grouped together.\n\nTriangulation and data compilation\n\nTo ensure credibility, reliability and trustworthy scientific accuracy, triangulation of the three data sources was adopted.35 To develop the Delphi questionnaire, data captured from all three sources, were systematically compiled. An Excel (Microsoft Inc) spreadsheet was used to collate the data from the literature search, onsite observations, and expert-enumerated items into a comprehensive list. Using the Open Coding System 4.034 the compiled data were systematically coded and categorised. In this process, SM, UN and RS mapped all the items, removed duplicates, grouped similar items, and identified themes as accessibility indicators. The refined list of items was then formatted into a structured Delphi questionnaire, ensuring clarity and relevance for the experts. The instructions and items were provided in English to accommodate all experts in Round 2.\n\nRound-2: Delphi questionnaire rating\n\nIn this round, experts were asked to rank the items identified from Round-1 using a 5-point Likert scale based on three criteria: affordability, feasibility, and priority. Each item was scored on a scale of 1 to 5, where 1 represented “least score” and 5 represented “highest score.” The total score for each item was generated by summing the scores across all three criteria. The instructions provided were: “Each of the items listed below is imperative to render public buildings in the city of Udupi entirely accessible to individuals with motor disabilities. We kindly request that you score each aforementioned element according to its relative significance, utilizing a 5-point Likert scale.” Extended file 3 provides the original scoring sheet given to experts.36\n\nAfter collecting the ratings from experts, we analysed the items using descriptive statistics to calculate the mean, median scores, and agreement percentages for each item. Despite the possibility of ranking an item as “1- least score,” none of the items were excluded or rearranged in this round. Also, items with low consensus were also retained until the final meeting to ensure discussion and evaluation of all items.\n\nRound-3: Delphi questionnaire rating\n\nIn this round, the same group of 35 experts were contacted with the same set of 117 items. We provided the overall ranking data from Round-2 with the possibility of ranking items differently in this round. The experts were asked to score all the items using the same Likert scale as in Round-2. The experts were prompted to give reasons for any disagreement, and it was recorded. Despite potential changes in rankings, all items were retained for the final consensus meeting to ensure comprehensive evaluation.\n\nFor Round 2 and 3, Microsoft Excel 2016 was used to assess the descriptive statistics including mean, median, interquartile range (IQR), ranking and agreement. IQR was to determine the level of agreement on the 5-point scale for each item on the questionnaire.\n\nTo compare the scores between these rounds, we performed the Wilcoxon signed-rank test to determine if there were statistically significant differences between the two rounds thereby check stability in ratings by experts. The p values from this test indicated whether the changes in scores were significant. Additionally, we calculated the Kappa statistic to measure the level of agreement between the two rounds. This was done using Jamovi Project 1.4.37 The order of items presented to experts remained fixed.\n\nTo identify key factors influencing the rankings and provided a visual representation of the decision-making process among the experts, we utilized R programming language with the ‘rpart’ package to develop a Decision Tree.38 Although the use of machine learning was not initially included in the study protocol, it was later incorporated to strengthen the validation of the expert scoring process. This helped identifying and validating items with the highest agreement, ensuring a robust and reliable final set of recommendations. To develop the Decision Tree the following steps were used:\n\nData Preparation: The dataset included the total scores for each item on Affordability, Feasibility, and Priority from both Round-2 and 3. Each item was categorized as either “acceptable” or “not acceptable” based on a threshold score (i.e. items with a score above 12 out of 15 were considered acceptable).\n\nModel Building: We first assessed all 117 items using the Decision Tree to identify the main factors influencing the rankings in both rounds. We then focused on items with high agreement (>80%) to build a more targeted Decision Tree, highlighting the most consistently prioritized items.\n\nValidation and Pruning: Cross-validation were performed to validate the model and assess its performance\n\nOutput and Interpretation: The Decision Tree output included nodes that represent decision points and branches that represent the outcomes based on specific criteria. Each terminal node (leaf) of the tree provided the final categorization of items as acceptable or not acceptable based on the experts’ ratings.\n\nStatistical measure used for evaluating the performance of Decision Tree analysis are Accuracy (Acc), 95% Confidence Interval (CI), No Information Rate (NIR), P-Value [Acc > NIR] Kappa, McNemar’s Test p value, Sensitivity, Specificity, Positive Predictive Value (PPV), Negative Predictive Value (NPV), Detection Rate, Detection Prevalence, and Balanced Accuracy. Extended file 4 gives the Decision tree coding.39\n\nRound-4: Consensus meeting\n\nAll experts from Round-3 were invited to the consensus meeting, which was conducted as two focus group discussions (FGDs). Sixteen experts consented to participate in the final discussion. The 117 items generated from the prior rounds were independently sorted by three researchers (SM, RS, and UN) according to their average rank from both rounds and presented to the experts. The top 40 items, with an agreement of over 80%, were presented separately. If any constituent items were contradictory or included multiple strategies, a common neutral statement was created to facilitate discussion among the experts.\n\nAs a result of the discussions, the number of items was reduced to a final list, with some items coalesced by the consensus group and others removed for not reaching the required consensus level. The final consensus statements were crafted to reflect the experts’ agreement on the most critical practices for enhancing accessibility to public buildings for individuals with mobility disabilities\n\nData from FGDs was used to refine and group the items. The final consensus statements were generated, reflecting the experts’ agreement using thematic analysis. These statements were designed to encapsulate all relevant items and address any contradictions or multiple strategies identified during the discussions.\n\nBy combining qualitative insights from the FGDs with the quantitative agreement data from previous rounds, the final set of best practices was developed. These practices provide a comprehensive guide for enhancing accessibility to public buildings for individuals with mobility disabilities in Udupi.\n\nThe study was approved by the Institutional Research Committee, Manipal College of Health Professions, and the Institutional Ethical Committee-Kasturba Hospital, Manipal (IEC 769/2017) to perform the study. The date of approval from ethics committee was received on 14th November 2017. The study period was approved from 14th November 2017 to 30th November 2024. The study was registered under the Clinical Trial Registry- India (CTRI/2018/07/014763). The study adheres to the Declaration of Helsinki. A written informed consent was obtained from experts detailing nature of study and their involvement.\n\n\nResults\n\nForty-eight individuals, self-identified as experts involved in city development, accessibility, and disability rights, were approached to participate in the study. Following the screening, ten individuals involved in city development were excluded due to low or no experience in the accessibility domain. Experts who did not respond to three reminders at the end of three consecutive weeks were categorized as non-respondents. The flow of experts and their response rates in each round, is displayed in Figure 3.\n\nThe individuals involved in the planning and development of the city of Udupi comprised a variety of professionals. Among them were engineers, auditors, and certifiers who were engaged in town planning and urban development. Additionally, policy implementers and executives, including legislative, Commissioners, and public office administrators, who played a significant role in public building developments and inspections of building guidelines, participated in the panel. Furthermore, designers, architects, and structural engineers, who were experts in assessing user needs and planning building designs, were also part of the panel.\n\nThe group representing individuals with mobility disabilities was composed of three categories of people. Firstly, individuals with mobility disabilities and disability rights activists were included. Caregivers accompanying individuals with disabilities to public spaces were also part of this panel. Furthermore, professionals involved with persons with mobility disabilities, including community physiotherapists and occupational therapists, also participated. The participants had an average of 7 years of experience in their respective fields, with some having over 20 years of experience in disability-related projects. While the experts primarily practiced in Udupi, it is important to acknowledge that some had experience in other geographical areas as well. Eleven participants were involved in research on accessibility or disability studies including health professionals (n=5), architects (n=5) and engineer (n=1). Eight experts identified themselves with various forms of mobility disability. They were from the disciplines of architecture (n=1), engineering (n=1), rehabilitation workers at the municipality level (n=2), and disability rights activists (n=4). A detailed description of all the experts is given in Table 2.\n\n* Health Professionals included experts from the disciplines of Physiotherapy, Occupational Therapy, Prothesis, and Orthosis with expertise in neurological, orthopedic, and community rehabilitation.\n\nItem generation\n\nA comprehensive, credible and contextually relevant list of practices and requirements to enhance accessibility to public buildings, a multiple methods triangulation led to generation of an exhaustive 1418 items list. The literature search identified a total of 125 articles relevant to the development of the Delphi questionnaire. After the data extraction process was completed, a total of 862 items were documented under the categories of built environment and non-built environment factors that impact the accessibility of individuals with mobility disabilities.\n\nThe onsite unobtrusive observations focused on the contextually relevant factors to be included in the best practices. The common spaces at six public buildings were categorized as external and internal accessible spaces including entrance, interior navigation, facility access, safety measures, services. Observations yielded 231 items for inclusion. Each item was meticulously documented and categorised under built environment and non-built environment factors. Additionally, 12 experts approved to provide a list of requirements for enhancing accessibility. A total of 325 open-ended responses were acquired from the group. Sample codes by experts are given in extended file 5.40\n\nTriangulation and finalisation\n\nThe items generated from the three above-mentioned methods were carefully compiled and all duplicates were removed, resulting in a final count of 117 items as given in extended file 6.41 In the subsequent round, the 117 items were subjected to a ranking by experts.\n\nThirty-eight experts eligible for participation were provided with the questionnaire as shown in Figure 3. Only 35 experts responded (92.1%) on all the items using the scoring sheet with a total score of 15. Forty-five items had a median score ≥13 (Top Priority) and forty-one items had a median score of 12 (High Priority), and only 4 items had median score of 10 (Unsure). No items were considered low scores by the group. Total 69 items had an agreement of more than 80%. Rankings of this round are presented in Tables 3 and 4. The scores are given in the extended file 7.42\n\nThis round was completed by 33 (82%) of experts who participated in Round 2 as shown in Figure 3. Seventy-nine items scored ≥ 80% agreement. None of the item scores when compared between Round-2 and 3 had significant p-value indicating consistency in the scoring. The Kappa value between 0.81 to 1.0 across the 61 items indicates moderate agreement between Rounds 2 and 3, highlighting some consistency in expert ratings over rounds for the group as a whole but also pointing to the need for further discussion. Final ranks with highest and lowest scored items are presented in Tables 3 and 4. Multiple items had tied ranks. The overall ranks secured by 117 items is given in extended file 8.43\n\nDecision tree\n\nTo test the consistency and validate the expert consensus from Round 2 and 3, a decision tress analysis was conducted in three stages as shown in Table 5. In the first stage, responses for all 117 items were analysed giving a significant p value of 0.02. This significant difference in the rating between the two rounds indicates a change in the perspectives of the experts during the Delphi process. This implies that the experts’ ratings of the items changed between rounds, potentially due to varying interpretations of the items or evolving perspectives during the Delphi process.\n\n* p value ≤ 0.05 and\n\n** p value ≥ 0.05.\n\nTo address this inconsistency, we moved to the second stage of the analysis, which focused on items with a Kappa value greater than 80%. This stage was crucial for isolating items with strong expert consensus and reducing the variability observed in the initial analysis. Here, the p value of 1.0 indicates no significant difference in ratings between rounds for these items, demonstrating that the experts had a more consistent evaluation for items with high Kappa values.\n\nIn the final stage, items with an agreement rate higher than 80% were analysed. Focusing on these widely agreed-upon items helped validate and strengthen the expert consensus. Higher accuracy (71.43%) and an insignificant p value of 0.79 suggests improved consistency and agreement among the experts for the items with high agreement rates, thus guiding the consensus meeting towards the final prioritization of items. Results from Decision Tree analysis is given extended file 9.44\n\nAll 117 items generated with the overall ranks were presented at the final focused group discussion conducted by SM and RS. The top ranked 30 items with agreement of over 80%, were presented separately. Any contradictory or multi-strategy items were rephrased into neutral statements to facilitate discussion. The lowest ranked items were also presented separately. Through the FGDs, the experts worked to refine and group the items, resulting in a final list of items. These were reviewed by 19 panelists (7 advocates and persons with disabilities and 12 experts) in the two FGDs. Some items were coalesced, while others were removed for not reaching the required consensus level. The final consensus statements were crafted to reflect the experts’ agreement on the most critical practices for enhancing accessibility to public buildings for individuals with mobility disabilities Following this meeting, the total number of items reduced from 117 to 86, as 12 items that had failed to reach level of consensus (80%) were now removed and 19 other items were coalesced by the consensus group. All 86 items generated by the Delphi panel were grouped by topic as in the process described above, generating 10 consensus statements summarised in Table 6. Final ranking was generated based on the mean ranking of constituent items.\n\n\nDiscussion\n\nThis paper describes a study that sought to generate a list of best practices to guide municipalities, design professionals, advocates, rehabilitation workers, and users of public buildings in identifying approaches to augment accessibility to public buildings. This study represents the first-ever multidisciplinary investigation to scrutinize public building accessibility related practices and methodologies from diverse stakeholders using the Delphi method. Our research has yielded identification of ten priority areas. These areas are discussed under the overarching themes, incorporating the novel insights of people, governance, cost vs. opportunity cost, design process, research and evidence-based implementation, indigenous technological solutions, data on needs, rehabilitation and medical partnerships, user involvement and cultural relevance in design, and capacity building.\n\nThe elements of the public building are categorized as internal and external structures. External structures prioritized for immediate accessibility implementation include parking space, access route and entrances. Internal environment structures include doors, sanitary and hygiene and other amenities. Experts particularly highlighted the importance of building entrances and prioritized public toilets among the amenities. Research indicates that these elements are commonly studied in accessibility research.13,21 Considering the buildings purpose during planning and implementation is an essential step. This will encourage flexible implementation without undue burden.\n\nThe importance of maintaining public buildings and spaces in terms of pathways, potholes, climate protection, and stagnation of rainwater were highlighted. These are contextually relevant environmental determinants influencing public buildings accessibility.45 Further, removal of movable barriers like dustbins, stray animals and ensuring accessibility services remain unlocked were also prioritized.\n\nA practical focus is evident in the study participants’ emphasis on immediate, actionable solutions, such as maintaining pathways and ensuring essential areas are free of obstructions. Furthermore, the study’s user-centered perspective adds a novel, practical dimension to broader policy discussions by highlighting the importance of considering the user experience. This perspective underscores the need for real-time solutions, such as ensuring accessibility services remain unlocked and addressing climate protection, which are often overlooked but crucial for daily accessibility.\n\nThe identified key strategies encompass a shift in the attitudes of both the community and stakeholders, through awareness and advocacy. Unfortunately, disability is still frequently perceived as a state of (in)capability. To create meaningful change at the foundation of this issue, it is crucial to recognize that disability is not a dichotomy, but rather a fluid and evolving process.46 There is increasing acknowledgment that the benefits of accessible built environments are not only limited to advancements of persons with disabilities but extend to the general public.47 It is essential to promote the universal need for accessibility, as doing so will have a positive impact on all levels of society. By increasing visibility and sharing experiences of persons with disabilities, as well as compiling adequate prevalence data, advocates can change the minority perspectives of disability among stakeholders and the general public.48\n\nThis paper posits that enhancing comprehension about disability needs could result in companies implementing disability-inclusive practices. Active engagement with the users, with and without disabilities, is required for property managers,20,49 professionals in the built environment and administrators to implement these practices.50\n\nFurthermore, advocacy and awareness campaigns are instrumental in fostering an empathetic attitude among the people. By cultivating empathy, there is an upsurge in the demand for accessible buildings, which serves as a stimulus for developers and government officials. Users with disabilities can further augment the demand for such buildings by adopting a self-advocacy approach, thereby exerting pressure on the providers.51\n\nDisability inclusive public buildings, have been viewed as an economic burden, aesthetically substandard and catering to minority groups.52 In many jurisdictions that are perceived as an entitlement and not a necessity. According to the Theory of Symbolic Interactionism, actions of people are determined by what they deem important.53,54 People’s perception of importance is shaped by social and environmental interactions.53 Thus, beliefs of community, administrators, planners and property managers play an important role in accessibility implementation. Encouraging usage of public buildings, enhancement of community involvement and self-advocacies are three strategies recommended to enhance visibility of persons with disabilities. Furthermore, these interactions and strategies will make accessibility a right rather than an entitlement.\n\nThe implementation of accessibility measures is linked to effective policies, compliance and governance especially at the municipal level. Recognizing disability is a complex phenomenon that is shaped by an individual’s interaction with their physical, structural, social, and political environment is crucial.55,56 However, a conventional portrayal of disability as a minority and dichotomous representation deviates administrators from realizing that accessibility is a basic human right. Therefore, municipalities must identify users and acknowledge accessibility as a fundamental requirement. Inadequate awareness, lack of data, and a lack of understanding the needs of users with disabilities in public infrastructures, result in ineffective advocacy. Hence, to bring about a systemic transformation and foster a change in perspective, it is crucial for municipalities to engage with all stakeholders.57\n\nOther approaches to promote good governance in the implementation of accessibility measures at the municipal level include encouraging ethical practices,58 collaborating with private organizations and users, promoting coordination among departments,57,59 and establishing well-defined and measurable plans such as accessibility metrics.60,61\n\nCollaboration with robust institutions possessing the capacity for advanced research and technology, as well as civic organizations dedicated to promoting a rights-based approach, will lead to the development of more accessible infrastructure and other positive societal transformations. Planners, architects, and engineers operating at the municipal level must prioritize accessibility in both the construction of new public buildings and the retrofitting of existing ones.\n\nExperts emphasized the need for establishment of committees at the municipal level committed to planning and continuous monitoring to break the cycle of conflict that frequently arises between the users of public buildings and municipal administrators.59,62,63\n\nThe framework considers bridging the gap between preferences of municipal administrations, politicians, planners to that of accessibility needs of persons with disabilities. Economic, aesthetic and structural demands of a public infrastructure may conflict with the accessibility needs.57 Builders and property managers are primarily concerned that accessibility measure may increase the cost of the property.17 Similarly, aesthetic demands of clients may create conflict with the planners’ desire to provide accessibility. Strategies to address these conflicts at private, public administration clients, planners, and implementations level are included in this framework.57,59\n\nIt should be understood that users of public buildings are “faceless”. Thus, planners at municipal level must take diverse groups into account in the planning process. Persons with motor disabilities are only one of many groups among other users in need of accessible infrastructure. According to Saha et al. local government officials encounter challenges with regards to data collection, community engagement, resource allocation, lack of analytical tools, and unclear or complex lines of responsibility.63\n\nProperty developers show reservations to retrofitting and accessibility implementations due to the associated cost.64,65 Many researchers argue that lack of advocacy within construction industry65 and inability to fully account for the long-term benefits of accessibility retrofitting due to a focus on immediate costs thus contesting this view about the actual cost.66 Even more there are no studies on the opportunity cost incurred due to inaccessible public buildings. Transportation expenditures, healthcare expenditure, lower employment and inadequate access to services are few of the challenges experienced by persons with disabilities.\n\nWe propose strategies to reduce economic burden and increase opportunities to participation. Awareness among property managers to understand the long-term value of property over short-term gain through accessibility violation can be provided. Using positive advisements, accessibility as a rating domain under public-building user experience are methods suggested to attract clients and users. Similarly using these techniques, the builders can improve marketability, and commercial profit from the buildings. The suggestion is in line with the challenges reported by planners and property managers in previous studies.67,68\n\nSuccessful implementation requires intrinsic and extrinsic motivation. Intrinsic drive includes universalization, rights-based approach, social interactions, and personal/professional experiences. Extrinsic motivation includes positive strategies (e.g. advertisements, user ratings, incentivization) and negative strategies (e.g. audits, penalization) for accessibility implementation. Among all strategies, external audits by national bodies for services and accreditation was deemed a top priority for implementation.69\n\nSpace constraints pose significant challenges when retrofitting historical buildings for accessibility.70 As stated by experts, historical buildings often become “thorny issues” when accessibility solutions are introduced due to their architectural and cultural significance.71,72 Built-area space limitations can impede the incorporation of accessibility features like ramps and elevators, which require substantial external and internal space. For example, constructing a ramp according to building codes may demand a large outdoor area, while installing an elevator might necessitate a considerable underground foundation and specific internal space allocation.73,74\n\nTo overcome these constraints, low-cost and innovative technologies offer potential solutions. Modular ramps, portable lifts, or platform stairlifts can provide accessibility without compromising the building’s structural integrity. Furthermore, historical buildings often face the challenge of balancing modernization with preservation, making value-based conservation critical.72 This approach ensures that the historical and aesthetic value of a building is maintained, while innovative, low-tech solutions are introduced to improve accessibility without altering the original structure excessively.\n\nThe design of buildings and the design process are a crucial component in the achievement of accessibility. The outcome, which encompasses the design of new buildings or the renovation of existing structures and facilities, must ensure the active participation of users through the process of co-design.51 By using CoDesign, developers can capture and incorporate user perspectives and needs during products, services, or programs development.75 Approaches such as interviews, community walks, user audits, focus groups, and photovoice methods are utilized to document the narratives of users with varying needs. Codesign as a strategy is capable of transforming mindsets, behaviors, empathetic engagement among individuals, planners, and government officials by establishing secure and meaningful avenues for user engagement.76,77\n\nInadequate information regarding users with disabilities and the perception of disabilities as a constant phenomenon has led planners and policymakers to assume that there will be low user turnout and high costs associated with accessible solutions for public buildings.57 The lack of data also results in a lack of knowledge, attention, and insufficient implementation of accessibility policies at the municipal level.50 Participatory research with the users throughout the process could alter the approach to accessibility and their requirements in public buildings.\n\nThe framework includes research on planning and monitoring accessibility. User audits or surveys with yes/no checklists are commonly used for accessibility evaluation but are costly, time-consuming, laborious, and difficult to interpret.78 Researchers have developed alternative evaluation methods using sensors, drones, robotics, mobile apps, and building information models.79,80 Municipalities can adopt these efficient and cost-effective tools to improve accessibility data.\n\nThe framework also highlights a need for evidence-informed recommendations for public buildings and knowledge dissemination to all the stakeholders. Along these lines, the framework priorities a need for feasible solution. Few strategies under the feasible solutions is to develop indigenous technologies that are affordable, user-centered, and long-lasting indigenous technologies.\n\nWe adopted a rights-based approach towards accessibility meaningfully involving individuals with disabilities and effective partnerships-with governmental, non-governmental, academia, disabled people’s organization, and civil societies. The methodological strengths lie in its comprehensive, multi-round consensus-building process, diverse stakeholder inclusion, and combining quantitative analysis with qualitative insights, ensuring robust and contextually relevant findings. Triangulation of data sources and adherence to ethical guidelines enhance the study’s credibility. The framework proposed can be adopted as a best practice ensuring specific, measurable and achievable targets for municipalities during planning and monitoring of public projects. The practices proposed can be replicable, in other countries and contexts.\n\nThough the study aim was to develop justice-centered best practices however the proposed practices focus specifically on individuals with motor disabilities. The research does not address the needs of other groups who may also face exclusion, such as older people, people with multiple disabilities, or those affected by gender-based issues. Additionally, while the framework covers many barriers in the built environment, it does not consider cultural or religious practices, such as kneeling or navigating thresholds in religious places, which could also impact access to public buildings.\n\nThe use of convenience and snowball sampling techniques may have introduced selection bias, as the sample may not fully represent all stakeholders, limiting the generalizability of the findings. Since the study involved a complex social phenomenon requiring extensive expertise, and a lengthy Delphi process could have impacted the expert’s responses. Also, the geographic focus on Udupi means the results may not be directly applicable to other regions. Despite these challenges, the study provides a well-founded basis for improving accessibility in public buildings for individuals with motor disabilities.\n\n\nConclusion\n\nThe priorities identified in this study represent a broad spectrum of crucial areas for municipal authorities, advocacy groups, planners, builders and property managers to address. Proposed strategic interventions range from micro-level actions—such as raising awareness, promoting ethical practices, and fostering motivation—to macro-level measures, including the creation of dedicated committees, the development of comprehensive data collection systems, and ongoing monitoring. This study’s implications extend from individual needs to broader societal impacts, aiming to enhance accessibility and inclusivity in Udupi city. Future research should employ robust methodologies to evaluate the effectiveness of the proposed priorities and their impact on achieving a more accessible and inclusive urban environment.\n\nDespite a trend towards urbanization and increasing population in cities, accessibility still remains a major challenge. Non-inclusive cities impact opportunities for all citizens, disabled and non-disabled. The best practice framework proposed in this study is dynamic and takes a rights-based approach to support local administration to develop policies that tackle exclusion of individuals with disabilities. The strategies highlight that focus on design modifications alone cannot achieve full participation. It should be remembered that for an inclusive city, accessibility is a main pillar to prevent exclusion and attain the Sustainable Development Goals (SDGs).\n\nFor international audiences, this study gives a practice framework to initiate, implement and exchange ideas about accessibility at municipal levels. At the national and international level, tier II cities are fast being recognised as emerging places of economic growth. The Government of India’s Smart Cities initiative has highlighted the importance of these cities, which often receive less attention compared to metros and tier I cities. Tier II cities are not as well researched as tier I cities. However, The Smart city initiative aims to equip local authorities with resources to foster inclusivity. Accessibility should be viewed not only through the lens of the built environment, but also in terms of human rights. This includes raising awareness, improving attitudes among planners, understanding opportunity costs, and emphasizing the need for planning, research, collaboration, and advocacy. These aspects are relevant to both national and international agencies.\n\nThe study was approved by the Institutional Research Committee, Manipal College of Health Professions, and the Institutional Ethical Committee-Kasturba Hospital, Manipal (IEC 769/2017) to perform the study. The date of approval from ethics committee was received on 14th November 2017. The study period was approved from 14th November 2017 to 30th November 2024. The study was registered under the Clinical Trial Registry- India (CTRI/2018/07/014763). The study adheres to the Declaration of Helsinki. A written informed consent was obtained from experts detailing nature of study and their involvement.", "appendix": "Data availability\n\nFigshare: Justice-centered best-practices for accessibility to public buildings in a tier II city: Insights from a Delphi expert consensus: https://doi.org/10.6084/m9.figshare.27084319.v1 81\n\nThe project contains the following underlying data:\n\n• Data Set (Total scores in Round 2 and Round 3 by experts).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Extended file 1: Network of experts. https://doi.org/10.6084/m9.figshare.27078994 31\n\nThis project contains the following extended data:\n\n• Extended file 1. Network of experts.docx\n\nFigshare: Extended file 2: Search strategy, https://doi.org/10.6084/m9.figshare.27079003 32\n\nThis project contains the following extended data:\n\n• Extended file 2. Search strategy.docx\n\nFigshare: Extended file 3: Scoring sheet, https://doi.org/10.6084/m9.figshare.27079015 36\n\nThis project contains the following extended data:\n\n• Extended file 3. Scoring sheet.xlsx\n\nFigshare: Extended file 4: Decision Tree Coding, https://doi.org/10.6084/m9.figshare.27079042 39\n\nThis project contains the following extended data:\n\n• Extended file 4. Decision Tree Coding.docx\n\nFigshare: Extended file 5. Sample codes from experts, https://doi.org/10.6084/m9.figshare.27079045 40\n\nThis project contains the following extended data:\n\n• Extended file 5. Sample codes.xlsx\n\nFigshare: Extended file 6. Round 1 list, https://doi.org/10.6084/m9.figshare.27079048 41\n\nThis project contains the following extended data:\n\n• Extended file 6. Round 1 list.xlsx\n\nFigshare: Extended file 7. Round scores, https://doi.org/10.6084/m9.figshare.27079057 42\n\nThis project contains the following extended data:\n\n• Extended file 7. Rounds scores.xlsx\n\nFigshare: Extended file 8. Overall final ranking, https://doi.org/10.6084/m9.figshare.27079063 43\n\nThis project contains the following extended data:\n\n• Extended file 8. overall final.xlsx\n\nFigshare: Extended file 9. Result from Decision tree analysis, https://doi.org/10.6084/m9.figshare.27079066 44\n\nThis project contains the following extended data:\n\n• Extended file 9. Result Decision tree.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: CREDES Reporting Guidelines, https://doi.org/10.6084/m9.figshare.27079075 28\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nAuthors would like to acknowledge all the experts and organisations who participated in the Delphi Consensus.\n\n\nReferences\n\nButler D: Global survey reveals impact of disability. Nature. 2012 Dec 18; 492(7429): 322–322. Publisher Full Text\n\nPinilla-Roncancio M: The reality of disability: Multidimensional poverty of people with disability and their families in Latin America. Disabil. Health J. 2018 Jul; 11(3): 398–404. PubMed Abstract \| Publisher Full Text\n\nODEP\|U.S. Department of Labor: [cited 2024 Jul 12]. Reference Source\n\nPinilla-Roncancio M, Mactaggart I, Kuper H, et al.: Multidimensional poverty and disability: A case control study in India, Cameroon, and Guatemala. SSM Popul. Health. 2020 Aug; 11: 100591. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConvention on the Rights of Persons with Disabilities\|OHCHR: [cited 2024 Jul 12]. Reference Source\n\nTHE 17 GOALS\|Sustainable Development: [cited 2024 Jul 12]. Reference Source\n\nLópez ME, Oyebanji O, Gora M: State of the World’s Cities 2010/2011- Cities for All: Bridging the Urban Divide\|UN-Habitat.[cited 2023 Jul 12]. Reference Source\n\nBrucker DL: Social capital, employment and labor force participation among persons with disabilities. J. Vocat. Rehabil. 2015 Jul 29; 43(1): 17–31. Publisher Full Text\n\nPinilla-Roncancio M, Alkire S: How Poor Are People With Disabilities? Evidence Based on the Global Multidimensional Poverty Index. J. Disabil. Policy Stud. 2021 Mar 17; 31(4): 206–216. Publisher Full Text\n\nBotticello AL, Rohrbach T, Cobbold N: Disability and the built environment: an investigation of community and neighborhood land uses and participation for physically impaired adults. Ann. Epidemiol. 2014 Jul; 24(7): 545–550. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBezmez D: Urban Citizenship, the Right to the City and Politics of Disability in Istanbul. Int. J. Urban Reg. Res. 2013 Jan 2; 37(1): 93–114. Publisher Full Text\n\nCrenshaw K: Mapping the Margins: Intersectionality, Identity Politics, and Violence against Women of Color. Stanford Law Rev. 1991 Jul; 43(6): 1241. Publisher Full Text\n\nCarlsson G, Slaug B, Schmidt SM, et al.: A scoping review of public building accessibility. Disabil. Health J. 2022 Apr; 15(2): 101227. Publisher Full Text\n\nCardoso RV, Meijers EJ: Contrasts between first-tier and second-tier cities in Europe: a functional perspective. Eur. Plan. Stud. 2016 May 3; 24(5): 996–1015. Publisher Full Text\n\nChen L, Mu T, Li X, et al.: Population Prediction of Chinese Prefecture-Level Cities Based on Multiple Models. Sustainability. 2022 Apr 18; 14(8): 4844. Publisher Full Text\n\nUnited Nations Human Settlements Programme (UN-Habitat), The United Nations Economic and Social Commission for Asia and the Pacific (ESCAP): The State of Asian and Pacific Cities 2015 Urban transformations Shifting from quantity to quality.2015 [cited 2023 Feb 12]. Reference Source\n\nImrie R, Hall P: An Exploration of Disability and the Development Process. Urban Stud. 2001 Feb 2; 38(2): 333–350. Publisher Full Text\n\nImrie R: Housing Quality and the Provision of Accessible Homes. Hous. Stud. 2003 May 14; 18(3): 387–408. Publisher Full Text\n\nWright CJ, Muenchberger H, Whitty JA: The choice agenda in the Australian supported housing context: a timely reflection. Disabil Soc. 2015 Jul 3; 30(6): 834–848. Publisher Full Text\n\nYau Y, Lau KW: Disability Awareness for Inclusive Built Environment: A study of Hong Kong s Property Management Industry. Second International Conference on Advances In Economics, Social Science and Human Behaviour Study - ESSHBS 2015. Institute of Research Engineers and Doctors; 2015; pp. 44–48.\n\nImrie R, Hall P: Inclusive Design. Taylor & Francis; 2003.\n\nChiwandire D, Vincent L: Wheelchair users, access and exclusion in South African higher education. Afr. J. Disabil. 2017 Sep 8; 6: 6. Publisher Full Text\n\nLakhani A, Zeeman H, Wright CJ, et al.: Stakeholder priorities for inclusive accessible housing: A systematic review and multicriteria decision analysis. J. Multi-Criteria Decis. Anal. 2020 Jan 30; 27(1–2): 5–19. Publisher Full Text\n\nAvella JR: Delphi Panels: Research Design, Procedures, Advantages, and Challenges. Int. J. Dr. Stud. 2016; 11: 305–321. Publisher Full Text\n\nJian IY, Luo J, Chan EHW: Spatial justice in public open space planning: Accessibility and inclusivity. Habitat Int. 2020 Mar; 97: 102122. Publisher Full Text\n\nBass JD, Marchant JK, de Sam Lazaro SL , et al.: Application of the Person–Environment–Occupation–Performance Model: A Scoping Review. OTJR. 2024 Jul 22; 44(3): 521–540. PubMed Abstract \| Publisher Full Text\n\nJünger S, Payne SA, Brine J, et al.: Guidance on Conducting and REporting DElphi Studies (CREDES) in palliative care: Recommendations based on a methodological systematic review. Palliat. Med. 2017 Sep 13; 31(8): 684–706. PubMed Abstract \| Publisher Full Text\n\nMohapatra S, Maiya GA, Nayak UU, et al.: CREDES Reporting Guidelines. figshare. Journal contribution. 2024.\n\nAbout District \|Udupi District\|India: [cited 2024 Jul 12]. Reference Source\n\nHome\|udupi City Municipal Council: [cited 2024 Jul 12]. Reference Source\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 1. Network of experts. figshare. Journal contribution. 2024.\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 2. Search strategy. figshare. Journal contribution. 2024.\n\nHelle T, Iwarsson S, Brandt Å: Validation of Housing Standards Addressing Accessibility. J. Appl. Gerontol. 2014 Oct 23; 33(7): 848–869. Publisher Full Text\n\nICT Services and System Development and Department of Epidemiology and Global Health. OpenCode. 2015 [cited 2024 Jul 12]; 4. Reference Source\n\nSantos K d S, Ribeiro MC, de Queiroga DEU , et al.: The use of multiple triangulations as a validation strategy in a qualitative study. Ciênc. Saúde Colet. 2020 Feb; 25(2): 655–664. PubMed Abstract \| Publisher Full Text\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 3. Scoring sheet. figshare. Journal contribution. 2024.\n\njamovi - open statistical software for the desktop and cloud: [cited 2024 Jul 12]. Reference Source\n\nR: The R Project for Statistical Computing: [cited 2024 Jul 12]. Reference Source\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 4. Decision Tree Coding. figshare. Journal contribution. 2024.\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 5. Sample codes from experts. figshare. Journal contribution. 2024.\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 6. Round 1 list. figshare. Journal contribution. 2024.\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 7. Round scores. figshare. Journal contribution. 2024.\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 8. Overall final ranking. figshare. Journal contribution. 2024.\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Extended file 9. Result from Decision tree. figshare. Journal contribution. 2024.\n\nSaito Y: Awareness of universal design among facility managers in Japan and the United States. Autom. Constr. 2006 Jul; 15(4): 462–478. Publisher Full Text\n\nBarnartt S: Disability as a Fluid State. Barnartt SN, editor. Emerald Group Publishing Limited; 2010; vol. 5. . (Research in Social Science and Disability. Publisher Full Text\n\nA/RES/48/96 - Standard Rules on the Equalization of Opportunities for Persons with Disabilities - UN Documents: Gathering a body of global agreements.[cited 2024 Aug 5]. Reference Source\n\nNtombela S: Inclusive education and training in South African higher education: Mapping the experiences of a student with physical disability at university. Afr. Educ. Rev. 2013 Sep; 10(3): 483–501. Publisher Full Text\n\nYau Y, Lau WK: Property management, disability awareness and inclusive built environment. Prop. Manag. 2016 Oct 17; 34(5): 434–447. Publisher Full Text\n\nOrmerod MG, Newton RA: Briefing for accessibility in design. Facilities. 2005 Jun 1; 23(7/8): 285–294. Publisher Full Text\n\nJackson MA: Models of Disability and Human Rights: Informing the Improvement of Built Environment Accessibility for People with Disability at Neighborhood Scale? Laws. 2018 Mar 8; 7(1): 10. Publisher Full Text\n\nNeath J: Social Causes of Impairment, Disability, and Abuse. J. Disabil. Policy Stud. 1997 Apr 13; 8(1–2): 195–230. Publisher Full Text\n\nMaines DR, Charon JM: Symbolic Interactionism: An Introduction, An Interpretation, An Integration. Contemp. Sociol. 1981 May; 10(3): 466. Publisher Full Text\n\nCarter MJ, Fuller C: Symbols, meaning, and action: The past, present, and future of symbolic interactionism. Curr. Sociol. 2016 Oct 9; 64(6): 931–961. Publisher Full Text\n\nBricout JC, Gray DB: Community Receptivity: The Ecology of Disabled Persons’ Participation in the Physical, Political and Social Environments. Scand. J. Disabil. Res. 2006 Jan; 8(1): 1–21. Publisher Full Text\n\nEricsson S, Wojahn D, Sandström I, et al.: Language that Supports Sustainable Development: How to Write about People in Universal Design Policy. Sustainability. 2020 Nov 17; 12(22): 9561. Publisher Full Text\n\nHallgrimsdottir B, Wennberg H, Svensson H, et al.: Implementation of accessibility policy in municipal transport planning – Progression and regression in Sweden between 2004 and 2014. Transp. Policy (Oxf). 2016 Jul; 49: 196–205. Publisher Full Text\n\nSkarstad K: Human rights through the lens of disability. Netherlands Quarterly of Human Rights. 2018 Mar 9; 36(1): 24–42. Publisher Full Text\n\nWennberg H, Ståhl A, Hydén C: Implementing accessibility in municipal planning: planners’ view. J. Transp. Land Use. 2009 Sep 15; 2(2). Publisher Full Text\n\nBoisjoly G, El-Geneidy AM: The insider: A planners’ perspective on accessibility. J. Transp. Geogr. 2017 Oct; 64: 33–43. Publisher Full Text\n\nCurl A, Nelson JD, Anable J: Does Accessibility Planning address what matters? A review of current practice and practitioner perspectives. Res. Transp. Bus. Manag. 2011 Nov; 2: 3–11. Publisher Full Text\n\nEgard H, Hansson K, Wästerfors D: Accessibility Denied. Understanding Inaccessibility and Everyday Resistance to Inclusion for Persons with Disabilities. London: Routledge; 2021.\n\nSaha M, Chauhan D, Patil S, et al.: Urban Accessibility as a Socio-Political Problem. Proc. ACM Hum. Comput. Interact. 2021 Jan 5; 4(CSCW3): 1–26. Publisher Full Text\n\nBruce T, Zuo J, Rameezdeen R, et al.: Factors influencing the retrofitting of existing office buildings using Adelaide, South Australia as a case study. Struct. Surv. 2015 May 11; 33(2): 150–166. Publisher Full Text\n\nHussey M, MacLachlan M, Mji G: Barriers to the Implementation of the Health and Rehabilitation Articles of the United Nations Convention on the Rights of Persons with Disabilities in South Africa. Int. J. Health Policy Manag. 2016 Aug 28; 6(4): 207–218. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcClain L: Shopping Center Wheelchair Accessibility: Ongoing Advocacy to Implement the Americans with Disabilities Act of 1990. Public Health Nurs. 2000 May 25; 17(3): 178–186. PubMed Abstract \| Publisher Full Text\n\nGuo Y, Agrawal S, Peeta S, et al.: Impacts of Property Accessibility and Neighborhood Built Environment on Single-Unit and Multiunit Residential Property Values. Transp. Res. Rec. 2016 Jan 1; 2568(1): 103–112. Publisher Full Text\n\nNurlaela S, Pamungkas A: Assessing the Impact of Accessibility Improvement on Property Value Capitalization Post Perth – Mandurah Railway Opening. Procedia. Soc. Behav. Sci. 2014 Aug; 135: 96–105. Publisher Full Text\n\nShah M, Nair S: The Influence of Strategy and External Quality Audit on University Performance: An Australian perspective. Tert. Educ. Manag. 2011 Jun; 17(2): 139–150. Publisher Full Text\n\nMachado L d V, de Oliveira UR : Analysis of failures in the accessibility of university buildings. J. Build. Eng. 2021 Jan; 33: 101654. Publisher Full Text\n\nKristl Ž, Temeljotov Salaj A, Roumboutsos A: Sustainability and universal design aspects in heritage building refurbishment. Facilities. 2019 Dec 2; 38(9/10): 599–623. Publisher Full Text\n\nKusnierz-Krupa D: Historical Buildings and the Issue of their Accessibility for the Disabled. IOP Conf. Ser. Mater. Sci. Eng. 2019 Sep 1; 603(5): 052007. Publisher Full Text\n\nOrmerod MG, Newton RA: Moving Beyond Accessibility: The Principles of Universal (inclusive) Design as a Dimension in nD Modelling of the Built Environment. Archit. Eng. Des. Manag. 2005 Jan 6; 1(2): 103–110. Publisher Full Text\n\nJoseph S, Namboodiri V: Measuring Economic Benefits of Built Environment Accessibility Technologies for People with Disabilities. Stud. Health Technol. Inform. 2023; 381–388. Publisher Full Text\n\nTrischler J, Pervan SJ, Kelly SJ, et al.: The Value of Codesign. J. Serv. Res. 2018 Feb 10; 21(1): 75–100. Publisher Full Text\n\nMelis Y, Halime D: Reflection of Empathic Design Process on Interior Architecture Students’ Universal Design Solutions. METU J. Fac. Archit. 2023 Jun 30; 40(1): 59–82. Publisher Full Text\n\nIedema R, Merrick E, Piper D, et al.: Codesigning as a Discursive Practice in Emergency Health Services: The Architecture of Deliberation. J. Appl. Behav. Sci. 2010 Mar 31; 46(1): 73–91. Publisher Full Text\n\nAndersson JE, Skehan T: Accessibility in public buildings: efficiency of checklist protocols. Studies in Health Technology and Informatics. IOS Press; 2016; pp. 101–110.\n\nNewton S, Carnemolla P, Darcy S: Building information modelling and related technologies applied to the post occupancy evaluation of accessible bathrooms for people with disability. Smart and Sustainable. Built Environ. 2023 Jun 9. Publisher Full Text\n\nAkanmu AA, Olayiwola J, Olatunji OA: Automated checking of building component accessibility for maintenance. Autom. Constr. 2020 Jun; 114: 103196. Publisher Full Text\n\nMohapatra S, Maiya GA, Nayak UU, et al.: Data Set. Dataset. figshare. 2024." }	[ { "id": "343827", "date": "28 Dec 2024", "name": "Satendra Singh", "expertise": [ "Reviewer Expertise Disability justice" ], "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\nReview of Manuscript The authors of this multidisciplinary study sought to generate a list of best practices to guide municipalities, design professionals, advocates, rehabilitation workers, and users of public buildings in identifying approaches to augment accessibility to public buildings. Using a four-round Delphi method, the study identified ten priority areas to establish what they termed Justice-Centered Best Practices (JCBPs) for accessibility provisions for individuals with mobility disabilities. The research is highly relevant and timely, especially as the Supreme Court of India is currently deliberating on matters of accessibility, highlighting the inadequate implementation of universal accessibility in India. I approve the manuscript for acceptance subject to the following revisions: Major Revisions\nIntroduction:\nIn the second paragraph, include a mention of the United Nations Convention on the Rights of Persons with Disabilities (UNCRPD) as it is a key human rights instrument and has been ratified by the Indian Parliament. Clarify the term \"justice-centered perspective\" mentioned in the manuscript. Specify whether it refers to distributive justice or disability justice, as both have different implications. Provide relevant references.\n\nFigures and Legends:\nIn Figure 2, include the full forms of VRWs and MRWs in the legends or footnotes for clarity.\n\nEthics Committee Approval:\nThe manuscript mentions that machine learning was incorporated later to validate the expert scoring process, which was not part of the initial study protocol. Indicate whether this amendment was communicated to the ethics committee. If not, provide justification.\n\nThemes and Coverage:\nOn page 17, the theme of \"Built and non-built environment considerations and maintenance\" is discussed. However, the paragraph omits details about the non-built environment. Ensure this aspect is addressed. Additionally, while the study focuses on individuals with motor disabilities, sensory aspects (e.g., accessibility of websites) are excluded, which should be clarified. On page 18, in the theme \"Policies and compliance for accessibility,\" emphasize existing legal provisions in the Rights of Persons with Disabilities Act (2016), such as:\nDistrict-level committees with disabled persons' organizations. Sections 40–45 as the legal mandate for accessibility. India's flagship Accessible India Campaign. Rajive Raturi case in Supreme court seeking stakeholder feedback on accessibility currently\n\nLimitations:\nAcknowledge that the study does not address sensory disabilities (e.g., visual and hearing disabilities) or invisible disabilities (e.g., neurodivergent individuals, those with chronic illnesses, and epilepsy). On page 20, note that the research excludes other marginalized groups, such as older adults, people with multiple disabilities, and those facing gender-based issues.\n\nStrategies to Reduce Economic Burden:\nUnder \"Proposed strategies to reduce economic burden and increase opportunities for participation,\" reference provisions mandated in the Rights of Persons with Disabilities Act (2016), such as:\nNo establishment shall be granted permission to build any structure without adhering to government rules. No completion certificate or occupancy permit shall be issued unless accessibility rules are followed. A timeline for making existing public buildings accessible. Accessibility action plan on the website for essential services like primary health centers, civil hospitals, schools, railway stations, and bus stops. Promotion of universally designed consumer products and accessories.\n\nReferences:\nReferences 31, 32, and 39–44 are linked to the study supplement. Confirm whether these need to remain in the primary reference list or should be shared separately as supplementary material.\n\nAdditional Recommendation I strongly agree with the authors' assertion that accessibility is a human rights issue. It should also be framed as a process toward quality improvement. The following reference may be relevant: [ref 1]\nConclusion The manuscript is a valuable contribution to the field, addressing an urgent need to enhance accessibility for individuals with disabilities. Incorporating the revisions suggested above will strengthen its clarity, relevance, and impact.\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": "343823", "date": "30 Dec 2024", "name": "Adesola C Odole", "expertise": [ "Reviewer Expertise Musculoskeletal Physiotherapy", "Disability-inclusion", "Health outcomes assessment and climate change" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for asking me to review this manuscript titled “Justice-centered best practices for accessibility to public buildings in a tier II city: Insights from a Delphi expert consensus” for F1000Research. The study appears original and interesting. It is an attempt to provide a clear guidance for implementing accessible solutions for individuals with mobility disabilities. The methodological rigor for data collection is scientific and sound. However, there are minor comments of interest. Please find below specific comments:\n1. Abstract -Under Results: The number of identified items for the final list should be specified under feasibility, affordability and priority. The question of concern is what happens if an item scored low on any of the three domains of feasibility, affordability and priority?\nIntroduction (third paragraph) The word between in the sentence “…….. mitigating the symbiotic relationship between poverty, exclusion and disability….” Should be replaced with among. There should be a consistency in the use of either mobility or motor disabilities throughout the entire manuscript. There should be a consistency in the use of either mobility impairments or mobility disabilities throughout the entire manuscript. Authors to check inclusion and exclusion criteria.\n2.Inclusion and exclusion criteria\nWas there any specific limit for the experts’ years of experience in advocating for disability rights?\n3. Data collection -Why were the instructions given in both English and Kannada? Were the instructions translated from English to Kannada in a standardized manner or interpreted? -Did the authors set out to involve specific number of professionals, policy implementers and executives? How many of these individuals were involved in the study?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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/13-1145
https://f1000research.com/articles/13-1144/v1	07 Oct 24	{ "type": "Study Protocol", "title": "Standardised and Objective Dietary Intake Assessment Tool (SODIAT): Protocol of a dual-site dietary intervention study to integrate dietary assessment methods", "authors": [ "Eka Bobokhidze", "Michelle Weech", "Katerina Petropoulou", "Thomas Wilson", "Jennifer Pugh", "Rosalind Fallaize", "Isabel Garcia-Perez", "Frank P.-W. Lo", "Adrian R Solis", "Juliet Vickar", "Stamatia Giannarou", "George Mylonas", "Benny Lo", "Amanda J Lloyd", "Albert Koulman", "Manfred Beckmann", "John Draper", "Gary Frost", "Julie A Lovegrove", "Eka Bobokhidze", "Michelle Weech", "Katerina Petropoulou", "Thomas Wilson", "Jennifer Pugh", "Rosalind Fallaize", "Isabel Garcia-Perez", "Frank P.-W. Lo", "Adrian R Solis", "Juliet Vickar", "Stamatia Giannarou", "George Mylonas", "Benny Lo", "Amanda J Lloyd", "Albert Koulman", "Manfred Beckmann", "John Draper", "Gary Frost" ], "abstract": "Introduction Current dietary assessment methods face challenges in accurately capturing individuals’ dietary habits, undermining the efficacy of public health strategies. The ‘Standardised and Objective Dietary Intake Assessment Tool’ (SODIAT)-1 study aims to assess the effectiveness of three emerging technologies (urine and capillary blood biomarkers, and wearable camera technology) and two online self-reporting dietary assessment tools to monitor dietary intake.\n\nMethods This randomised controlled crossover trial will recruit 30 participants (aged 18-70 years and BMI of 20-30 kg/m2) from Imperial College London and the University of Reading. Exclusion criteria include recent weight change, food allergies/intolerances, following restrictive diets, certain health conditions and medication use. Interested volunteers will be directed to an online screening questionnaire via REDCap and eligible participants will attend a pre-study visit. Volunteers will consume, in a random order, two highly-controlled diets (compliant and non-compliant with UK guidelines) for four days each. Each study arm will be separated by at least one-week. During each test period, dietary intake will be monitored continuously using wearable cameras and self-recorded using eNutri (food frequency questionnaire) and Intake24 (24-hour dietary recall). Urine and capillary blood samples will be collected for biomarker analysis. Data analysis will assess the accuracy of dietary reporting across these methods using Lin’s concordance correlation coefficient.\n\nDiscussion and ethical considerations This study introduces a novel approach to dietary assessment, addressing the limitations of traditional methods by reducing misreporting and enhancing inclusivity, particularly for underrepresented populations with literacy or language barriers. However, challenges persist, such as variability in biomarker data due to failure to adhere to sample storage requirements and the practicalities of continuously wearing cameras. To protect privacy, participants will be instructed to remove cameras at inappropriate times, and artificial intelligence will be used to blur all images captured apart from food.", "keywords": [ "Nutrition", "Health", "Research", "Dietary reporting", "Underreporting", "Misreporting", "Biomarkers" ], "content": "Introduction\n\nOptimal nutrition is fundamental for maintaining good health and preventing diseases across the life course.1 The relationship between dietary habits and noncommunicable diseases (NCDs) is globally recognised,2,3 and evidence suggests unhealthy diets are strongly associated with increased prevalence of diabetes, various forms of cancer, and cardiovascular diseases.4–6 The impact of diet on population health has been highlighted by the Global Burden on Disease study that reported over 11 million deaths worldwide per year can be attributed to suboptimal diets.7\n\nNutrition research has a significant role in reducing the detrimental health impact of poor diets globally. Assessing population food intake can provide substantial data on the nation’s nutritional status and may be used in planning and implementation of evidence-based public health interventions.8 However, lack of accurate dietary assessment measures continuously undermines the strength and efficacy of public health strategies.9,10 Traditional subjective methods of dietary assessment, such as food frequency questionnaires (FFQs), 24-hour dietary recalls, and food diaries, are widely used to capture individuals’ dietary information.11 Despite being non-invasive, easy to use and suitable for large scale studies (depending on method), these self-reporting methods face notable challenges that can compromise the accuracy and reliability of collected dietary data.12–15 Memory recall bias is a common challenge, as participants may struggle to remember all consumed items, leading to potential underreporting or inaccuracies,14 whereas social desirability bias occurs when respondents align their reported food choices with perceived societal expectations, impacting the representation of true dietary habits.16 In addition, estimating portion sizes poses a challenge, as individuals may struggle with accuracy and perceptions of portion sizes differ between individuals (e.g., small, medium and large).17 Finally, response burden and fatigue, particularly prevalent when individuals weigh and record their dietary consumption over extended periods, can result in incomplete records, whereas day-to-day variability in dietary habits (such as oily fish and alcohol that are not typically eaten daily) may not be adequately captured for shorter recording periods.9\n\nCultural and social influences, lack of standardisation in reporting procedures, and limited detail on food preparation methods further contribute to the complexity of self-reported dietary assessments.13 The phenomenon of underreporting or overreporting in dietary assessments adds another layer of complexity, for example, obese individuals, particularly women, are most likely to underestimate their energy intake by under-reporting high energy foods considered socially undesirable.18 Mitigating these challenges and improving accuracy is essential for advancing the assessment methodology of population food intake.14\n\nIn addition to subjective measures, objective methods can also be used to assess dietary intake. These do not rely on participants’ self-reported intakes, instead dietary intake is assessed using various physical, biochemical, physiological or environmental measures, such as direct observation, nutritional biomarkers and duplicate diets.12 The development of advanced technologies, such as sensor-based and image-based tools, has increased the possibilities to address the limitations of self-reporting in nutrition research.19 Additionally, detecting dietary biomarkers in bodily fluids can reflect food intake and complement traditional dietary assessment methods.20 Implementing these methods minimise the biases associated with subjective measures, however, each objective method has its own limitations, and there is no universally accepted “gold standard”.12\n\nTo address this problem, the ‘Standardised and Objective Dietary Intake Assessment Tool’ (‘SODIAT’)-1 study will explore the ability of three emerging objective technologies and two subjective online tools to accurately assess what people eat and drink. The objective measures will include: 1. Urine biomarker metabolomics,21 2. Capillary blood biomarkers22 and 3. Wearable camera technology,23 and the subjective measures will include eNutri (online FFQ tool)24 and Intake24 (online 24h recall tool).13,24,25 The primary objective of the study is to calibrate the above dietary assessment technologies and tools for effectiveness to monitor exposure to foods/food groups commonly consumed in the UK in a controlled diet intervention. By conducting a comprehensive evaluation of their capabilities in accurately reporting dietary intake, the study aims to identify the most promising features of each technology. Subsequently, the research team will collaboratively integrate these features to create a combined optimal tool that maximises accuracy and usability which will be tested in future studies in the home environment (not described in this protocol).\n\n\nMethods\n\nIn randomised cross over study SoDiat-1 thirty male and female participants aged between 18-70 years will be recruited by the research teams at Imperial College London and University of Reading, with an equal distribution per study location. Participants of all ethnicities with a body mass index (BMI) 20-30 kg/m2 will be eligible. Exclusion criteria are as follows:\n\n• Involvement in any other study during the previous 12 weeks, is unable to commit to the study (e.g., travel commitments) or unwilling to collect urine and blood samples and wear the micro-camera.\n\n• A weight change of more than 3kg in the preceding 3 months or following a weight-loss diet.\n\n• Excess alcohol intake (more than 21 alcohol units per week).\n\n• Unwilling to abstain from drinking alcohol and avoid strenuous exercise during the two 5-day test periods.\n\n• Unwilling to follow the study menus (e.g., dislike of food items, following a restrictive/specialised diet or receiving specialised dietary advice for a medical condition).\n\n• Unable to eat fish and/or meat (e.g., are vegan or vegetarian).\n\n• Allergy/intolerance to any of the food items in the menu.\n\n• Use of dietary supplements (e.g., multivitamins, fish oils), unless willing to have a washout of at least 2 weeks prior to taking part in the study.\n\n• Pregnant or lactating.\n\n• Diagnosed with any of the following: eating disorder, diabetes, cancer, gastrointestinal disorders (e.g., inflammatory bowel disease or irritable bowel syndrome), kidney disease, liver disease, pancreatitis, HIV or AIDS or any other chronic illness.\n\n• Taking any of the following medications: anti-inflammatory drugs or steroids, antibiotics, androgens, phenytoin, erythromycin, or thyroid hormones.\n\n• Illicit substance use.\n\n• Diagnosed with dementia or other conditions affecting memory.\n\n• Difficulty using laptops/tablets (e.g., cannot use these devices without assistance, are blind or have other conditions affecting sight, or have physical disabilities/conditions that affect ability to press buttons).\n\n• Cannot read and understand English.\n\nVarious methods of recruitment will be employed, including distributing posters around the university campuses, emails sent to the respective clinical unit’s volunteer databases and university mailing lists, and social media advertisements for groups within the universities and surrounding areas. Recruitment will start in December 2023 and finish when required sample size is achieved. Recruitment materials will include a link and QR code that takes interested participants to REDCap, a secure web application for administering online surveys and recording datasets in research studies (https://www.project-redcap.org/), where they can view and download the participant information sheet.\n\nScreening\n\nInterested participants will complete an online screening questionnaire on REDCap, after which the respective research teams will determine their eligibility and/or request further information from the interested volunteers.\n\nConsent and pre-study visit\n\nPrior to starting the study, participants will attend the NIHR Imperial Clinical Research Facility at Hammersmith Hospital or the Hugh Sinclair Unit of Human Nutrition (HSUHN) at the University of Reading (depending on their preferred location as specified on the screening form). Researchers will explain the study in full, reconfirm eligibility (such as ensuring all food items on the menu can be consumed) and allow the participant to ask questions before informed written consent will be taken. During the pre-study visits, participants will be provided with a study handbook and the technologies used during the study will be explained and demonstrated to them. Their self-reported BMI will also be confirmed by measuring height and weight using a bioelectrical impedance analyser (Tanita MC780 MA P (Imperial) and BC-418 (Reading), TANITA UK Ltd, UK) to ensure the participant is within the correct BMI range. If the volunteer is happy to proceed, they will be invited to schedule the two 4-day study visits. They will also be provided with urine kits to take home and a reminder checklist/log form for the evening/morning prior to their first visit. A schematic diagram (Figure 1) illustrating the study process from recruitment through to completion.\n\nAfter the pre-study visit, participants will be assigned a study ID code and randomisation will be undertaken using REDCap. Participants will be randomly allocated to one of two diet orders: Diet 1 followed by Diet 2 or Diet 2 followed by Diet 1. Randomisation will be stratified by study centres. The research team and participant will not be blinded to the randomisation, as study menus are provided in advance, making it clear which diet they will follow each week.\n\nParticipants will consume two controlled diets, one per study period, provided in a random order: Diet 1: non-compliant with UK dietary guidelines (e.g., high in saturated fat, free sugars, and salt and low in fibre); Diet 2: compliant with UK dietary guidelines, e.g., within the dietary reference values for saturated fat (≤10% total energy (TE)), free sugars (≤5 %TE), salt (≤6 g/d) and fibre (≥30 g/d) (Table 1). The diets are matched for energy, protein, total fat and carbohydrate. Foods and drinks selected for each diet were selected to allow investigation of specific biomarkers.21 Each diet consists of a 2-day repeating menu (e.g., menu A served on days 1 and 3, and menu B served on days 2 and 4) as shown in Tables 2 and 3. Bottled spring water will also be available to drink throughout the day. Meals and snacks will be consumed at 2-hour intervals throughout the study days (9 am breakfast, 11 am morning snack, 1 pm lunch, 3 pm afternoon snack, and 5 pm dinner) and will be served using identical tableware at each research unit (white crockery and clear glass on days 1 and 2 and patterned crockery and coloured glass on days 3 and 4); no foods/drinks will be consumed directly from their packaging. Participants will also be provided with a snack and bottled water to take home to consume before 8 pm and instructed not to eat or drink anything else before returning to the research unit the following day.\n\n* Mean of menu 1 and menu 2 per study diet.\n\nThe study visits will take place at the NIHR/Imperial Clinical Research Facility at Hammersmith Hospital or the HSUHN at the University of Reading and will include two study periods each consisting of four full-day (8 am to 6 pm) visits from Monday to Thursday with a short visit on the fifth study day (Friday) to return final urine samples and all study equipment. A washout period of at least one week between study periods will be required (menstruating women will attend study visits at the same phase of their menstrual cycle).\n\nThe day before starting each study period, participants will be asked to restrict their caffeine and alcohol intakes and exercise levels to amounts that are usual for them and fast for 12 hours overnight (not consuming any food or drink, except water). Upon waking, participants will also collect a first morning void (FMV) urine sample.\n\nParticipants will attend the research unit at 8 am on day 1 (Monday) of each study period. Upon arrival, blood pressure, height and body weight will be measured. A fasted capillary blood sample (OneDraw) will also be self-collected and participants will be set up with the wearable camera (which will be worn continuously) before being provided with breakfast. Habitual diet will be recorded using the eNutri tool. With the exception of mealtimes, participants will have the rest of the day as free time but must remain in the research unit. At the end of the study day (6 pm), participants will be provided with bottled water and a snack for the evening, urine kits (for last evening void (LEV) and FMV samples) and a reminder checklist/log. Days 2-4 will repeat day 1 except: 1) Intake24 will be used on days 2-4 to record dietary intake during the previous 24 hours, 2) eNutri will be repeated at the end of day 4 (Thursday) to record dietary intake during the previous 4 days, and 3) capillary blood samples will not be collected on day 3 (Wednesday). On day 5 (Friday), participants will collect a final FMV, complete Intake24 and return samples/equipment to the research unit.\n\nSpot urine samples\n\nParticipants will collect spot urine samples using previously described methods.21 For each collection, participants will be provided with four additive-free vacuum collection tubes (4 mL) (plus two spares), urine transfer straws and a disposable collection cup (Figure 2). Participants will collect their FMV urine and LEV urine for all four study days in each study period as well as a FMV sample on day 5 using the collection cup. Participants will then transfer samples to four tubes via the transfer straw and store at 4 °C. During each study day, samples will be processed in the research unit using previously described methods to render them acellular then they will be stored at -80 °C until the end of the study.26\n\nUrinary biomarkers of dietary intake will be measured at Aberystwyth University using a combination of Ultra-High Performance Liquid Chromatography (UHPLC) Triple Quadrupole Mass Spectrometry (QqQ-MS) and high-resolution mass spectrometry (HRMS). Previous studies have determined a list of dietary intake biomarkers that reflect intake of common UK diet components and are sufficiently robust and reproducible in spot urine samples from dietary intervention studies.27 Global dietary patterns will be assessed by measuring the urine samples using Proton Nuclear Magnetic Resonance (1H-NMR) at Imperial College London. A global dietary score will be generated from the 1H-NMR urinary metabolic profiles following a previously validated methodology28 that will indicate the quality of the diet in combination with a complementary set of urinary dietary biomarkers.\n\nCapillary blood samples\n\nCapillary blood samples will be self-collected by participants prior to breakfast on days 1, 2 and 4 using a OneDraw kit (Drawbridge, Thorne Research, Summerville SC, US) as shown in Figure 3. The single-use device attaches to the upper arm or thigh via a hydrogel adhesive and vacuum and collects capillary blood with little discomfort for the participant. The capillary blood is directly collected onto two paper strips.22 When the collection is finished, the cartridge containing the blood samples will be placed in the transport sleeve then left at room temperature for at least 48 hours to allow the blood to dry prior to storage at -80 °C.\n\nThe dried blood samples will be extracted at the University of Cambridge using a standard protocol for dried blood spots29 and the lipid profile will be analysed using a combination of UHPLC and HRMS, and lipids will be quantified against internal standards as published previously.22\n\nWearable camera technology\n\nTo effectively capture the dietary habits and food-related activities of individuals in UK households, a comprehensive passive dietary assessment system has been meticulously designed for this study. This system is a fusion of both hardware and software components, each with distinct functionalities to enhance the accuracy and efficiency of dietary data collection.\n\nHardware\n\nFor this pilot study, prototype of the camera was developed - wearable camera capable of recording up to 20hrs called M2.1. The wearable camera device is a high-definition camera with a maximum resolution of 2592x1944 pixels, mounted on the side arm of lens-less eye glasses frames to align with the user’s viewpoint and is connected to a rechargeable powerpack whilst in use (Figure 4). It is designed to be used during daytime, capturing images of the eating process at frequency of one image every 1.5 seconds. The camera is powered by a built-in STM32 microcontroller with a 32-bit arm processor. The device begins recording upon the insertion of an empty 128 GB SD card and the camera is turned on. The camera is turned on automatically once is connected to the external battery.\n\nPrior to breakfast on day 1, participants will receive a camera device mounted on a glasses frame (or they can mount this on their own glasses frame) and instructed to wear this continuously until they go to bed, with the exception of when it is not suitable for the camera to be worn (such as when getting dressed and using the bathroom) in which case the glasses will be temporarily removed and details noted on the camera log. Upon arrival to the research unit on days 2-5, the SD cards will be removed from the camera device by the research team and uploaded in duplicate to two encrypted external hard drives. Whilst the cameras are not in use overnight, participants will be instructed to fully charge the power packs and start wearing the cameras the following morning before returning to the research unit (days 2-4).\n\nSoftware\n\nTo ensure the anonymity of individuals, all footage captured by wearable cameras will undergo pre-processing prior to analysis. Initially, a large foundation model known as the Recognize Anything Model (RAM)30 will be employed. RAM specializes in image tagging and has been developed through extensive training on a large number of general images. This model will play a crucial role in identifying images captured by our customized wearable camera. Its function will be to detect the presence of food items within these images. Upon detection of food items, RAM will assign a ‘food tag’ to the relevant images. This tagging mechanism is both efficient and precise, ensuring that only images with clear food content are marked for inclusion. The images that receive a ‘food tag’ from RAM will then be segregated from the rest and earmarked for further analysis, forming the core dataset for the study. Meanwhile, we have also designed ‘excluding tags’ for our model, which include around 20 categories of items such as bathrooms, mobile phone screens, and PC screens, with the flexibility to add or remove items as needed. This design is intended to prevent sensitive items from appearing alongside food in the collected data. Furthermore, for the retained images, an additional layer of protection will be implemented by blurring the faces of the participants and other individuals residing with them, as well as any other visible phone and computer screens that were unintentionally missed in the previous step. This step will use YOLOv8,31 a deep learning technique renowned in the field of image recognition, to prevent the inadvertent disclosure of identities and personal information. Only after this pre-processing will the images be subjected to further analysis.\n\nFollowing pre-processing is the food recognition phase, where we will leverage large language models (LLMs)32 capable of processing both text and images. These models have been extensively trained on vast datasets, allowing them to recognize a wide range of food types without the need for additional training or fine-tuning. Portion size estimation also plays a pivotal role in dietary assessment, and our approach is tailored to address the unique challenges associated with using a wearable camera that captures only red-greed-blue (RGB) images, without the depth information provided by stereo imaging. This brings us to the issue of scale ambiguity, which is a significant problem given that our system cannot rely on stereoscopic methods to estimate the volume of food items. To circumvent the need for users to place a reference object next to their food - which would be an inconvenience and could disrupt the natural eating environment - we are exploring the potential of leveraging large-scale AI foundation models to learn the general context of objects and their environmental surroundings in relation to food. By understanding these contextual relationships, the model can make more accurate inferences about the portion sizes of the food being consumed.\n\n24-hour dietary recall\n\nParticipants will complete a self-administered 24-hour dietary recall following each study day to measure both the accuracy of self-reporting and usability of repeated 24-hour dietary recalls. Participants will use Intake24 (intake24.com), which is a validated, web-based, open-source computerised dietary recall system based on the multiple pass method.33 The tool, currently maintained by the University of Cambridge, Monash University and Newcastle University, is used by the UK’s National Diet and Nutrition Survey Rolling Programme.25,33 Participants will use Intake24 to record everything they ate and drank the day before from midnight to midnight by using free text to list each food/drink item consumed per meal as part of the initial ‘quick list’. Next, the detailed pass stage involves searching Intake24’s food database for the closest match for each item then estimating their portion size using the images presented on the screen. Intake24 will also prompt the participant about foods usually consumed together, e.g., if they recorded coffee then it will ask if they added milk and/or sugar, as well as frequently forgotten foods, such as condiments. Additional questions will be presented if Intake24 identifies long time gaps without food or very low energy intakes, and the recall ends with the participant reviewing their entries. Prior to completing Intake24 for the first time, participants will be encouraged to watch the tutorial video (accessible via the Intake24 menu). At the end of the study, data will be exported from Intake24 including the quantities and nutritional intakes for each food item recorded per recall, after which mean daily intakes per day per participant will be calculated.\n\nFFQ\n\nThe eNutri web app, developed by researchers from the University of Reading, includes an FFQ based on UK diets.34 The current version includes 157 food, drink and supplement items. For each food and drink item, users first select how often they consumed it during the previous 4 weeks from 10 frequency buttons (such as ‘not in the last 4 weeks’ and ‘once a day’). If consumed, they then select their typical portion size from 7 portion size photos/buttons. Certain items (n=37) also request additional details, for example, the type of milk (if any) added to their coffee and whether the item consumed was a low-fat or low-sugar variety (e.g., soft drinks, yogurts); each of these items also has an ‘I’m not sure’ option. Users also report frequency of use of salt (added at the table and/or during cooking) and 8 dietary supplements. Using this information, eNutri automatically calculates mean daily intakes (g/d) of each food item, from which it estimates a large range of food group intakes (e.g., vegetables, dairy) and nutrient intakes (e.g., protein, vitamin C). In addition to dietary intake, eNutri also records certain demographic and lifestyle information about the users (such as age, sex, ethnicity, education level, physical activity levels and smoking status).\n\nFor this study, participants will use the eNutri FFQ tool on day 1 of study period 1 to measure their habitual diet by recording what they ate and drank during the previous 4 weeks. Prior to using eNutri for the first time, participants will watch the short tutorial video on the web app. To measure dietary intake during the two 4-day study periods, a separate version of eNutri was created that adapted the frequency options to reflect 4 days of dietary intake (such as ‘not in the last 4 days’ and ‘1x in the past 4 days’).\n\nParticipants will complete the system usability scale (SUS) questionnaire following their first use of eNutri (day 1, week 1) and Intake24 (day 2, week1) via REDCap. The SUS questionnaire is widely-used to “measure people’s subjective perceptions of the usability of a system” and comprises of 10 alternating positive and negative statements regarding the user experience (Table 4).35 For each statement, respondents rate their agreement on a 5-response-scale from “Strongly Disagree” to “Strongly Agree” and, using the method described by Brooke (1995), a SUS score ranging from 0 to 100 is calculated, with higher scores indicating better usability.36 Overall usability is also evaluated with a general question: “Overall, I would rate the user-friendliness of this system as:” with 7 options from “Worst Imaginable” to “Best Imaginable”.\n\n* System usability scale.\n\nAt the end of the study (day 4, week 2), participants will also provide feedback about all of the tools used during the study. This includes free text and Likert questions and will be completed via REDCap.\n\nPrevious studies have shown that the misreporting rate of total energy expenditure between self-reported dietary assessment tools and double labelled water was 35 % with a standard deviation of 33 %.37 To reduce the misreporting rate to <10%, an a priori sample size calculation determined that to achieve a power of 80 % with a type 1 error of 5%, a total of 27 participants are required. This was increased to 30 participants to account for potential dropouts. Two separate clinical research centres will be used, with both centres recruiting participants to ensure consistent demographics between sites (sex, age, and BMI).\n\nBootstrapped Lin’s concordance correlation coefficient (CCC) with 95% confidence intervals will be used to test the extent of agreement between each dietary assessment tool/technology and the nutrient composition of known diets and recorded compliance.\n\nThe primary outcome will be the accuracy of dietary reporting, measured at the end of each intervention week using dietary data collected from wearable cameras, spot urine samples, capillary blood samples, and self-reported dietary assessments.\n\nSecondary outcome measures include: 1) the creation of a multiplatform model of dietary intake using g/day measured from wearable cameras and self-report dietary assessments, and μg/ml of dietary exposure biomarkers from spot urine samples and capillary blood samples at the end of the study, and 2) the design of a dietary intake study in a free-living population that will be informed by the results of the current dietary intake study protocol.\n\nThe results of this study will be presented at medical meetings, research conferences and published open access in peer-reviewed scientific journals and lay publications, approximately six months following the end of the study. They will also be used by research students who are associated with this project in work that will contribute to their degree (BSc, MSc, PhD) or other qualification, and shared with the press and media. The datasets will be made available and deposited in public databases at the point of publication. All data will be released within 2 years of the project’s completion and will be made accessible.\n\n\nDiscussion\n\nThis study provides a novel approach to dietary assessment by addressing the significant limitations present in traditional methods, such as those used in the National Diet and Nutrition Survey10 and other population surveys.33 The novel methods to be tested in SODIAT-1 will reduce participant burden, requiring less detailed recording of foods and drinks consumed. For individuals with conditions affecting memory, this approach also eliminates reliance on recall, thus reducing the risk of inaccurate data collection.13 Furthermore, the methodology will particularly be helpful to capture dietary intake of underrepresented populations, including individuals with illiteracy, language and cultural differences as well as marginalised groups such as homeless people, whose dietary intake is difficult to capture accurately through traditional self-reporting methods and are often left out from the nationwide studies.38 The ability to access these populations broadens the scope and applicability of dietary assessments, providing a more comprehensive understanding of dietary patterns across different demographics.\n\nDespite these strengths, there are also limitations to this this approach when used in less controlled conditions. For instance, participants will be asked to keep their urine samples refrigerated before returning them to the study centre, but failure to comply could affect biomarker detection during analysis, potentially compromising the accuracy of the data.20 The use of cameras to record dietary intake also presents challenges. For example, accurately measuring foods and drinks consumed directly from their packaging (e.g., cans of fizzy drinks and packets of crisps) remains difficult and amount of the leftovers cannot be detected. Additionally, distinguishing between types of foods and drinks (e.g., low-fat versus whole yoghurts or sugar-free versus sugar-sweetened drinks) through visual means can be challenging. Moreover, this method relies on participants consistently wearing and correctly using the cameras, which may not always be practical or adhered to.19\n\nThe study received a favourable opinion for conduct by the Camden & Kings Cross Research Ethics Committee (23/LO/0437) on 4th July, 2023 and the University of Reading Research Ethics Committee (23/19) on 19th May, 2023. The study will be conducted according to the principles expressed in the Declaration of Helsinki.\n\nPrior to screening, potential participants will receive an ethically approved participant information sheet containing full details of the study. They will have adequate time to consider taking part in the study and have an opportunity to ask questions before attending the pre-study visit where they will give written informed consent.\n\nWhen participants wear the cameras, they will collect images of the participant, people around them and their devices (e.g. smartphones). To ensure everyone’s anonymity and privacy, any people and device screens recorded on the images will be automatically blurred prior to analysis, as described above. In addition, any non-food related images will be removed from the dataset. Both processing steps will be achieved via an artificial intelligence methodology and only the pre-processed dataset will be analysed by the research team. Participants will also be advised to remove their camera when it is not appropriate to wear them (such as when in the bathroom and dressing) and to log these instances.\n\nThe data collected through the SoDiat-1 study will be pseudonymised and anonymised. Pseudonymised data will be shared among research partners for data analysis purposes. The confidentiality of study participants will be preserved under the Data Protection Act. Acellular urine samples will be transferred to Aberystwyth university and dried blood samples will be sent to the University of Cambridge in compliance with the Human Tissue Authority (HTA) regulation. The data generated from the wearable cameras will be stored on encrypted hard drives and transferred to Imperial College London after the data collection is completed. For subjective dietary assessment tools eNutri and Intake24, participants will use pre-generated weblinks and/or login details to avoid using personal information such as email addresses and names. Other data will be input on REDCap by study researchers, which will be double checked by the study coordinator at each site before the records are locked.\n\nRecruitment for this study concluded in May 2024, with data collection completed in mid-June 2024. At the time of paper submission, blood and urine samples, as well as camera images, have been transferred to the respective research teams, and data analysis is currently in progress.\n\nThe study was registered at ISRCTN (ISRCTN13562899).", "appendix": "Data availability\n\nNo data is associated with this article.\n\nZenodo: A-dual-site-dietary-intervention-study-to-integrate-dietary-assessment-methods. https://zenodo.org/records/13360114\n\nThis project contains the following extended data:\n\n• Dual_site_dietary_intervention_Menus.pdf (Study Meal Plans)\n\n• Dual_site_dietary_intervention_PIS.pdf (Participant Information Sheet)\n\n• Protocol_Version1.0_15032023.pdf (Study Protocol)\n\n• Consent form\n\n• SPIRIT 2013 Checklist\n\nData are available under the terms of the Creative Commons Zero v1.0 Universal License (CC0).\n\n\nAcknowledgements\n\nInfrastructure support for the studies run at Imperial College London will be provided by the NIHR Imperial Biomedical Research Centre (BRC) and the NIHR Imperial Clinical Research Facility. TW and MB acknowledge funding from the UK Medical Research Council (MRC Grant Ref: MR/S010483/1). GF is an NIHR senior investigator and is funded through the NIHR, BBSRC, MRC and EU horizon 2020. AK was supported by the NIHR Cambridge Biomedical Research Centre (NIHR203312). IGP is supported by a NIHR Career Development Research Fellowship (NIHR-CDF-2017-10-032), Horizon Europe project DOMINO (grant number 101060218), the Horizon Europe project CoDiet (grant number 101084642) and Medical Research Council (MRC) funded GI tools project (MR/V012452/1). EB’s PhD was supported by LEPL International Education Center of Georgia. JV’s PhD was supported by the UK FoodBioSystems Doctoral Training Partnership (DTP) (BB/T008776/1).\n\n\nReferences\n\nRodríguez-Mañas L, Murray R, Glencorse C, et al.: Good nutrition across the lifespan is foundational for healthy aging and sustainable development. Front. Nutr. 2023; 9: 9. Publisher Full Text\n\nKrieger JP, Pestoni G, Frehner A, et al.: Combining recent nutritional data with prospective cohorts to quantify the impact of modern dietary patterns on disability-adjusted life years: A feasibility study. Nutrients. 2020; 12(3). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWHO, FAO: Diet, nutrition and the prevention of chronic diseases: report of a joint WHO/FAO expert consultation.2002.\n\nDominguez LJ, Bes-Rastrollo M, Basterra-Gortari FJ, et al.: Association of a dietary score with incident type 2 diabetes: The dietary-based diabetes-risk score (DDS). PLoS One. 2015; 10(11): e0141760. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMicha R, Shulkin ML, Peñalvo JL, et al.: Etiologic effects and optimal intakes of foods and nutrients for risk of cardiovascular diseases and diabetes: Systematic reviews and meta-analyses from the nutrition and chronic diseases expert group (NutriCoDE). PLoS One. 2017; 12(4): e0175149. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Cancer Research Fund, American Institute for Cancer Research: Diet, nutrition, physical activity and cancer: A Global Perspective. A summary of the third expert report.2018.\n\nAfshin A, Sur PJ, Fay KA, et al.: Health effects of dietary risks in 195 countries, 1990–2017: A systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2019; 393: 1958–1972. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhluwalia N, Dwyer J, Terry A, et al.: Update on NHANES dietary data: Focus on collection, release, analytical considerations, and uses to Inform public policy. Adv. Nutr. 2016; 7: 121–134. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKipnis V, Midthune D, Freedman L, et al.: Bias in dietary-report instruments and its implications for nutritional epidemiology. Public Health Nutr. 2002; 5(6A): 915–923. PubMed Abstract \| Publisher Full Text\n\nNDNS Years 5-9: Appendix X. Misreporting in the National Diet and Nutrition Survey Rolling Programme: Summary of results and their interpretation.2008.\n\nKirkpatrick SI, Vanderlee L, Raffoul A, et al.: Self-Report dietary assessment tools used in Canadian research: A scoping review. Adv. Nutr. 2017; 8(2): 276–289. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDAPA Measurement Toolkit: Dietary Assessment Domain 2024.Reference Source\n\nGibson RS, Charrondiere RU, Bell W: Measurement errors in dietary assessment using self-reported 24-hour recalls in low-income countries and strategies for their prevention. Adv. Nutr. 2017; 8: 980–991. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRavelli MN, Schoeller DA: Traditional self-reported dietary instruments are prone to inaccuracies and new approaches are needed. Front. Nutr. 2020; 7: 7. Publisher Full Text\n\nStrahan RF: Regarding some short forms of the Marlowe-Crowne social desirability scale. Psychol. Rep. 2007; 100(2): 483–488. PubMed Abstract \| Publisher Full Text\n\nHebert JR, Hurley TG, Peterson KE, et al.: Social desirability trait influences on self-reported dietary measures among diverse participants in a multicenter multiple risk factor trial. J. Nutr. 2008; 138(1): 226–234.\n\nFerreira GR, da Silva DG , Taconeli CA, et al.: Assessment of bias and associated factors for food portion quantification with photos in Brazil. Measurement: Food. 2021; 3: 100007. Publisher Full Text\n\nConnor S: Underreporting of dietary intake: Key issues for weight management clinicians. Curr. Cardiovasc. Risk Rep. 2020; 14(16). Publisher Full Text\n\nRantala E, Balatsas-Lekkas A, Sozer N, et al.: Overview of objective measurement technologies for nutrition research food-related consumer and marketing research. Trends Food Sci. Technol. 2022; 125: 100–113. Publisher Full Text\n\nGao Q, Praticò G, Scalbert A, et al.: A scheme for a flexible classification of dietary and health biomarkers. Genes Nutr. 2017; 12: 34. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLloyd AJ, Wilson T, Willis ND, et al.: Developing community-based urine sampling methods to deploy biomarker technology for the assessment of dietary exposure. Public Health Nutr. 2020; 23(17): 3081–3092. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKoulman A, Prentice P, Wong MCY, et al.: The development and validation of a fast and robust dried blood spot based lipid profiling method to study infant metabolism. Metabolomics. 2014; 10(5): 1018–1025. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang W, Min W, Li T, et al.: A review on vision-based analysis for automatic dietary assessment. Trends Food Sci. Technol. 2021; 122: 223–237.\n\nZenun Franco R, Fallaize R, Weech M, et al.: Effectiveness of web-based personalized nutrition advice for adults using the eNutri Web App: Evidence from the EatWellUK Randomized Controlled Trial. J. Med. Internet Res. 2022; 24(4): e29088. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFoster E, Lee C, Imamura F, et al.: Validity and reliability of an online self-report 24-h dietary recall method (Intake24): a doubly labelled water study and repeated-measures analysis. J. Nutr. Sci. 2019; 8: e29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilson T, Garcia-Perez I, Posma JM, et al.: Spot and cumulative urine samples are suitable replacements for 24-Hour urine collections for objective measures of dietary exposure in adults using metabolite biomarkers. J. Nutr. 2019; 149(10): 1692–1700. PubMed Abstract \| Publisher Full Text\n\nBeckmann M, Wilson T, Zubair H, et al.: A standardized strategy for simultaneous quantification of urine metabolites to validate development of a biomarker panel allowing comprehensive assessment of dietary exposure. Mol. Nutr. Food Res. 2020; 64(20): e2000517. PubMed Abstract \| Publisher Full Text\n\nGarcia-Perez I, Posma JM, Gibson R, et al.: Objective assessment of dietary patterns by use of metabolic phenotyping: a randomised, controlled, crossover trial. Lancet Diabetes Endocrinol. 2017; 5(3): 184–195. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFurse S, Koulman A: Lipid extraction from dried blood spots and dried milk spots for untargeted high throughput lipidomics. Molecular Omics. 2020; 16: 563–572. PubMed Abstract \| Publisher Full Text\n\nZhang Y, Huang X, Ma J, et al.: Recognize anything: A strong image tagging model. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. 2023; pp. 1724–1732.\n\nJocher G, Chaurasia A, Qiu J: Ultralytics YOLOv8. Version 8.0.0.2023. Reference Source\n\nLo FP, Qiu J, Wang Z, et al.: Dietary assessment with multimodal ChatGPT: A systematic analysis. IEEE J. Biomed. Health Inform. 2024; 1–11. Publisher Full Text\n\nPublic Health England, Food Standards Agency: Evaluation of changes in the dietary methodology in the National Diet and Nutrition Survey Rolling Programme from Year 12 (2019 to 2020).2021.\n\nFallaize R, Weech M, Franco RZ, et al.: The eNutri app: Using diet quality indices to deliver automated personalised nutrition advice. Agro Food Ind Hi Tech. 2020; 31(2).\n\nBrooke J: SUS: A quick and dirty usability scale. Usability evaluation in industry. 1995; p. 189.\n\nBangor A, Kortum P, Miller J: Determining what individual SUS scores mean: Adding an adjective rating scale. J. Usability Stud. 2009; 4(3): 114–123.\n\nPettitt C, Liu J, Kwasnicki RM, et al.: A pilot study to determine whether using a lightweight, wearable micro-camera improves dietary assessment accuracy and offers information on macronutrients and eating rate. Br. J. Nutr. 2016; 115(1): 160–167. PubMed Abstract \| Publisher Full Text\n\nHolmes B, Dick K, Nelson M: A comparison of four dietary assessment methods in materially deprived households in England. Public Health Nutr. 2008; 11(5): 444–456. PubMed Abstract \| Publisher Full Text" }	[ { "id": "341524", "date": "17 Dec 2024", "name": "Cătălina Cuparencu", "expertise": [ "Reviewer Expertise biomarkers of food intake", "dietary assessment", "nutrition research", "metabolomics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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: The manuscript describes the protocol for a study designed to integrate dietary assessment tools covering traditional technologies (FFQs and recalls) with last-generation technologies (biomarkers of food intake measured in biological samples and wearables). The study is great in many ways and has the potential to shed light into the applicability and cost-effectives of the new dietary assessment tools, as well as providing a first attempt to cross-validate these tools against each other. The concept is novel and highly needed to move dietary assessment forward in nutrition research and provide a more accurate estimate of the human diet.\nSome considerations: Abstract: The cross-over design is 2x4 days with wash out. How will the FFQs information be integrated with the acute dietary information? Dietary intake will be monitored continuously through wearable cameras (abstract). I would imagine the cameras (glasses) have to be taken off at times (also stated by the authors later in the abstract)? Maybe “continuously” is not the best term here. In the discussion point (abstract) it is unclear how the study will enhance the inclusivity of underrepresented populations with literacy or language barriers, since the study will primarily recruit from Imperial College London and Reading University. If this is a perspective (future application of this methodology / impact), it should be seeded in the introduction, for coherence.\n\nI suggest the authors be somewhat more cautious when stating “reducing misreporting and enhancing inclusivity”. The methodologies they will test are far from being validated and fully accurate, and the cross-validation still relies on participants turning the wearables on. It is therefore yet to be investigated if this integrative approach will indeed reduce misreporting.\nIntroduction - I suggest cautiousness in classifying wearables as part of “objective” measures, since they essentially also rely on the will of the study population to actually record everything.\nRecruitment – it is stated that recruitment will start in December 2023 -> change to started? although later in the manuscript it is stated that it is also already completed. This can be already stated from the start.\nStudy design:\nIn what cases will the washout before study not be needed? (Figure 1) Habitual diet will be recorded with the eNutri tool. How is this data relevant to the study? It is slightly unclear if day 2-4 are conducted also at the research center? I would assume not, but some clarification with help the reader\nObjective dietary assessment tools\nHow will the spot urines be normalized? Is the blood collection device standardized for volume of blood, or how would this be quantified? Wearables: very interesting technology developed, that takes into account some limitations of such technologies (eg privacy). Few points: is the recorded dietary data connected to the same food composition database as the subjective tools used (eNutri, intake24)? How does the dietary recording work with stacked foods (i.e., burgers or sandwiches) to disentangle the identity and quantities of the ingredients? What about composite meals? Wearables: here it is stated that participants come to the research center days 2-4; yet, later the authors refer to “natural eating environment”. This should be clarified, as an experimental diet, even if designed according to national dietary guidelines, it is by no means a natural eating environment, even more so if it is consumed at a research center\nPrimary outcome: what will be the “golden standard” among the 4 methodologies? In other words, how do the authors define “the accuracy of dietary reporting”? Logically, it would be the reflection of the diet in comparison with the dietary intervention – if this is correct, it should be clearly stated. Moreover, will this be measure at the nutrient, food group or dietary pattern level?\nSecondary outcome: ug/ml of dietary exposure biomarker indicates quantitative biomarkers. This may be true for nutrients, but most foods are not covered by quantitative biomarkers reflecting their intake. Considering the spot sampling with potential imprecise information of volume (leading to inaccurate urines concentration, potentially also for blood spots, depending on the device used), quantifying amounts consumed with biomarkers can be challenging. What are the authors’ thoughts on this?\nEthics: how is the data privacy through AI being monitored?\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": "359796", "date": "03 Feb 2025", "name": "Emily B. Hill", "expertise": [ "Reviewer Expertise dietary assessment", "metabolomics", "nutrition intervention", "behavior change" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOVERVIEW AND GENERAL COMMENTS\nThis protocol describes a controlled feeding study designed to assess the effectiveness of three technologies (urine biomarkers, capillary blood biomarkers, wearable camera technology) alongside two self-report dietary assessment tools. While this is a well-defined population and study design, it is unclear if the proposed correlational analyses will be sufficient to determine “effectiveness” of these tools. Generally, this is a well-written protocol to address a need in dietary assessment that is highly relevant. It is acceptable for indexing given the general concern above and below comments are addressed.\nSPECIFIC COMMENTS\nAbstract: Which of the assessment methods are considered novel? Diet records and food frequency questionnaires are commonplace in nutrition research, and details regarding biomarkers and wearable technology are quite limited in the description provided. Further, is “actual” food intake (i.e., weighed/portioned food delivered in a controlled setting) the comparator for each of the five proposed assessment methods?\nAbstract: It seems a food frequency questionnaire would be an odd choice for assessment of a four-day diet, as the purpose of this instrument is to assess usual intake over a defined period of time (typically 30 days or more). Has the eNutri tool been validated for this recall period? How will data be integrated between diet assessment instruments?\nAbstract: Which urine and capillary biomarkers will be measured? How will they be measured (e.g., targeted vs untargeted approaches)?\nAbstract: Authors do not describe how this study will reduce misreporting or enhance inclusivity.\nIntroduction: While a good point, stating that shorter recording periods for dietary assessment are problematic for capturing day-to-day variability seems to be counterproductive to the main rationale for conducting a study with four-day controlled feeding periods that may not be reflective of usual intake.\nIntroduction: Consider person-first language; “obese individuals” could be re-written as “individuals with obesity.”\nMethods, Study population: What is the rationale for the BMI I/E criterion of 20-30 kg/m2? This does not fully capture the “normal” range (18.5-24.9 kg/m2) and does include those with obesity (BMI³30 kg/m2). Thus, this range seems a bit arbitrary.\nMethods, Study diets: Were diets designed only to be matched in terms of nutrient composition, or were similar foods/food groups balanced as well? Authors state “foods and drinks for each diet were selected to allow investigation of specific biomarkers,” but this does not shed much light on the details for these selections.\nMethods, Study diets: It remains unclear which specific biomarkers will be employed/tested, though references are provided under the “spot urine samples” and “capillary blood samples” sections. It may be helpful to include examples of these compounds in table format. Is a one-week washout period adequate based on the expected half-life of these biomarkers, and are they expected to be sufficiently different between diets?\nMethods, Study visit procedures/24-hour dietary recall/FFQ: It appears habitual diet as assessed on Day 1 of the protocol using the eNutri tool reflects usual intake prior to the study period? How is it used in this study? Why is Intake24 not used on Day 1?\nMethods, Objective dietary assessment tools: Information on the type of analysis (metabolomics at minimum) would be helpful to include earlier in the protocol.\nMethods, Objective dietary assessment tools/Capillary blood samples: Is a capillary blood draw completed only in the morning of each study visit on Days 1, 2, and 4? What is the rationale for excluding day 3?\nMethods, Wearable camera technology: It is not clear why the participants will be asked to continuously wear the mounted camera outside of eating windows.\nMethods, FFQ: As mentioned in the abstract, it is not clear that the eNutri tool has been validated for four-day recall periods – is part of the objective of this study to validate the “separate version” that was created? If so, how will this be done?\nMethods, Statistical analysis: Are simple measures of correlation between instruments adequate to measure accuracy? Are the biomarkers selected indicative of specific nutrients (e.g., fat, sodium), foods, or food groups? If the latter are not controlled for or not substantially different between diets, what is the expectation for how accuracy will be determined if the biomarkers do not distinguish at this level? Where will participants report/record compliance? Or is the study team measuring this? Details are lacking for evaluation of these methods.\nMethods, Primary outcomes: How will “accuracy” be determined amongst the data collected? Which measure is “true?”\nMethods, Secondary outcomes: It is not clear how this multiplatform model will be designed or how all of the assessment measures will be integrated together. Further, with no detail on the biomarkers of interest, it is impossible to evaluate if the goal of assessing ug/mL of dietary exposure biomarkers is realistic. Many untargeted metabolomics assays do not provide data at this level (e.g., relative abundance vs quantitative measures/concentrations). While the use of triple quad indicates some targeted panels may be run and thus this may be possible, the stated goal to create a simple “global dietary score” from NMR data does not align with this stated objective.\nDiscussion: While the end goal is to reduce participant burden, this reviewer would argue the study increases it given the number of data collection procedures. Consider specifying that if the methods tested are reliable, reproducible, etc. and can be incorporated into clinical practice and/or future research, this could reduce burden.\nDiscussion: Similar to comments in the abstract, it is not immediately clear how these methods will improve assessment in underrepresented populations, particularly those who are experiencing homelessness, as stated in text. It would be near impossible to give someone the wearable technology or ask them to appropriately collect and store biospecimens such as urine under those conditions.\nDiscussion: Consider adding to strengths/limitations the length of collection for blood (small capillary sample vs venous draw) and urine (spot vs 24 hour). While these methods may reduce participant burden, they also weaken the ability to capture precise measures reflective of longer periods of intake.\nEthical considerations: While perhaps outside the scope of this protocol manuscript, it is not clear how AI technology being employed is protective of personally identifiable information – what program “sees” this? The reviewer notes the software availability statement but feels this may be inadequate.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-1144
https://f1000research.com/articles/13-1142/v1	07 Oct 24	{ "type": "Research Article", "title": "Expression of microRNA-21 in acute ischemic stroke: relationship with inflammatory cytokines, clinical severity, and clinical outcome", "authors": [ "Ashari Bahar", "Muhammad Akbar", "Andi Kurnia Bintang", "Muhammad Nasrum Massi", "Rusdina Bte Ladju", "Agussalim Bukhari", "Jumraini Tammasse", "Wijoyo Halim", "Gita Vita Soraya", "Irawan Satriotomo", "Muhammad Akbar", "Andi Kurnia Bintang", "Muhammad Nasrum Massi", "Rusdina Bte Ladju", "Agussalim Bukhari", "Jumraini Tammasse", "Wijoyo Halim", "Gita Vita Soraya" ], "abstract": "Background When the brain is deprived of oxygen and nutrients due to stenosis or arterial rupture, neurons in the affected area suffer irreversible damage and cellular death. MicroRNA has been shown to regulate target genes implicated in arterial hypertension, atherosclerosis, and diabetes mellitus, all of which influence the risk of ischemic stroke through inflammation, oxidative stress, cell proliferation, and apoptosis. The study aims to determine the changes in miRNA expression, namely miRNA-21, between acute ischemic stroke patients and controls and their relationship to proinflammatory cytokines, clinical severity, and outcome.\n\nMethods Serum samples from tertiary hospitals and controls were used to evaluate miRNA-21 expression as well as cytokines TNF-α, IL-10, ICAM-1, and CCL5 levels within 7 days of stroke onset. The 30-day clinical severity and outcome were assessed using the National Institute of Health Stroke Scale (NIHSS) and modified Rankin Scale (mRS), respectively.\n\nResult A total of 64 acute ischemic stroke patients and 22 age-matched controls were recruited, with median ages of 56 and 55.5 years old, respectively. There were more male subjects than females (35 to 29). A statistically significant difference was observed in miRNA-21 expression between patients and controls (p<0.001). This finding implies that miRNA-21 expression may have a contribution in acute stroke patients. This was followed by an increase in proinflammatory markers TNF-α, IL-10, ICAM-1, and CCL5. However, no association was found between miRNA-21 and any pro-inflammatory cytokine. There was no significant correlation between miRNA-21 or cytokines markers with clinical severity or prognosis.\n\nConclusion Our study demonstrated increased miRNA-21 expression and proinflammatory cytokine expression in acute ischemic stroke patients relative to controls. However, this was not related to clinical severity or clinical outcomes.", "keywords": [ "miRNA", "acute ischemic stroke", "proinflammatory cytokine", "clinical outcome" ], "content": "Introduction\n\nStroke is the world’s second leading cause of death and the major cause of long-term impairment in people. When the brain experiences a lack oxygen and nutrients, either due to blockage, constriction, or rupture of an artery, the neurons in the afflicted area suffer irreversible damage and cellular death, resulting in disability.1 The global prevalence of all types of stroke is approximately 89.13 million cases, up 2.17% from 2010 to 2020. The largest prevalence occurs in Sub-Saharan Africa, Southeastern and Eastern USA, and Southeast Asia.2,3 According to current data from 2018, around 7.6 million people in the United States have had a stroke, with the majority of those over the age of 20. While this prevalence is rising in both sexes,4 males are far more susceptible to the disease than females.5 In China, for example, ischemic stroke accounts for 70% of all stroke cases, while hemorrhagic stroke is less common.1\n\nRecent investigations in ischemic stroke have highlighted the importance of microRNAs (miRNA), which are small noncoding RNA molecules (16-29 nucleotides) that act as post-transcriptional regulators of gene expression in mammalian cells. MiRNAs can modulate “base pairing to complementary sequences” in messenger RNA (mRNA), resulting in reduced gene activity via “translational repression.” These molecules play critical roles in the most fundamental biological processes, including cell cycle control, cell metabolism, apoptosis, and immune response.4–6 MiRNAs have been linked to the regulation of target genes involved with arterial hypertension, atherosclerosis, and diabetes. These genes can regulate inflammation, oxidative stress, cell proliferation, and apoptosis, all of which may contribute to the development of ischemic stroke.7–9 MiRNAs have also been linked to stroke risk.8 The high prevalence of ischemic stroke emphasizes the need to detect early warning signs of risk factors in order to choose an immediate and effective treatment option against the disease process.\n\nWe chose miRNA-21 as a marker in this study for a variety of reasons. First, in ischemic stroke patients, miRNA-21 is highly dysregulated relative to healthy controls. Studies have found that miRNA-21 levels are significantly reduced in the peripheral blood of ischemic stroke patients.5 Second, miRNA-21 protects against ischemic injury. It can bind to the IL-6R gene and suppress IL-6R expression,5 reducing endothelial cell damage following oxygen-glucose deprivation (OGD), suggesting that miRNA-21 has neuroprotective properties. Third, miRNA-21 levels are associated with stroke severity and outcomes. According to several studies, increased miRNA-21 expression correlated to better treatment response and disease-free survival.6 Fourth, miRNA-21 remains stable and detectable in blood samples.9 All of this evidence leads to miRNA-21 as a prognostic biomarker, making it a viable candidate for non-invasive liquid biopsy approaches that are easier to use clinically than tissue-based markers.\n\nInflammation has a critical role in stroke pathogenesis. Neurovascular units become dysfunctional after stroke due to a lack of oxygen and nutrients. During ischemia, the brain releases glutamate and produces reactive oxygen species (ROS), which cause oxidative stress and microglial activation. This may influence the release of inflammatory mediators.10 Following a stroke, serum TNF-α levels increase within 6 hours and remain high for 10 days.11 Similarly, CSF levels of interleukin-1β (IL-1β) increase and peak 2-3 days post-stroke. Interleukin-1β damages neurons, glia, and blood vessels, leading to ischemia and excitotoxic brain injuries. CCL5, a member of the circulating chemokine family, is produced by a variety of cells, including T lymphocytes, platelets, endothelial cells, and glial cells. It can bind to chemokine receptors, attracting white blood cells to the injured area and letting them migrate along the inner lining of blood vessels, causing arterial damage.12 T-cell recruitment and activation in the damaged brain tissue may result in further ischemia injury.13 Furthermore, intercellular adhesion molecule-1 (ICAM-1) is a type I transmembrane protein that secretes soluble ICAM-1, which can be detected in a variety of body fluids.14 Previous studies have shown that ICAM-1 levels are elevated in conditions such as atherosclerosis, cardiovascular diseases, metabolic vascular neuropathy, and acute ischemic stroke. Similarly, IL-6 levels are elevated in the CSF of severe stroke patients, with peak levels recorded on days 2 and 4, or in some investigations, on days 3 and 7.15–19 In contrast, transforming growth factor-β (TGF-β) and IL-10 are anti-inflammatory cytokines that reduce inflammation following ischemic stroke by inhibiting proinflammatory cytokines. These pro- and anti-inflammatory agents predict and influence the prognosis of ischemic injury; hence, the balance of beneficial and detrimental effects of cytokines is significantly influenced by the brain’s biochemical and physiological condition.20,21 Surprisingly, miRNAs and proinflammatory cytokines interact both directly and indirectly. For example, miR-124, miR-9, and miR-219 were reported to be lower in acute ischemic stroke (AIS), which may contribute to neuroinflammation and brain damage by reducing MMP-9 levels, a pro-inflammatory marker.22\n\nGiven the potential role of miRNAs and inflammatory cytokines in stroke mechanisms, as well as their potential interactions with inflammatory pathways, we hypothesize that these factors may influence patient clinical severity and prognosis. This study will compare the expression of miRNA-21 and proinflammatory cytokines (TNF-α, IL-10, CCL5, and ICAM-1) between ischemic stroke patients and controls, as well as their relationship with clinical severity and outcomes.\n\n\nMethods\n\nThis case-control study was conducted at the Wahidin Sudirohusodo General Hospital, Makassar, Indonesia, from January to May 2024. Physical examination and imaging using non-contrast computed tomography (CT) scans and/or magnetic resonance imaging (MRI) were used to identify subjects with acute ischemic stroke. Inclusion criteria are acute ischemic stroke less than 7 days of onset, age 18-80 years old, with no history of coronary artery disease, malignancy, or peripheral arterial disease. Infection and myocardial infarction during follow-up were both considered exclusion criteria. In addition, age-matched controls were chosen. Written permission to conduct the studies for the purposes of this research was obtained by all subjects, who were fully informed about the purposes of this research and how their data would be used and stored. Ethical approval was obtained from the Ethics Committee of Faculty of Medicine, University of Hasanuddin (98/UN4.6.4.6.5.31/PP36/2024) on February 21st, 2024. We obtained the patients’ serum within 7 days of onset. The clinical severity was evaluated using the National Institute of Health Stroke Scale (NIHSS), and the clinical outcome was determined using the modified Rankin Scale (mRS) 30 days after onset.\n\nSubjects were recruited sequentially from the Neurology Inpatient Unit Wahidin Sudirohusodo General Hospital in Makassar, Indonesia until the sample size was sufficient. A total of 5 mL of whole blood samples were collected from each individual in EDTA-containing tubes, centrifuged, separated into serum, and stored at -80°C for analysis. To determine the expression of miRNA-21, we used Homo sapiens hsa-miR-21-3p mature miRNA taken from microRNA database (https://mirbase.org), which has the following sequences: 46-CAACACCAGUCGAUGGGCUGU-66. DNA was isolated from the whole blood sample using a preamplification kit (miScript preAmp, Cat. No. #331452, Qiagen, Germany), and expression was measured using DNA complementary amplification with reverse transcriptase-polymerase chain reaction (PCR) and real-time PCR.\n\nThe miRCURY LNA RT Kit (catalog number 339340) was used for first-strand cDNA synthesis. The template RNA samples were diluted to 5 ng/μl using nuclease-free water. The reverse transcription reactions were prepared on ice by mixing 2 μl of 5x miRCURY SYBR® Green RT Reaction Buffer + 4.5 μl of RNase-free water + 1 μl of 10x miRCURY RT Enzyme Mix + 0.5 μl of UniSp6 RNA spike-in (optional) and 2 μl of Template RNA (5 ng/μl) up to a total reaction volume of 10 μl. Samples were incubated at 42°C for 60 minutes, followed by heat inactivation at 95°C for 5 minutes, and immediate cooling to 4°C for real-time PCR procedure.\n\nDilution of cDNA was performed at 1:60 by adding 590 μl RNase-free water to the 10 μl RT reaction. A reaction mix was made using 2x miRCURY SYBR Green Master Mix. A 10 μl reaction was added to PCR tubes and placed in the real-time cycler. The PCR protocol consisted of 2 minutes heat activation at 95°C, followed by 2 steps of cycling, 10 seconds of denaturation at 95°C, and 60 seconds annealing/extension at 56°C, all at a rapid ramp rate. The Roche LightCycler 480 was used capture The SYBR Green fluorescence data, with 45 cycles each step and melting curve analysis done between 60 and 95°C. Raw Cq and CT values were then retrieved for analyzed.\n\nAll inflammatory cytokines were analyzed with the enzyme-linked immunosorbent assay (ELISA) technique in accordance with the manufacturers’ instructions outline below. All laboratory values were assessed at the Hasanuddin University Medical Research Center laboratory.\n\nThe TNF-α assay utilized the human TNF-α ELISA Kit (BMS223-4, Invitrogen, Austria). After allocating 50 μL of buffer, either standards, controls, or samples were added into the well (100 μL). After mixing and washing, TNF-α biotin conjugate solution was added to the well for 1-hour incubation, washed and followed by 30 minutes incubation with 100 μL 1x streptavidin-HRP solution. After washing, 100 μL of Stabilized Chromogen was applied and incubated in the dark for 30 minutes. The experiment was terminated with 100 μL stop solution and read at 450 nm.\n\nIL-10 was measured using the human IL-10 ELISA Kit (BMS215-2, Invitrogen, Austria). Add 100 μL of blank assay buffer and 50 μL sample assay buffer to the corresponding wells. Add 50 μL of sample to each well, then 50 μL of biotin-conjugate and incubate for 2 hours. After washing, 100 μL streptavidin-HRP was added to each well, followed by an hour of incubation and washing. Incubate 100 μL TMB substrate for 10 minutes. Then, add 100 μL of stop solution and read at 450 nm.\n\nThe CCL5 assay (Human CCL5 (RANTES) ELISA Kit Cat. No. 440807, BioLegend USA) was initiated by adding of 50 μL wash buffer, 50 μL standard or sample, followed by 2 hour incubation. After washing, add 100 μL detection antibody solution and incubate for 1 hour. Wash again, add 100 μL of Avidin-HRP and incubate for 30 minutes. After washing, add 100 μL substrate solution and incubate for 10 minutes in the dark. Terminate with 100 μL stop solution and measure absorbance at 450 nm and 570 nm.\n\nFor the ICAM-1 sandwich ELISA (Human ICAM-1/CD54 ELISA Kit Cat. No. E-EL-H6114, Elabscience, USA): 100 μL of standards or samples were incubated in wells for 90 minutes. After discarding, add 100 μL of biotinylated detection antibody solution and incubate for 60 minutes. Then, wash and add 100 μL HRP conjugate working solution for another 30 minutes of incubation. After washing, add 90 μL of substrate reagent, incubate for 15 minutes, finish with 50 μL of stop solution, and read at 450 nm.\n\nThe data were analyzed using IBM SPSS version 27 (https://www.ibm.com/products/spss-statistics#110). The levels of miRNA expression and proinflammatory cytokines were compared between patients and controls using the t-test and the Mann-Whitney test. Spearman correlation analysis was utilized to examine the relationship between miRNA expression and the pro-inflammatory cytokine levels, as well as clinical severity and clinical outcomes. Data are presented as means ± standard deviation (SD). A p-value < 0.05 was considered significant.\n\n\nResults\n\nIn this study, we recruited 64 patients for the acute ischemic stroke case group and 22 age-matched subjects for the control group, with a median age of 56 and 55.5 years old, respectively. Table 1 illustrates the similarity in median age between cases and controls due to sample matching. Table 2 displays gender characteristics, with 35 males (54.7%) and 29 females (45.3%). The control group had an equal number of males and females (n = 11). Table 3 lists the individuals’ risk factors, with hypertension and smoking being the most common among men.\n\nIn addition, Table 4 shows a significant difference in miRNA-21 expression between acute ischemic stroke patients and controls (5.01 ± 9.27 versus 0.21 ± 0.38, p < 0.001). Table 5 shows the serum levels of each proinflammatory cytokine in both ischemic stroke patients and controls. Stroke patients have significantly higher serum levels of TNF-α than controls (5.04 ± 3.82 versus 3.79 ± 0.88, p < 0.05, respectively). In patients, IL-10 inflammatory cytokines levels are three times greater than in controls (1.42 ± 2.71 versus 0.39 ± 0.29, p < 0.001, respectively). Stroke patients also exhibited considerably higher serum levels of CCL5 (1973.28 ± 1281.41 versus 1434.15 ± 173.18, p < 0.001) and ICAM-1 (18.26 ± 8.74 versus 13.17 ± 3.62, p < 0.001).\n\nAccording to the Spearman test analysis, we found no significant correlation between miRNA-21 with TNF-α (r = 0.013, p = 0.931), IL-10 (r = 0.276, p = 0.058), CCL5 (r = 0.033, p = 0.824), and ICAM-1 (r = 0.054, p = 0.717) inflammatory cytokines (Table 6). There was also no link between miRNA-21 and either NIHSS (r = 0.229, p = 0.118) or mRS (r = -0.022, p = 0.88) scores (Table 7).\n\n\nDiscussion\n\nThis study aimed to compare the expressions of miRNA-21 and inflammatory cytokines (TNF-α, IL-10, CCL5, and ICAM-1) in acute ischemic stroke patients and controls, analyzing their relationship with clinical outcomes and severity. A recent study has demonstrated that miRNAs have a role in the pathological process of ischemic injury via mechanisms that change inflammatory signaling by targeting cytokine production in immune cells.16 MicroRNA-21 is involved in a wide range of biological processes, including proliferation, apoptosis, and inflammation.23 In this study, we observed a significantly difference in miRNA-21 expression between acute ischemic stroke patients and controls (Table 5). This is consistent with Zhou J’s (2014) experiments, which showed that miRNA-21 and miRNA-24 levels in cultured N2A cells increased 3.3 and 4.9 times, respectively, during the 24-hour recovery period and 3 hours after oxygen-glucose deprivation (OGD). Furthermore, the difference in miRNA-21 and miRNA-24 levels between acute cerebral infarction and controls was statistically significant and positively associated, indicating that release occurred during or after the ischemia event, elucidating their mechanisms in acute cerebral ischemia as plasma markers. This suggests that miRNA-21 and miRNA-24 may operate as protective and anti-apoptotic agents in cerebral ischemia, making them potential therapeutic agents for stroke.23,24\n\nOur data findings support the concept that miRNA-21 regulates inflammatory processes during ischemic stroke, most likely by modulating gene expression associated with inflammatory responses, immune cell migration, and atherosclerotic plaque formation.25–28 MicroRNA-21 has emerged as a potential therapeutic target for inflammation-related disorders.29 Zhou and Zhang (2014) discovered miRNA-21 as a possible early-stage marker of acute cerebral infarction. Inhibiting miRNA-21 has been proposed as a therapeutic strategy for controlling endothelial cell dysfunction and vascular inflammation.27,30 Zhan et al. (2023) found that miRNA-21 protects against ischemic stroke by inhibiting IL-6R. These collective findings provide evidence for miRNA-21’s involvement in neuroprotection and its potential as a therapeutic target in neurological disorders.\n\nIn this study, we discovered that acute stroke patients had significantly higher levels of all proinflammatory cytokines than controls. We found that the TNF-α level in the stroke patients is greater compared to healthy subjects. This finding is similar to a recent study, which reported that patients with acute ischemic stroke had significantly greater levels of TNF-α in both cerebrospinal fluid (CSF) and serum within 24 hours after stroke onset compared to healthy controls.31 A previous study reveals that TNF-α, a proinflammatory protein present throughout the body, may contribute to ischemic damage in cerebral tissue.32 Using TNF-α for prognosis yielded varied outcomes. Although earlier research has indicated that levels of TNF-α in brain tissue may remain high for 24 hours following ischemic injury and may be linked to the severity of the injury,31 we observed no relationship between TNF-α levels and the severity of symptoms or outcomes in the patients we evaluated.\n\nIn several animal stroke models, IL-10 mRNA and protein levels, as well as IL-10R mRNA levels, were elevated on microglia and astrocytes in the ischemic penumbra. Low IL-10 levels are associated with increased inflammatory responses and poorer stroke outcomes.33 Indeed, in transgenic mice overexpressing IL-10, infarct size decreased and apoptosis was reduced 4 days after an ischemic stroke.34 Furthermore, overexpression of IL-10 increased the neuroprotective benefits of mesenchymal stem cell transplantation by controlling inflammation, hence promoting neuron survival following acute ischemia.33–35 Our findings are consistent with previous studies that have demonstrated higher levels of IL-10 in ischemic stroke patients compared to healthy subjects.36,37 Vila et al. (2003) found that lower plasma IL-10 concentrations (<6 pg/mL) were associated with clinical deterioration in acute ischemic stroke patients.37 Increased IL-10 levels in female patients were associated with poorer outcomes after ischemic stroke, although they were not the only independent predictor.38 This suggests that IL-10 effects may be influenced by other factors such as gender, age, and stroke severity.\n\nRANTES (Regulated upon Activation, Normal T Cell Expressed and Presumably Secreted) chemokines (C-C motif) ligand 5, or CCL5, is a kind of chemokine that plays an important role in stroke progression via angiogenesis and endothelial repair.32,39 We observed that CCL5 levels were higher in ischemic stroke patients than in healthy subjects. We found no correlation between CCL5 levels and the severity of symptoms or outcomes in the stroke patients. Our findings are comparable with Pawluk et al. (2023), who discovered that when compared to healthy persons, this chemokine was elevated in less than 4.5 hours, 24 hours, and 7 days. Furthermore, they also determined the effect of CCL5 concentration on probability of patient death, finding that concentrations greater than 75 ng/mL resulted in a significant increase in stroke mortality. A similar relationship was also seen on the first day and during the onset of stroke, with CCL5 levels higher than 60 ng/mL and 100 ng/mL, respectively, making this chemokine an excellent biomarker for mortality during stroke progression.32 However, differences in CCL5 levels may vary depending on the type of stroke and the onset. CCL5 levels were shown to be different in ischemic and hemorrhagic stroke patients, with hemorrhagic stroke patients having lower levels than acute ischemic stroke patients.32 Julián-Villaverde (2022) discovered that patients suffering from either an ischemic or hemorrhagic stroke had different levels of CCL5. CCL5 levels were significantly lower in hemorrhagic stroke patients that persisted for at least 7 days. However, no association was found between CCL5 levels and the outcome of patients with hemorrhagic stroke.32,39,40 Similarly, Pawluk et al. (2023) also found no significant correlations between CCL5 levels and mRS and NIHSS score after an acute ischemic stroke. Thus, assessing CCL5 levels upon admission can be used as a predictive biomarker for the progression of ischemic stroke in patients, as well as a promising diagnostic biomarker for distinguishing between different types of strokes.\n\nWe observed that ICAM-1 serum levels were elevated in ischemic stroke patients. Our findings are aligning with Wu et al. (2018), who discovered that ischemic stroke patients had considerably greater serum soluble ICAM-1 (sICAM-1) levels than healthy controls. Nielsen et al. (2020) also found that stroke patients had significantly higher ICAM-1 levels than controls within the first 8 hours of symptom onset but not beyond 72 hours. In contrast, Supanc et al. (2011) showed no significant difference in serum levels of soluble ICAM-1 between acute ischemic stroke patients and healthy controls. The disparities in these findings might be attributed to differences in the timing of sample collection, stroke subtypes, or other methodological factors. Overall, while some studies reported higher ICAM-1 levels in acute ischemic stroke, particularly in the early phase, the evidence is not entirely consistent across investigations. Further study may be required to elucidate the association between ICAM-1 levels and ischemic stroke, taking into consideration parameters such as stroke subtype and timing of assessment.33,40,41\n\nThis study also evaluated the correlation between miRNA-21 and serum inflammatory cytokines TNF-α, IL-10, CCL5, and ICAM-1. We found no significant relationship between miRNA-21 and the four examined cytokines. Despite the lack of correlation in our study, other studies have demonstrated that miRNA-21 plays an important role in regulating inflammatory responses in the brain following an ischemic stroke, which is supported by studies showing its involvement in inflammation resolution and negative regulation of proinflammatory responses.28 MicroRNA-21 is also implicated in attenuating inflammatory responses in cerebrovascular disease, indicating its potential role in modulating inflammation in the brain following ischemic events.33 Understanding these complex regulatory networks is critical for determining miRNA’s functions in development and cerebrovascular disease progression. Future studies with large samples at a multi-research institution are required to evaluate the clinical application of miRNA-21 as a potential biomarker for ischemic stroke diagnosis.\n\nEthical approval was obtained from the Ethics Committee of Faculty of Medicine, University of Hasanuddin (98/UN4.6.4.6.5.31/PP36/2024) on February 21st, 2024. Written permission to conduct the studies for the purposes of this research was obtained by all subjects, who were fully informed about the purposes of this research and how their data would be used and stored.\n\n\nDisclosures\n\nThe authors report no relevant disclosures.", "appendix": "Data availability\n\nFigshare: Result of analysis samples re pcr - Gene Expression Results - Bar Chart aLL dATA.xlsxResult of Statistical Analysis.spv, we present the following article accordance with the STREGA guideline checklist DOI: https://doi.org/10.6084/m9.figshare.27146649.v1 42\n\nThe project contains the following underlying data:\n\n• Result of analysis samples re PCR - Gene Expression Results - Bar Chart aLL dATA.xlsx\n\n• Result of Statistical Analysis.spv\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 author wants to acknowledge all the patients and all the supporting systems.\n\n\nReferences\n\nJiang Q, Li Y, Wu Q, et al.: Pathogenic role of microRNAs in atherosclerotic ischemic stroke: Implications for diagnosis and therapy. Genes Dis. 2022 May; 9(3): 682–696. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDela Peña IC, Yoo A, Tajiri N, et al.: Granulocyte Colony-Stimulating Factor Attenuates Delayed tPA-Induced Hemorrhagic Transformation in Ischemic Stroke Rats by Enhancing Angiogenesis and Vasculogenesis. J. Cereb. Blood Flow Metab. 2015 Feb; 35(2): 338–346. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYemisci M, Caban S, Gursoy-Ozdemir Y, et al.: Systemically Administered Brain-Targeted Nanoparticles Transport Peptides across the Blood—Brain Barrier and Provide Neuroprotection. J. Cereb. Blood Flow Metab. 2015 Mar; 35(3): 469–475. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMa Q, Zhang L, Pearce WJ: MicroRNAs in brain development and cerebrovascular pathophysiology. Am. J. Physiol.-Cell Physiol. 2019 Jul 1; 317(1): C3–C19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhan L, Mu Z, Jiang H, et al.: MiR-21-5p protects against ischemic stroke by targeting IL-6R. Ann. Transl. Med. 2023 Jan 31; 11(2): 101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZedain A, Badrawy H, Fawzy M, et al.: Evaluation the Possibility of Using of miRNA-21 as a Prognostic and Predictive Factor in Colorectal Cancer (South Egypt Experience). J. Cancer Ther. 2020; 11(02): 88–97. Publisher Full Text\n\nTian R, Wu B, Fu C, et al.: miR-137 prevents inflammatory response, oxidative stress, neuronal injury and cognitive impairment via blockade of Src-mediated MAPK signaling pathway in ischemic stroke. Aging. 2020 Jun 4; 12(11): 10873–10895. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTodoran R, Falcione SR, Clarke M, et al.: microRNA as a therapeutic for ischemic stroke. Neurochem. Int. 2023 Feb; 163: 105487. Publisher Full Text\n\nZhao X, Xiao Z, Li B, et al.: miRNA-21 may serve as a promising noninvasive marker of glioma with a high diagnostic performance: a pooled analysis of 997 patients. Ther Adv Med Oncol. 2021 Jan; 13: 175883592098765. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBulygin KV, Beeraka NM, Saitgareeva AR, et al.: Can miRNAs be considered as diagnostic and therapeutic molecules in ischemic stroke pathogenesis?—Current status. Int. J. Mol. Sci. 2020; 21(18): 6728. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHussein M, Magdy R: MicroRNAs in central nervous system disorders: current advances in pathogenesis and treatment. Egypt J. Neurol. Psychiatry Neurosurg. 2021 Dec; 57(1): 36. Publisher Full Text\n\nCao DD, Li L, Chan WY: MicroRNAs: Key Regulators in the Central Nervous System and Their Implication in Neurological Diseases. Int. J. Mol. Sci. 2016 May 28; 17(6): 842. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXue Y, Zeng X, Tu WJ, et al.: Tumor Necrosis Factor-α: The Next Marker of Stroke. Hsu SP, editor. Dis. Markers. 2022 Feb 27; 2022: 1–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZeng L, He X, Wang Y, et al.: MicroRNA-210 overexpression induces angiogenesis and neurogenesis in the normal adult mouse brain. Gene Ther. 2014 Jan; 21(1): 37–43. PubMed Abstract \| Publisher Full Text\n\nLiesz A, Suri-Payer E, Veltkamp C, et al.: Regulatory T cells are key cerebroprotective immunomodulators in acute experimental stroke. Nat. Med. 2009 Feb; 15(2): 192–199. PubMed Abstract \| Publisher Full Text\n\nBartholomäus I, Kawakami N, Odoardi F, et al.: Effector T cell interactions with meningeal vascular structures in nascent autoimmune CNS lesions. Nature. 2009 Nov; 462(7269): 94–98. PubMed Abstract \| Publisher Full Text\n\nRothlein R, Wegner C: Role of intercellular adhesion molecule-1 in the inflammatory response. Kidney Int. 1992 Mar; 41(3): 617–619. Publisher Full Text\n\nMarzolla V, Armani A, Mammi C, et al.: Essential role of ICAM-1 in aldosterone-induced atherosclerosis. Int. J. Cardiol. 2017 Apr; 232: 233–242. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMohammadi H, Khoshnam M, Khoshnam E: Effects of different modes of exercise training on body composition and risk factors for cardiovascular disease in middle-aged men. Int. J. Prev. Med. 2018; 9(1): 9.\n\nJin HY, Park TS: Role of inflammatory biomarkers in diabetic peripheral neuropathy. J. Diabetes Investig. 2018 Sep; 9(5): 1016–1018. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWegeberg AML, Okdahl T, Fløyel T, et al.: Circulating Inflammatory Markers Are Inversely Associated with Heart Rate Variability Measures in Type 1 Diabetes. Mediat. Inflamm. 2020 Aug 18; 2020: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang L, Chen Y, Feng D, et al.: Serum ICAM-1 as a Predictor of Prognosis in Patients with Acute Ischemic Stroke. Xu Y, editor. Biomed. Res. Int. 2021; 2021: 1–6. Publisher Full Text\n\nLi Y, Mao L, Gao Y, et al.: MicroRNA-107 contributes to post-stroke angiogenesis by targeting Dicer-1. Sci. Rep. 2015 Aug 21; 5(1): 13316. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJayaraj RL, Azimullah S, Beiram R, et al.: Neuroinflammation: friend and foe for ischemic stroke. J. Neuroinflammation. 2019; 16(1): 1–24.\n\nQin C, Yang S, Chu YH, et al.: Signaling pathways involved in ischemic stroke: molecular mechanisms and therapeutic interventions. Signal Transduct. Target. Ther. 2022 Jul 6; 7(1): 1–29. Publisher Full Text\n\nZhou J, Zhang J: Identification of miRNA-21 and miRNA-24 in plasma as potential early stage markers of acute cerebral infarction. Mol. Med. Rep. 2014 Aug 1; 10(2): 971–976. PubMed Abstract \| Publisher Full Text\n\nYu X, Li Z: MicroRNAs regulate vascular smooth muscle cell functions in atherosclerosis (Review). Int. J. Mol. Med. 2014 Oct; 34(4): 923–933. Publisher Full Text\n\nSheedy FJ: Turning 21: Induction of miR-21 as a Key Switch in the Inflammatory Response. Front. Immunol. 2015; 6: 19. Publisher Full Text\n\nJenike AE, Halushka MK: miR-21: a non-specific biomarker of all maladies. Biomark. Res. 2021 Dec; 9(1): 18. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCanfrán-Duque A, Rotllan N, Zhang X, et al.: Macrophage deficiency of miR-21 promotes apoptosis, plaque necrosis, and vascular inflammation during atherogenesis. EMBO Mol. Med. 2017 Sep; 9(9): 1244–1262. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZaremba J, Losy J: Early TNF-α levels correlate with ischaemic stroke severity: TNF-α and stroke. Acta Neurol. Scand. 2001 Nov; 104(5): 288–295. PubMed Abstract \| Publisher Full Text\n\nPawluk H, Kołodziejska R, Grześk G, et al.: The Potential Role of RANTES in Post-Stroke Therapy. Cells. 2023 Sep 6; 12(18): 2217. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSupanc V, Biloglav Z, Kes VB, et al.: Role of cell adhesion molecules in acute ischemic stroke. Ann. Saudi Med. 2011 Jul; 31(4): 365–370. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJulián-Villaverde FJ, Serrano-Ponz M, Ramalle-Gómara E, et al.: CCL5 Levels Predict Stroke Volume Growth in Acute Ischemic Stroke and Significantly Diminish in Hemorrhagic Stroke Patients. Int. J. Mol. Sci. 2022 Sep 1; 23(17): 9967. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeruzzaro ST, Andrews MMM, Al-Gharaibeh A, et al.: Transplantation of mesenchymal stem cells genetically engineered to overexpress interleukin-10 promotes alternative inflammatory response in rat model of traumatic brain injury. J. Neuroinflammation. 2019 Jan 5; 16(1): 2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPelidou S, Kostulas N, Matusevicius D, et al.: High levels of IL-10 secreting cells are present in blood in cerebrovascular diseases. Eur. J. Neurol. 1999 Jul; 6(4): 437–442. PubMed Abstract \| Publisher Full Text\n\nVila N, Castillo J, Dávalos A, et al.: Levels of Anti-Inflammatory Cytokines and Neurological Worsening in Acute Ischemic Stroke. Stroke. 2003 Mar; 34(3): 671–675. PubMed Abstract \| Publisher Full Text\n\nZhou S, Liu C, Wang J, et al.: CCL5 mediated astrocyte-T cell interaction disrupts blood-brain barrier in mice after hemorrhagic stroke. J. Cereb. Blood Flow Metab. 2024 Mar; 44(3): 367–383. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConway SE, Roy-O’Reilly M, Friedler B, et al.: Sex differences and the role of IL-10 in ischemic stroke recovery. Biol. Sex Differ. 2015 Dec; 6(1): 17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu BN, Wu J, Hao DL, et al.: High serum sICAM-1 is correlated with cerebral microbleeds and hemorrhagic transformation in ischemic stroke patients. Br. J. Neurosurg. 2018 Nov 2; 32(6): 631–636. PubMed Abstract \| Publisher Full Text\n\nNielsen HH, Soares CB, Høgedal SS, et al.: Acute Neurofilament Light Chain Plasma Levels Correlate With Stroke Severity and Clinical Outcome in Ischemic Stroke Patients. Front. Neurol. 2020 Jun 11; 11: 448. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBahar A: Result of analysis samples re pcr - Gene Expression Results - Bar Chart aLL dATA.xlsxResult of Statistical Analysis.spv. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "341357", "date": "04 Dec 2024", "name": "Josephine Fullerton", "expertise": [ "Reviewer Expertise Stroke", "neuropathology", "extracellular vesicles and microRNAs." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 investigates the expression of microRNA-21 following acute ischemic stroke (AIS), and the relationship with levels of specific inflammatory cytokines, clinical severity and patient outcome. This study assessed serum samples from AIS patients (n=64) and aged-matched controls (n=22), within 7 days of stroke onset. The paper concluded that although miR-21 and proinflammatory cytokine expression levels increased when compared to controls, there was no correlation to clinical severity or clinical outcomes. The authors provide a clear background and rationale for their scientific reasoning for investigating the relationship between this miR following AIS, however, there are a few details I would like to gain clarification on in the methods and results sections. For qRT-PCR, was there a control microRNA used as a “housekeeper” for the samples? Many studies utilise U6 or some form of exogenous housekeeper, yet in the detailed methods there is only mention of UniSp6 RNA spike in, which is listed as optional, was this the exogenous control that was used? In the results section, specifically Table 4, miR-21 expression in AIS patients is compared to non-stroke controls. However, it is not clear what data are being compared here, the methods state that raw Cq and CT values were used for analysis – please clarify if this is a fold change, or how the data is presented. It may be more visually appealing to be detailed as a graph. Also, the number of cases listed is n=48 and n=14 for the miR data, and not the full cohort – is this detailed anywhere? Throughout the results section, there are numbers without units, it is again unclear if these changes are fold changes or cytokine concentrations. The samples were taken within 7 days of stroke onset, across a wide range of ages (34-80 years). It may be useful analyses to investigate the effect of time/age on miR and cytokine expression or mention if this was looked at. The discussion section refers well to current literature and understanding of miRs, AIS and cytokine expression. It would be useful to add a limitations section (if word count allows) which may explain the lack of correlation observed compared to other studies. This manuscript examines the relationship between post-stroke miR-21 expression, cytokine levels, and patient outcome, and could be strengthened with a number of small adjustments.\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": [] }, { "id": "345113", "date": "27 Dec 2024", "name": "Shuya Li", "expertise": [ "Reviewer Expertise stroke" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 investigates the expression of microRNA-21 (miR-21) following acute ischemic stroke (AIS), and its relationship with levels of specific inflammatory cytokines, clinical severity, and patient outcomes. While the study provides a clear background and rationale for exploring the link between miR-21 and AIS, there are several points that need clarification and consideration. 1. Methods and Clarification Needed:\nThe manuscript mentions the use of an exogenous control for miRNA expression analysis, but only briefly refers to UniSp6 RNA spike-in as an optional component. It is unclear whether this was indeed the exogenous control employed. Clarification on this point is necessary. In the results section, specifically Table 4, miR-21 expression in AIS patients is compared to non-stroke controls. However, the presentation of the data lacks clarity. The methods state that raw Cq and CT values were used for analysis, but it is not specified whether these represent fold changes or how the data is presented exactly. For better comprehension, it would be more informative to present these data as a graph. Additionally, the number of cases mentioned for miR data (n=48 for AIS patients and n=14 for controls) does not correspond to the full cohort size. This discrepancy should be explained or clarified elsewhere in the manuscript.\n2. Results Presentation and Units:\nThroughout the results section, numbers are presented without units, making it unclear whether these represent fold changes or cytokine concentrations. Providing units or explicitly stating what these numbers represent would greatly enhance the clarity of the manuscript. The samples were collected within 7 days of stroke onset, spanning a wide age range (34-80 years). It would be insightful to investigate the potential effects of time from stroke onset and age on miR and cytokine expression, even if such analyses were not the primary focus of the study.\n3. Limitations and Correlation:\nThe manuscript reports no correlation between the increased expression of proinflammatory cytokines and clinical severity or outcomes. Given this lack of correlation, it would be useful to include a limitations section (if word count allows) discussing potential reasons for this discrepancy compared to other studies.\n4. Technical Soundness and Replication:\nThe study design appears appropriate, and the technical aspects of the work seem sound. However, the level of detail provided in the methods and analysis section is only partly sufficient to allow replication by others. More comprehensive methodological details would be beneficial.\n5. Statistical Analysis:\nThe statistical analysis and its interpretation appear appropriate. However, given the concerns about data presentation and clarity, it is important to ensure that all statistical tests and their results are presented with sufficient detail and accuracy.\nOverall Assessment: I confirm that I have read this submission and believe that I have an appropriate level of expertise to assess its scientific standard. However, I have significant reservations, as outlined above. Addressing these points would greatly strengthen the manuscript and enhance its overall quality.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1142
https://f1000research.com/articles/10-1313/v1	23 Dec 21	{ "type": "Research Article", "title": "A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.", "authors": [ "Rizone Al Hasib", "Md. Chayan Ali", "Md. Shahedur Rahman", "Md. Mafizur Rahman", "Fee Faysal Ahmed", "Md. Abdullah Al Mashud", "Md. Azizul Islam", "Mohammad Abu Hena Mostofa Jamal", "Rizone Al Hasib", "Md. Chayan Ali", "Md. Shahedur Rahman", "Md. Mafizur Rahman", "Fee Faysal Ahmed", "Md. Abdullah Al Mashud", "Md. Azizul Islam" ], "abstract": "Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization (WHO) declared it as a global pandemic on 11th March, 2020. Many endeavors have been made to find appropriate medications to restrain the SARS CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating ADMET profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates against the SARS-CoV-2 main protease. The crystallized SARS-CoV-2 main protease structure was collected from the RCSB PDB database (PDB ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Out of 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as our top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. MD simulations disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but for experimental validation, they will require more in vivo trials.", "keywords": [ "SARS-CoV-2", "Main protease", "ADMET analysis", "Molecular docking", "Molecular dynamics simulation", "Essential oil." ], "content": "Introduction\n\nA new strain of coronavirus termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for a variety of respiratory diseases that emerged in Wuhan, Hubei province, China towards the end of 2019, and since then has spread globally.1,2 SARS-CoV-2 is a positive sense, enveloped RNA virus that belongs to the β genus of the coronaviridae family.3 Live animals like bats sold at the local Huanan seafood wholesale market are thought to be a possible point of origin of SARS-CoV-2 as most of the fatalities are inhabited nearby it.4 Patients with SARS-CoV-2 infection suffer from a fever at the preliminary stage of the disease as a clinical symptom with some other symptoms including headache, dry cough, difficulty breathing, and pneumonia.5 Progressive respiratory failure due to alveolar damage with the initiation of the disease can even cause the death of the patient.6 Considering the potential health risks associated with this disease, a therapeutic strategy to reduce the transmission rate is urgently needed, but no specific drugs have yet been discovered.7 Several medications like ritonavir, lopinavir, oseltamivir, and ganciclovir have been assayed as yet for the inhibition of SARS-CoV-2. All such drugs are repurposed, and though they may have shown some effectiveness against SARS-CoV-2, but their adverse effects and poor success rate against emerging diseases cannot be neglected.8 Simultaneously, lopinavir-ritonavir based treatment in hospitalized adult patients with severe SARS-CoV-2 has not shown any significant effect.9 Combined doses of hydroxychloroquine and azithromycin exhibited more satisfactory results in the removal of viral load of SARS-CoV-2 than hydroxychloroquine alone, as claimed by Gautret et al., in their study10 but was refuted by another study mentioning the clinical failure of these two drugs in severe cases.11\n\nA protease enzyme called main protease (Mpro) or chymotrypsin-like protease (3CLPro) and a papain-like protease act in the maneuvering of two polyproteins (1a and 1ab) into non-structural proteins (nsps), which are liable for viral replication.12,13 The SARS-CoV-2 main protease specifically cleaves polypeptide sequences after a residue of glutamine as like Leu-Gln↓ (Ser, Ala, Gly) (↓ indicates the cleavage site), which represents the main protease as a suitable drug target since no human host-cell proteases are identified with such substrate specificity.14–17 SARS-CoV-2 main protease maintains an amino acid sequence analogy of 96% in contrast to SARS-CoV-1 and varies merely at 12 out of 303 places in the amino acid sequence.18 Moreover, SARS-CoV-2 main protease comprises three major domains, namely chymotrypsin-like domain I (residues 10–99), picornavirus 3C protease-like domain II (residues 100–184); these two catalytic domains contain a six-stranded antiparallel β-barrel and the α-helical domain III (residues 201–303); necessary for dimerization. Domain II and domain III are linked together through an extended loop region between residues 185-200.19 A cleft between domains I and II holds the substrate-binding site, and the Cys145 and His41 catalytic dyad residues are also included here.20,21\n\nAs mentioned earlier, there is no appropriate medication for SARS-CoV-2; however, several previous studies indicated that phytochemicals and essential oils secreted from medicinal plants may have been used to prevent viral replication.22 Essential oils have been reported to exhibit antiviral effects along with their antibacterial and antifungal activity.23 Compounds derived from essential oils have been proven efficient against the herpes simplex virus (HSV-I and HSV-II) and SARS-CoV by numerous experiments.24,25 An in-silico investigation against SARS-CoV-2 reported that several antiviral agents or other alleviation of SARS-CoV-2 symptoms could be amplified by essential oils.26 So, through this research, we hope to provide evidence that our selected essential oil compounds could be effectively used as a treatment against the deadly SARS-CoV-2 infection. The goal of this study was to investigate the effects of essential oils and phytochemicals obtained from different plants against SARS-CoV-2 main protease using using absorption, distribution, metabolism, elimination, and toxicity (ADMET) profiling, molecular docking, and molecular dynamics simulation.\n\n\nMethods\n\nIn our study, we considered essential oil compounds as a possible anti-SARS-CoV-2 agent. In August 2020, we conducted a randomized study to identify relevant essential oil compounds for the current study. From previous research and observations, we formulated a repository of the bioactive compounds of essential oils. Through checking relevant studies in PubMed, PubChem, Google Scholar, the Web of Science, and Scopus databases, we built a catalog of biologically active essential oil molecules. As inclusion criteria, the compounds were evaluated for their antimicrobial and antiviral properties. Our research included the compounds that had previously shown these two characteristics. Compounds were excluded from the study if they did not have these two key features. The 3D conformation in spatial data file (SDF) format, InChI key, and canonical simplified molecular input line entry systems (SMILEs) of all the compounds were collected from the PubChem database once identified from the search databases.27,28 This research identified a total of 114 essential oil compounds, which were then investigated to see whether they had antiviral properties against SARS-CoV-2 (See extended data file for plant information of all the compounds including their binding affinity scores).29\n\nBased on their ADMET properties, all the essential oil compounds were filtered. Qikprop determined the absorption, distribution, metabolism, elimination (ADME) properties of the compounds.30 Physicochemical properties, pharmacokinetics, lipophilicity, water-solubility, medicinal chemistry are some of the ADME properties estimated to analyze drug profiles of top drug candidates.31 In this study, the rule of five, rule of three, solvent accessible surface area (SASA), aqueous solubility (QPlogS), human oral absorption, Caco-2 cell permeability, and other pharmacological and druglikeness properties like predicted octanol/water partition coefficient (QPlogPo/w), predicted water/gas partition coefficient (QPlogPw), and conformation-independent predicted aqueous solubility (CIQPlogS) were analyzed using Qikprop and the outputs were compared to the threshold values. The compounds were filtered in a stepwise process. The ligands were initially preprocessed for ADME profiling using the LigPrep module of the Schrödinger suite 2020–3 (https://www.schrodinger.com/products/ligprep). The processed ligands were then directly inserted as an input file (.maegz) into Qikprop (https://www.schrodinger.com/products/qikprop). For the pharmacokinetic properties mentioned above, an output file (.csv) was generated automatically.\n\nFirst, compounds that pursued the rule of five and the rule of three were included. Following that, these compounds that passed the rule of five and three tests were assessed based on their maximum oral absorption rate (cut-off value is equal to three). In addition, the toxicity of the compounds was analyzed via the online platform admetSAR (http://lmmd.ecust.edu.cn/admetsar2).32 admetSAR is a free tool that offers a user-friendly interface to search for ADMET properties. It is estimated that there are more than 210,000 ADMET specified datasets for more than 96,000 specific compounds in admetSAR, with 45 different kinds of ADMET-associated properties, which were collated from a wide range of previous studies.33 The toxicity assessment results were generated using the Canonical SMILES of the compounds obtained from PubChem as input data into admetSAR. Here, only negative outcomes in the hERG inhibition, AMES test, and carcinogenic test were taken into account. In summary, the following parameters were used to filter the compounds from the initial 114 identified: Rule of Five = 0 violations, Rule of Three = 0 violations, Human Oral Absorption = 3, hERG inhibition = non-inhibitor, AMES Toxicity = non-AMES Toxic, and Carcinogenic Property = non-carcinogen.\n\nThe crystallized structure of the SARS-CoV-2 main protease (PDB ID 6LU7) was compiled from the reserves of the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (https://www.rcsb.org).34–36 The RCSB PDB is the world's first open-access digital resource for experimentally determined 3D structures of biological macromolecules and their complexes.37 Using the search, visualisation, and analysis tools of RCSB PDB, users can easily explore chemical interactions that stabilize macromolecules and play a significant role in their interactions and functions.38 During receptor preparation, the water molecules and ligands had been eliminated from it, and the steepest descent and conjugate gradient techniques were utilized for energy minimization. The final receptor was configured using GROMACS 96 43B1 algorithm in Swiss-PdbViewer (version 4.0.4) (https://spdbv.vital-it.ch)39 and Chimera (Amber Force field, version 1.14) (https://www.cgl.ucsf.edu/chimera).40 Swiss-PdbViewer is a user-friendly platform that combines the functions for protein structure modeling, assessment, and manipulation. It has been improved with numerous features that allow users to identify and search for general structural motifs in a set of structures.41 In addition, UCSF Chimera is an interactive tool for visualizing molecular structures and is completely free for non-commercial purposes.42\n\nThe ligand preparation was carried out by utilizing the open-source virtual screening tool PyRx (https://pyrx.sourceforge.io). To minimize the energy of the ligands, the mmff94 (Merck molecular force field) force field,43 which is available in PyRx, was employed.44 For ligand optimization, the steepest descent technique was used, with a total number of 200 steps. After that, the ligands were transformed into a protein data bank (PDB) format by implementing the open-source chemical toolbox Open Babel (http://openbabel.org/wiki/Main_Page). For this, the SDF format of the ligands retrieved from the PubChem database was used as inputs in Open Babel. Then the autodock protein data bank (PDB), partial charge (Q), and atom type (T) [PDBQT] format of the ligands was created via PyRx for further study and analysis.45 The grid box generation and molecular docking study were performed by utilizing the autodock wizard of PyRx, version 0.8 as the free version (https://pyrx.sourceforge.io). PyRx provides an autodock wizard with a simple user interface, making it a useful tool for computer-aided drug design (CADD).46 During the molecular docking study, ligands were considered flexible, and the protein was assumed to be rigid.44,47 The grid parameter configuration file was initiated utilizing the auto grid engine in autodock (grid box size X, Y, Z; 31.93, 21.49, and 30.66, respectively). As potential inhibitors, ligands with the most negative docking scores were taken. Low-affinity ligand binding entails less intermolecular force between the ligand and its receptor than high-affinity ligand binding does. The lower the binding affinity of the ligand is, the better the binding of the ligand and the receptor will be. Finally, using Biovia discovery studio visualizer (v 4.5) (https://discover.3ds.com/discovery-studio-visualizer), molecular interactions between ligands and receptor were visualized.48\n\nTo attain detailed information about the predicted molecular interactions, the best-docked complexes were analyzed for 50 ns of MD simulations utilizing the GROMOS96 43al force field of the ‘GROMACS’ macromolecular simulation system (https://simlab.uams.edu/ProteinWithLigand/protein_with_ligand.html).49 In the beginning, topology parameters for the selected ligands were obtained from the ‘PRODRG’ webserver (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg). PRODRG delivers high-throughput protein-ligand crystallography with quick, automated, and consistent access to small-molecule topologies and parameters. PRODRG produced topologies are often of higher quality than topologies generated by other methods and are acceptable for MD simulation in the GROMACS environment.50\n\nIn this study, Mpro-ligand complexes were solvated in a cubic box (0.15 M) with the SPC (spc216) water model. Cubic boxes are generally utilized in molecular dynamics simulations for the sake of geometric simplicity.51 Despite considering polarization, the SPC water model is one the most reliable three-center waters models. It provides accurate water density and dielectric permittivity in molecular dynamics simulations.52\n\nFor each simulation method, the steepest gradient technique (5000 cycles) was implemented to minimize the energy. Under periodic boundary conditions with a predefined pressure of 1 bar, the equilibration period was accomplished for 100 ps at a constant temperature of 300 K. Finally, the simulation outputs like root mean square deviation (RMSD), root mean square fluctuations (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and the number of hydrogen bonds were calculated employing the built-in features of \"GROMACS\". The lower RMSD, Rg, and SASA value represents the compactness of the system where the high RMSF value indicates the structural flexibility. Likewise, intermolecular hydrogen bonds formed during protein-ligand MD simulation are crucial for the conformational stability of the complex.\n\n\nResults\n\nThe propensity of a drug to acquire pharmacologically active concentration at targeted therapies can be evaluated by a set of ADME parameters. Evaluation of ADME may be efficient in combination with toxicity appraisement in silico models.53 The ADMET properties and drug-likeness of each essential oil compound were determined in this study (See underlying data file, ADME.xlsx).54 We did not consider the ability of the compounds to cross the blood-brain barrier (BBB) because SARS-Cov-2 is not directly linked with our central nervous system. Out of 114 compounds tested, 41 were found to violate the rule of five, rule of three, or both. Just one of the remaining 73 compounds had an oral absorption rate of less than three. As a result, the remaining 72 compounds were screened based on the hERG inhibition, AMES, and carcinogenic tests (See underlying data file, Toxicity.xlsx).54 Finally, 53 essential oil compounds met the druglikeness and ADMET profiles requirements outlined in the methods. Following that, a molecular docking approach was then used to examine these 53 filtered compounds.\n\nSince there is no specific medication to date for the treatment of SARS-CoV-2, it is very urgent to identify feasible biological compounds which block SARS-CoV-2 main protease and act as potential anti-SARS-CoV-2 agents. In this investigation, we docked 53 essential oil molecules against SARS-CoV-2 main protease (PDB ID: 6lu7) that passed the ADMET criteria and evaluated the binding affinity of all these probable inhibitor compounds to the receptor-binding site (See underlying data file for all binding affinity scores).54 We chose the top three potential compounds based on their higher binding affinity scores. The PubChem Id, molecular formula, molecular weight, IUPAC name, 2D structures, and binding affinity of the selected hits including the positive control α-ketoamide are shown in Table 1.\n\nAmong the compounds, bisabololoxide B (obtained from Matricaria recutita) disclosed the highest binding affinity of −6.6 kcal/mol, and both eremanthin (obtained from Laurus nobilis) and leptospermone (obtained from Leptospermum scoparium) exhibited a binding affinity of −6.3 kcal/mol during docking analysis. Zhang et al.,53 have shown in a recent analysis that the positive inhibitor α-ketoamide interacts with the main protease residues His41, Gly143, Ser144, Cys145, His163, His164, Glu166, Pro168, and Gln189.55 The Cys-His catalytic dyad (Cys-145 and His-41) is the target region for the inhibitors to bind in. Our selected three hit compounds interact with either Cys-145 or His-41 or both by forming different types of bonds.\n\nBisabololoxide B is demonstrated in Figure 1(b), it interacted with A: HIS-41 and A: MET-49 by forming alkyl bonds. Eremanthin, demonstrated in Figure 1(c), formed conventional hydrogen bonds with A: SER-144 and A: GLY-143. At the same time, eremanthin interacted with A: CYS-145 by forming both conventional hydrogen and alkyl bonds, whereas it formed only alkyl bonds with A: HIS-163 and A: HIS-172. Leptospermone, demonstrated in Figure 1(d), interacted with A: CYS-145, A: SER-144, and A: GLY-143 through strong hydrogen bonds. It also interacted with A: HIS-41 and A: MET-49 by forming alkyl bonds and with A: MET-165 by carbon-hydrogen bond. Such findings indicated that our selected essential oil compounds could be effective in treating SARS-CoV-2.\n\n(a) Molecular interactions of positive control α-ketoamide with Mpro, (b) interactions between Bisabololoxide B and Mpro, (c) between Eremanthin and Mpro, and (d) between Leptospermone and Mpro.\n\nThe molecular interactions can describe biological systems in a dynamic fashion, but usually, molecular docking defines only a single whiff of protein-ligand interaction.56 Hence, we simulated the dynamic nature of all the top three complexes to capture their different conformations attained in the solvated condition. Five parameters, RMSD, RMSF, Rg, SASA, and the number of hydrogen bonds were utilized in our study to analyze the dynamic behavior of the top three protein-ligand complexes. The average RMSD values for α-ketoamide-Mpro, bisabololoxide B-Mpro, eremanthin-Mpro and leptospermone-Mpro complex were 0.34 Å, 0.33 Å, 0.32 Å, and 0.23 Å, respectively where leptospermone showed the lowest RMSD value (shown in Table 2). The positive control α-ketoamide had a stable conformation from 1 to 20 ns, but from 21 ns to the rest of the simulation, there was significant structural distortion. From 1 ns to 20 ns and 40 ns to 50 ns, the bisabololoxide B complex was relatively stable; however, it fluctuated noticeably from 21 ns to 40 ns. Eremanthin remained almost stable throughout the simulation process; only a small amount of structural drifting was found at 8 ns to 10 ns and from 48 ns to 50 ns. The leptospermone complex remained stable from 15 ns to 20 ns and 35 ns to 45 ns but exhibited significant structural instability during the rest of the time. Furthermore, to evaluate the local residual transition, the RMSF benchmark was used. There is a proportional relationship between the RMSF value and the flexibility of a system. If the RMSF value is greater, the system's flexibility will be greater.57 In comparison to the positive control α-ketoamide-Mpro complex (0.21 Å), all three hits had a lower average RMSF value. Eremanthin- Mpro complex showed the lowest average RMSF value (0.15 Å) compared to the other systems. Besides this, both bisabololoxide B-Mpro and leptospermone-Mpro complex displayed an average RMSF value of 0.16 Å (shown in Table 2). Consequently, the lower Rg value evaluates the compactness of the protein structure.58 In this study, bisabololoxide B-Mpro and eremanthin- Mpro complex showed the lowest Rg value (2.13 Å). On the other hand, leptospermone-Mpro complex exhibited the same Rg value (2.16 Å) as the positive control α-ketoamide-Mpro complex (shown in Table 2). A minimal fluctuation rate is always expected during a simulation process. Here also, we calculated the SASA for all systems to determine the compactness of the system (shown in Table 2). Both eremanthin-Mpro (134.31 nm2) and bisabololoxide B-Mpro complex (134.44 nm2) showed lower average SASA value than the positive control α-ketoamide-Mpro complex (139.03 nm2). However, the average SASA value of leptospermone-Mpro complex was 139.75 nm2 which is almost similar to the positive control α-ketoamide-Mpro complex (shown in Table 2). Furthermore, we calculated the total average number of hydrogen bonds for Mpro-ligand complexes, as intermolecular hydrogen bonds between protein-ligand complex plays a vital role in its conformational stability. Here, the positive control α-ketoamide-Mpro complex formed the highest average number of hydrogen bonds (213.79) during the simulation process. Similarly, the eremanthin-Mpro complex produced almost the same number (213.45) of hydrogen bonds as the positive control α-ketoamide-Mpro complex, whereas bisabololoxide B-Mpro and leptospermone-Mpro complex formed an average of 211.03 and 207.13 hydrogen bonds respectively (shown in Table 2).\n\n\nDiscussion\n\nIn reality, SARS-CoV-2 is a big concern for the scientific community due to its high infectivity.59 On 30 December 2019 and 30 January 2020, the World Health Organization (WHO) raised warnings and announced this viral infection a ‘public health emergency of international concern’. Since the first report of a coronavirus-related pneumonia outbreak in December 2019, the virus SARS-CoV-2 that causes the infection has emerged into a pandemic, with >100 million individuals infected in over 210 countries and around two million people dying from COVID-19 as of today.60\n\nNevertheless, no sufficient breakthrough in action against SARS-CoV-2 has been developed yet,61 but researchers are profoundly focused on implementing vaccines and methodologies to eradicate the disease.62,63 However, clinical trials of many candidates are still going on, and some of them pose contentious issues.31,64–66 For instance, An adenosine analogue named Remdesivir which inhibits viral RNA polymerases was known to be an advantageous antiviral agent against a diverse species of RNA viruses along with Ebola, SARS-CoV, and MERS-CoV and exhibited remedial activity in non-clinical models of these coronaviruses but had several undesirable effects in case of SARS-CoV-2 and failed in phase three clinical trials.55,67–69 Failure of hydroxychloroquine in preventing illness of patients with high or moderate-risk exposure to SARS-CoV-2 was also reported previously.70 Therefore, we desperately need potential anti-SARS-CoV-2 drugs to keep people's lives safe.71 New plant-based therapies compensate for around 60% of total Western medicines, and now they are being extensively studied to develop a cure for combating SARS-CoV-2.72,73 This study assayed several plant essential oil compounds through computational approaches to find out effective SARS-CoV-2 Mpro inhibitors.\n\nSince prehistoric periods, plants and their derivatives have been utilized to treat diseases in humans, and they were reported to be clinically safe for humans.74 Plant essential oils are considered to have a range of useful antimicrobial, antibacterial, antiviral, antiparasitic, and insecticidal properties, and now widely studied as a consequential source of drug development for their safety profiles and advantages over synthetic drugs.69,75,76 Some essential oils have shown to be effective against multiple RNA, and DNA viruses, including avian influenza A virus, herpes simplex virus, dengue virus, and poliovirus, as well as are being successful in the treatment of both infectious and chronic diseases.77–81\n\nThe protocol of new drug development is complicated, time-intensive, costly, and involves both preclinical and clinical stages. With the aid of computational biology and bioinformatics, manufacturing operations of new drugs are altered and optimized, and hence development costs are minimized.82 This approach focuses on ligands interacting with their target proteins to evaluate the clinical efficacy of specific compounds.83–85\n\nThe current study can help to explain the attributes of druglikeness and medicinal chemistry of the key metabolites against SARS-CoV-2. ADME properties estimated by the computational approach provide crucial perceptions into how the body treats or accepts a drug. Computational methods perform a vital role in predicting possible issues with ADME and toxicity and reducing the number of experiments that demand animal trials. Thus, supreme drug candidates were utilized to estimate their drug profiles with ADME analysis.86 In this experiment, all 114 compounds were firstly filtered based on their different ADMET properties. The rule of five and the rule of three were perfectly implemented in 72 compounds out of 114. There were no unfavorable outcomes discovered that could lead to a decrease in their ADME properties and druglikeness. The druglikeness property is assessed by Lipinski's rule of five, whereas Jorgensen's rule of three is more likely to suggest a compound's bioavailability.87,88\n\nFurthermore, when developing new drugs for oral administration, solubility is one of the most significant parameters influencing absorption, and it improves many drug development operations.89,90 The 72 filtered compounds are all water-soluble and have a high rate of oral absorption. Consequently, toxicity tests showed that 53 of the 72 compounds were non-hERG inhibitors and found to be non-Ames toxic and non-carcinogenic in the Ames test and carcinogenic test, respectively.\n\nThe 53 screened compounds were then evaluated by molecular docking study. We considered the compounds as a set of ligands in our current analysis and selected the top three hits (Bisabololoxide B, Eremanthin, and Leptospermone) based on their higher binding affinity scores over the other compounds. Results revealed that bisabololoxide B showcased the maximum binding affinity score of -6.6 and the remaining two metabolites (eremanthin and leptospermone) exhibited a binding affinity score of -6.3 kcal/mol, respectively. Bisabololoxide B possesses anti-inflammatory properties, and its pharmacological significance was previously noted.91 Antioxidant properties of eremanthin were previously assayed in STZ induced diabetic rats.92 In an earlier study, eremanthin exhibited notable cytotoxic effects on HeLa cervical cancer cells and hence acted as a promising anti-cancer agent against human cervical cancer.93 Leptospermone is an active compound of the β-triketone portion of manuka oil that exhibited good antiviral effects against HSV-1 and HSV-2 prior to infection. It works by interrupting the structure of the virion envelope and mask viral particles requires for adsorption.94 Leptospermone also showed antimicrobial effects against two bacterial strains, namely C. difficile and C. perfringens in an earlier study.95\n\nMoreover, molecular dynamics simulation was employed to define the exact physical movement and flexibility of ligand-receptor complexes to further evaluate the molecular docking performance.96 RMSD indicates the stability of ligand-protein complexes, where residual flexibility is characterized by RMSF.97 All of our hit compounds showed lower RMSD and RMSF values compared to the positive α-ketoamide control, which depicts their stable conformation with SARS-CoV-2 main protease. The lowest RMSD value was asserted by leptospermone-Mpro complex, which represents its structural compactness. Compared to other systems, eremanthin-Mpro complex displayed a lower RMSF value that denotes its conformational stability. In addition, we also computed the Rg value for each system to determine their compactness. Both bisabololoxide B-Mpro and eremanthin-Mpro complex showed a lower Rg value (2.13 Å), however, the leptospermone-Mpro complex depicted the same Rg value (2.16 Å) as the positive control α-ketoamide-Mpro complex. These outputs suggested that bisabololoxide B-Mpro and eremanthin-Mpro complex were more compact than the positive control α-ketoamide-Mpro complex. Likewise, to evaluate the nature of protein expansion, we estimated the SASA values for all complexes. Here, the eremanthin-Mpro (134.31 nm2) and bisabololoxide B-Mpro complex (134.44 nm2) disclosed a smaller SASA value compared to the positive control α-ketoamide-Mpro complex (139.03 nm2). Consequently, the leptospermone-Mpro complex exhibited a nearly identical but a bit higher SASA value (139.75 nm2) to that of the positive control α-ketoamide-Mpro complex, indicating that the Mpro expanded slightly when it interacted with leptospermone. Furthermore, we calculated the average mean value of total intermolecular hydrogen bonds generated during the simulation process to analyze the structural consistency of the complexes. The bisabololoxide B-Mpro and leptospermone-Mpro complex formed 211.03 and 207.13 hydrogen bonds during the molecular dynamics simulation, while the number of intermolecular hydrogen bonds for eremanthin-Mpro complex (213.45) is nearly equivalent to the positive control α-ketoamide-Mpro complex (213.79). All such outcomes obtained from molecular dynamics simulation indicate the conformational stability and compactness of our selected target compounds with the SARS-CoV-2 main protease.\n\nThroughout the current investigation, we unveiled the molecular interactions of the leading drug candidates with SARS-CoV-2 main protease. The catalytic domain of SARS-CoV-2 main protease owned the ligand-binding sites for each ligand, and His41 and Cys145 residues serve as a site for substrate recognition among the other active residues as it comprises the catalytic dyad.98–100 All of the top three drug candidates were well adjusted into the pocket of SARS-CoV-2 main protease in which several hydrophobic amino acid residues such as Met-49, Gly-143, His-41, Ser-144, His-163, Cys-145, and Met-165 constitute a fairly hydrophobic atmosphere to maintain conformational stabilization of the compounds.100 Thus, based on the findings of this study, we can claim that each of our lead compounds has the potential to act as an inhibitor of SARS-CoV-2, and we hope that the study will pave the way for the development of novel pharmaceutical drugs.\n\n\nConclusion\n\nThe rapid spreading of novel coronavirus threatens human life terribly, which needs to be stopped for reducing the mortality rate. The main objective of this study was to identify novel inhibitors against the SARS-CoV-2 main protease. To discover novel Mpro inhibitors derived from natural essential oil compounds, ADMET analysis, molecular docking, and MD simulation were successfully conducted here. A total number of 114 essential oil compounds were screened by ADMET profiling and molecular docking study, and the efficacy of the top three compounds was validated by MD simulation. During the 50ns simulation, all the hits (bisabololoxide B, eremanthin, and leptospermone) appeared stable and possessed high affinities against SARS-CoV-2 main protease but further in vivo studies are needed for experimental validation. We conclude that the findings of this study could lead to the development of promising natural pharmaceutical agents for SARS-CoV-2 in the future.\n\n\nData availability\n\nFigshare: Underlying data for ‘A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.’\n\nhttps://doi.org/10.6084/m9.figshare.16879777.v1.54\n\nThis project contains the following underlying data:\n\n• ADME.xlsx (spreadsheet of ADME properties for all the 114 compounds).\n\n• Toxicity.xlsx (spreadsheet of toxicity for screened 72 compounds).\n\n• Binding Affinity.xlsx (spreadsheet of binding affinity for screened 53 compounds).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Underlying data for ‘A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.’\n\nhttps://doi.org/10.6084/m9.figshare.16879777.v1.54\n\nThis project contains the following extended data:\n\n• Extended Data 1.docx (document file for the plant source with their corresponding binding affinity of all the 114 compounds).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthors contribution\n\nRAH and MCA conceived the plan of this research. RAH wrote the manuscript. RAH analyzed the data and made the figures. MSR, MMR, MAI, and FFA edited the manuscript. MCA did the molecular dynamics simulation, and MAHMJ supervised the whole project. All authors revised and approved the manuscript for final submission.", "appendix": "References\n\nFischer A, Sellner M, Neranjan S, et al.: Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds. Int J Mol Sci. 2020 May 21; 21(10). Epub 2020/05/28. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTang X, Wu C, Li X, et al.: On the origin and continuing evolution of SARS-CoV-2. Nat Sci Rev. 2020; 7: 1012–1023. Publisher Full Text\n\nWu C, Liu Y, Yang Y, et al.: Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 2020 May; 10(5): 766–788. Epub 2020/04/16. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen N, Zhou M, Dong X, et al.: Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020 Feb 15; 395(10223): 507–513. Epub 2020/02/03. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi YC, Bai WZ, Hashikawa T: The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients. J Med Virol. 2020 Jun; 92(6): 552–555. Epub 2020/02/28. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou P, Yang XL, Wang XG, et al.: A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar; 579(7798): 270–273. Epub 2020/02/06. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDas S, Sarmah S, Lyndem S, et al.: An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study. J Biomol Struct Dyn. 2020 May; 13: 1–11. Epub 2020/05/05. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhadka S, Yuchi A, Shrestha DB, et al.: Repurposing Drugs for COVID-19: An Approach for Treatment in the Pandemic. Altern Ther Health Med. 2020 Aug; 20. Epub 2020/08/23. eng. PubMed Abstract\n\nCao B, Wang Y, Wen D, et al.: A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19. N Engl J Med. 2020 May 7; 382(19): 1787–1799. Epub 2020/03/19. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGautret P, Lagier JC, Parola P, et al.: Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents. 2020 Mar; 56: 105949. Epub 2020/03/25. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMolina JM, Delaugerre C, Le Goff J, et al.: No evidence of rapid antiviral clearance or clinical benefit with the combination of hydroxychloroquine and azithromycin in patients with severe COVID-19 infection. Med Mal Infect. 2020 Jun; 50(4): 384. Epub 2020/04/03. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuralidharan N, Sakthivel R, Velmurugan D, et al.: Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. J Biomol Struct Dyn. 2020 Apr; 16: 1–6. Epub 2020/04/07. eng. PubMed Abstract\n\nAnand K, Ziebuhr J, Wadhwani P, et al.: Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science. 2003 Jun 13; 300(5626): 1763–1767. Epub 2003/05/15. eng. PubMed Abstract \| Publisher Full Text\n\nZhang L, Lin D, Kusov Y, et al.: α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment. J Med Chem. 2020 May 14; 63(9): 4562–4578. Epub 2020/02/12. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang L, Lin D, Sun X, et al.: Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science. 2020 Apr 24; 368(6489): 409–412. Epub 2020/03/22. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHilgenfeld R: From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. Febs J. 2014 Sep; 281(18): 4085–4096. Epub 2014/07/22. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUllrich S, Nitsche C: The SARS-CoV-2 main protease as drug target. Bioorg Med Chem Lett. 2020 Sep 1; 30(17): 127377. Epub 2020/08/03. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEstrada E: Topological analysis of SARS CoV-2 main protease. Chaos. 2020 Jun; 30(6): 061102. Epub 2020/07/03. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJin Z, Zhao Y, Sun Y, et al.: Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nat Struct Mol Biol. 2020 Jun; 27(6): 529–532. Epub 2020/05/10. eng. PubMed Abstract \| Publisher Full Text\n\nLee J, Worrall LJ, Vuckovic M, et al.: Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Nat Commun. 2020 Nov 18; 11(1): 5877. Epub 2020/11/20. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJoshi RS, Jagdale SS, Bansode SB, et al.: Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. J Biomol Struct Dyn. 2020 May; 5: 1–16. Epub 2020/04/25. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAstani A, Reichling J, Schnitzler P: Screening for antiviral activities of isolated compounds from essential oils. Evid Based Complement Alternat Med. 2011; 2011: 253643. Epub 2009/12/17. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMinami M, Kita M, Nakaya T, et al.: The inhibitory effect of essential oils on herpes simplex virus type-1 replication in vitro. Microbiol Immunol. 2003; 47(9): 681–684. Epub 2003/10/31. eng.PubMed Abstract\n\nLoizzo MR, Saab AM, Tundis R, et al.: Phytochemical analysis and in vitro antiviral activities of the essential oils of seven Lebanon species. Chem Biodivers. 2008 Mar; 5(3): 461–470. Epub 2008/03/22. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKoch C, Reichling J, Schneele J, et al.: Inhibitory effect of essential oils against herpes simplex virus type 2. Phytomedicine. 2008 Jan; 15(1-2): 71–78. Epub 2007/11/03. eng. PubMed Abstract \| Publisher Full Text\n\nSilva J, Figueiredo PLB, Byler KG, et al.: Essential Oils as Antiviral Agents. Potential of Essential Oils to Treat SARS-CoV-2 Infection: An In-Silico Investigation. Int J Mol Sci. 2020 May 12; 21(10). Epub 2020/05/16. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Q, Cheng T, Wang Y, et al.: PubChem as a public resource for drug discovery. Drug Discov Today. 2010 Dec; 15(23-24): 1052–1057. Epub 2010/10/26. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBolton EE, Chen J, Kim S, et al.: PubChem3D: a new resource for scientists. J Cheminform. 2011 Sep 20; 3(1): 32. Epub 2011/09/22. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHasib RA, Ali MC, Rahman MS, et al.: A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds. figshare.2021.\n\nSchrödinger L: QikProp, version 4.4. New York, NY: 2015.\n\nAzim KF, Ahmed SR, Banik A, et al.: Screening and druggability analysis of some plant metabolites against SARS-CoV-2: An integrative computational approach. Inform Med Unlocked. 2020; 20: 100367. Epub 2020/06/17. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCheng F, Li W, Zhou Y, et al.: admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model. 2012 Nov 26; 52(11): 3099–105. Epub 2012/10/25. eng. PubMed Abstract \| Publisher Full Text\n\nCheng F, Li W, Zhou Y, et al.: Correction to “admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties”. J Chem Inf Model. 2019 Nov 25; 59(11): 4959. Epub 2019/10/30. eng. PubMed Abstract \| Publisher Full Text\n\nBurley SK, Berman HM, Bhikadiya C, et al.: RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res. 2019 Jan 8; 47(D1): D464–D474. Epub 2018/10/26. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu X, Zhang B, Jin Z, et al.: The crystal structure of COVID-19 main protease in complex with an inhibitor N3. Protein DataBank. 2020.\n\nJin Z, Du X, Xu Y, et al.: Structure of M (pro) from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020 Jun; 582(7811): 289–293. Epub 2020/04/10. eng. PubMed Abstract \| Publisher Full Text\n\nBurley SK, Berman HM, Kleywegt GJ, et al.: Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. Methods Mol Biol. 1607; 1607: 627–641. Epub 2017/06/03. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZardecki C, Dutta S, Goodsell DS, et al.: RCSB Protein Data Bank: A resource for chemical, biochemical, and structural explorations of large and small biomolecules. ACS Publications. 2016; 93: 569–575. Publisher Full Text\n\nGuex N, Peitsch MC: SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997 Dec; 18(15): 2714–2723. Epub 1998/03/21. eng. PubMed Abstract \| Publisher Full Text\n\nPettersen EF, Goddard TD, Huang CC, et al.: UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct; 25(13): 1605–1612. Epub 2004/07/21. eng. PubMed Abstract \| Publisher Full Text\n\nJohansson MU, Zoete V, Michielin O, et al.: Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinformatics. 2012 Jul 23; 13: 173. Epub 2012/07/25. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang Z, Lasker K, Schneidman-Duhovny D, et al.: UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2012 Sep; 179(3): 269–278. Epub 2011/10/04. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHalgren TA: Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem. 1996; 17(5-6): 490–519. Publisher Full Text\n\nDallakyan S, Olson AJ: Small-molecule library screening by docking with PyRx. Methods Mol Biol. 2015; 1263: 243–250. Epub 2015/01/27. eng. PubMed Abstract \| Publisher Full Text\n\nO'Boyle NM, Banck M, James CA, et al.: Open Babel: An open chemical toolbox. J Cheminform. 2011 Oct 7; 3: 33. Epub 2011/10/11. eng. PubMed Abstract \| Free Full Text\n\nOunthaisong U, Tangyuenyongwatana P: Cross-docking study of flavonoids against tyrosinase enzymes using PyRx 0.8 virtual screening tool. TJPS. 2017; 41(2017).\n\nPagadala NS, Syed K, Tuszynski J: Software for molecular docking: a review. Biophys Rev. 2017 Apr; 9(2): 91–102. Epub 2017/05/17. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBiovia DS: Discovery studio visualizer. San Diego, CA, USA: 2017; vol. 936.\n\nVan Der Spoel D, Lindahl E, Hess B, et al.: GROMACS: fast, flexible, and free. J Comput Chem. 2005 Dec; 26(16): 1701–1718. Epub 2005/10/08. eng. PubMed Abstract \| Publisher Full Text\n\nSchüttelkopf AW, van Aalten DM : PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr. 2004 Aug; 60(Pt 8): 1355–1363. Epub 2004/07/24. eng. PubMed Abstract \| Publisher Full Text\n\nCao T, Ji X, Wu J, et al.: Correction of diffusion calculations when using two types of non-rectangular simulation boxes in molecular simulations. J Mol Model. 2019 Jan 4; 25(1): 22. Epub 2019/01/06. eng. PubMed Abstract \| Publisher Full Text\n\nPraprotnik M, Janežič D, Mavri J: Temperature dependence of water vibrational spectrum: a molecular dynamics simulation study. J Phys Chem A. 2004; 108(50): 11056–11062. Publisher Full Text\n\nRoy S, Kumar A, Baig MH, et al.: Virtual screening, ADMET profiling, molecular docking and dynamics approaches to search for potent selective natural molecules based inhibitors against metallothionein-III to study Alzheimer's disease. Methods. 2015 Jul 15; 83: 105–110. Epub 2015/04/30. eng. PubMed Abstract \| Publisher Full Text\n\nRizone Al H, Md. Chayan A, Md. Shahedur R, et al.: A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds. figshare. Dataset. 2021. Publisher Full Text\n\nWang M, Cao R, Zhang L, et al.: Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020 Mar; 30(3): 269–271. Epub 2020/02/06. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharma P, Joshi T, Mathpal S, et al.: Identification of natural inhibitors against Mpro of SARS-CoV-2 by molecular docking, molecular dynamics simulation, and MM/PBSA methods. J Biomol Struct Dyn. 2020 Nov; 4: 1–12. Epub 2020/11/05. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAli MC, Nur AJ, Khatun MS, et al.: Identification of potential SARS-CoV-2 main protease inhibitors from Ficus Carica Latex: An in-silico approach. Journal of Advanced Biotechnology and Experimental Therapeutics. 2020; 3: 57–67. Publisher Full Text\n\nLobanov M, Bogatyreva NS, Galzitskaia OV: Radius of gyration is indicator of compactness of protein structure. Mol Biol (Mosk). 2008 Jul-Aug; 42(4): 623–628. Epub 2008/10/17. rus. PubMed Abstract \| Publisher Full Text\n\nKhachfe HH, Chahrour M, Sammouri J, et al.: An Epidemiological Study on COVID-19: A Rapidly Spreading Disease. Cureus. 2020 Mar 18; 12(3): e7313. Epub 2020/04/22. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang C, Wang Z, Wang G, et al.: COVID-19 in early 2021: current status and looking forward. Signal Transduct Target Ther. 2021 Mar 8; 6(1): 114. Projects related to SARS-CoV-2 diagnostics and COVID-19 vaccine development. K.Z. filed patents on COVID-19 diagnosis and vaccines. The other authors declare no competing interests. Epub 2021/03/10. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPandeya KB, Ganeshpurkar A, Mishra MK: Natural RNA dependent RNA polymerase inhibitors: Molecular docking studies of some biologically active alkaloids of Argemone mexicana. Med Hypotheses. 2020 Jun 1; 144: 109905. Competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Epub 2020/06/15. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGordon DE, Jang GM, Bouhaddou M, et al.: A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Jul; 583(7816): 459–468. Epub 2020/05/01. eng. PubMed Abstract \| Publisher Full Text\n\nZhou Y, Hou Y, Shen J, et al.: Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov. 2020; 6: 14. Epub 2020/03/21. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou D, Dai SM, Tong Q: COVID-19: a recommendation to examine the effect of hydroxychloroquine in preventing infection and progression. J Antimicrob Chemother. 2020 Jul 1; 75(7): 1667–1670. Epub 2020/03/21. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDong L, Hu S, Gao J: Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discov Ther. 2020; 14(1): 58–60. Epub 2020/03/10. eng. PubMed Abstract \| Publisher Full Text\n\nHraiech S, Bourenne J, Kuteifan K, et al.: Lack of viral clearance by the combination of hydroxychloroquine and azithromycin or lopinavir and ritonavir in SARS-CoV-2-related acute respiratory distress syndrome. Ann Intensive Care. 2020 May 24; 10(1): 63. Epub 2020/05/26. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrein J, Ohmagari N, Shin D, et al.: Compassionate Use of Remdesivir for Patients with Severe Covid-19. N Engl J Med. 2020 Jun 11; 382(24): 2327–2336. Epub 2020/04/11. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGordon CJ, Tchesnokov EP, Feng JY, et al.: The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus. J Biol Chem. 2020 Apr 10; 295(15): 4773–4779. Epub 2020/02/26. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKulkarni SA, Nagarajan SK, Ramesh V, et al.: Computational evaluation of major components from plant essential oils as potent inhibitors of SARS-CoV-2 spike protein. J Mol Struct. 2020; 1221: 128823. Publisher Full Text\n\nBoulware DR, Pullen MF, Bangdiwala AS, et al.: A Randomized Trial of Hydroxychloroquine as Postexposure Prophylaxis for Covid-19. N Engl J Med. 2020 Aug 6; 383(6): 517–525. Epub 2020/06/04. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAsai A, Konno M, Ozaki M, et al.: COVID-19 Drug Discovery Using Intensive Approaches. Int J Mol Sci. 2020 Apr 18; 21(8). Epub 2020/04/25. eng. PubMed Abstract \| Free Full Text\n\nEgbuna C, Kumar S, Ifemeje JC, et al.: Phytochemicals as Lead Compounds for New Drug Discovery. Elsevier; 2019.\n\nPan SY, Zhou SF, Gao SH, et al.: New Perspectives on How to Discover Drugs from Herbal Medicines: CAM's Outstanding Contribution to Modern Therapeutics. Evid Based Complement Alternat Med. 2013; 2013: 627375. Epub 2013/05/02. eng. PubMed Abstract \| Free Full Text\n\nYuan H, Ma Q, Ye L, et al.: The traditional medicine and modern medicine from natural products. Molecules. 2016; 21(5): 559. Publisher Full Text\n\nKoroch AR, Juliani HR, Zygadlo JA: Bioactivity of essential oils and their components. Flavours and fragrances. Springer; 2007; 87–115.\n\nEl Omari K, Hamze M, Alwan S, et al.: In-vitro evaluation of the antibacterial activity of the essential oils of Micromeria barbata, Eucalyptus globulus and Juniperus excelsa against strains of Mycobacterium tuberculosis (including MDR), Mycobacterium kansasii and Mycobacterium gordonae. J Infect Public Health. 2019 Sep-Oct; 12(5): 615–618. Epub 2019/02/11. eng. PubMed Abstract \| Publisher Full Text\n\nElshafie HS, Camele I: An Overview of the Biological Effects of Some Mediterranean Essential Oils on Human Health. Biomed Res Int. 2017; 2017: 9268468. Epub 2017/12/13. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStea S, Beraudi A, De Pasquale D: Essential oils for complementary treatment of surgical patients: state of the art. Evid Based Complement Alternat Med. 2014; 2014: 726341. Epub 2014/04/08. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMossa AT, Refaie AA, Ramadan A, et al.: Antimutagenic effect of Origanum majorana L. essential oil against prallethrin-induced genotoxic damage in rat bone marrow cells. J Med Food. 2013 Dec; 16(12): 1101–1107. Epub 2013/11/08. eng.PubMed Abstract \| Publisher Full Text\n\nTariq S, Wani S, Rasool W, et al.: A comprehensive review of the antibacterial, antifungal and antiviral potential of essential oils and their chemical constituents against drug-resistant microbial pathogens. Microb Pathog. 2019 Sep; 134: 103580. Epub 2019/06/14. eng.PubMed Abstract \| Publisher Full Text\n\nPourghanbari G, Nili H, Moattari A, et al.: Antiviral activity of the oseltamivir and Melissa officinalis L. essential oil against avian influenza A virus (H9N2). Virusdisease. 2016 Jun; 27(2): 170–178. Epub 2016/07/02. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmbesi-Impiombato A, Bernardo D: Computational biology and drug discovery: From single-target to network drugs. Curr Bioinform. 2006; 1(1): 3–13. Publisher Full Text\n\nTerstappen GC, Reggiani A: In silico research in drug discovery. Trends Pharmacol Sci. 2001 Jan; 22(1): 23–26. Epub 2001/02/13. eng. PubMed Abstract \| Publisher Full Text\n\nHirono S: An introduction to the computer-aided structure-based drug design–applications of bioinformatics to drug discovery. Rinsho Byori. 2002 Jan; 50(1): 45–51. Epub 2002/03/02. jpn. PubMed Abstract\n\nEkins S, Mestres J, Testa B: In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol. 2007 Sep; 152(1): 9–20. Epub 2007/06/06. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWishart DS: Improving early drug discovery through ADME modelling: an overview. Drugs R D. 2007; 8(6): 349–362. Epub 2007/10/30. eng. PubMed Abstract \| Publisher Full Text\n\nLipinski CA, Lombardo F, Dominy BW, et al.: Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2001 Mar 1; 46(1-3): 3–26. Epub 2001/03/22. eng.PubMed Abstract \| Publisher Full Text\n\nJorgensen WL, Duffy EM: Prediction of drug solubility from Monte Carlo simulations. Bioorg Med Chem Lett. 2000 Jun 5; 10(11): 1155–1158. Epub 2000/06/24. eng. PubMed Abstract \| Publisher Full Text\n\nRitchie TJ, Macdonald SJ, Peace S, et al.: Increasing small molecule drug developability in sub-optimal chemical space. MedChemComm. 2013; 4(4): 673–680. Publisher Full Text\n\nOttaviani G, Gosling DJ, Patissier C, et al.: What is modulating solubility in simulated intestinal fluids?. Eur J Pharm Sci. 2010; 41(3-4): 452–457. Publisher Full Text\n\nPekić B, Zeković Z, Petrović L, et al.: Behavior of (–)-α-Bisabolol and (–)-α-Bisabololoxides A and B in camomile flower extraction with supercritical carbon dioxide. Sep Sci Technol. 1995; 30(18): 3567–3576. Publisher Full Text\n\nEliza J, Daisy P, Ignacimuthu S: Antioxidant activity of costunolide and eremanthin isolated from Costus speciosus (Koen ex. Retz) Sm. Chem Biol Interact. 2010 Dec 5; 188(3): 467–472. Epub 2010/08/17. eng.PubMed Abstract \| Publisher Full Text\n\nLiu T, Zhao X, Song D, et al.: Anticancer activity of Eremanthin against the human cervical cancer cells is due to G2/M phase cell cycle arrest, ROS-mediated necrosis-like cell death and inhibition of PI3K/AKT signalling pathway. J buon. 2020 May-Jun; 25(3): 1547–1553. Epub 2020/08/31. eng. PubMed Abstract\n\nReichling J, Koch C, Stahl-Biskup E, et al.: Virucidal activity of a beta-triketone-rich essential oil of Leptospermum scoparium (manuka oil) against HSV-1 and HSV-2 in cell culture. Planta Med. 2005 Dec; 71(12): 1123–1127. Epub 2006/01/06. eng.PubMed Abstract \| Publisher Full Text\n\nJeong E-Y, Jeon J-H, Kim H-W, et al.: Antimicrobial activity of leptospermone and its derivatives against human intestinal bacteria. Food Chem. 2009; 115(4): 1401–1404.\n\nLiu X, Shi D, Zhou S, et al.: Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov. 2018 Jan; 13(1): 23–37. Epub 2017/11/16. eng. PubMed Abstract \| Publisher Full Text\n\nTahir Ul Qamar M, Alqahtani SM, Alamri MA, et al.: Structural basis of SARS-CoV-2 3CL(pro) and anti-COVID-19 drug discovery from medicinal plants. J Pharm Anal. 2020 Aug; 10(4): 313–319. Epub 2020/04/17. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang H, Yang M, Ding Y, et al.: The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23): 13190–13195. Epub 2003/10/31. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMacchiagodena M, Pagliai M, Procacci P: Identification of Potential Binders of the Main Protease 3CL(pro) of the COVID-19 via Structure-Based Ligand Design and Molecular Modeling. Chem Phys Lett. 2020 Apr 18; 750: 137489. Epub 2020/04/22. eng.PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu C, Liu Y, Yang Y, et al.: Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 2020 Feb 27; 10(5): 766–788. Epub 2020/04/16. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "138870", "date": "31 May 2022", "name": "Thi Thanh Binh Nguyen", "expertise": [ "Reviewer Expertise medicine", "molecular in pharmacy", "clinical study" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nArticle \"A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds\". The manuscript is clearly presented and well substantiated and I recommend it for indexing in F1000Research with the following minor changes.\nSpecific Comments:\nWhat is the reason behind choosing the PDB ID 6LU7?\n\nPhysicochemical properties, pharmacokinetics, lipophilicity, water-solubility, and medicinal chemistry are some of the ADME properties estimated to analyze drug profiles of top drug candidates. Rewrite the sentence like this.\n\n'Despite considering polarization, the SPC water model is one the most reliable three-center waters models.' Fix the typological error in this sentence.\n\n“The propensity of a drug to acquire pharmacologically active concentration at targeted therapies can be evaluated by a set of ADME parameters”- please add at least two recent references.\n\n“The protocol of new drug development is complicated, time-intensive, costly, and involves both preclinical and clinical stages”- please add references.\n\nThere are some spelling mistakes in the manuscript. And please avoid acronyms in the abstract. Please check and correct.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "8367", "date": "15 Jun 2022", "name": "Mohammad Abu Hena Mostofa Jamal", "role": "Author Response", "response": "Thank you for your insightful feedback to improve our manuscript. Regarding your valuable feedback, we have addressed all the comments individually as follows: Comment 1: What is the reason behind choosing the PDB ID 6LU7? Response: Thanks for your valuable comment. The structure of PDB ID 6LU7 was obtained using the X-RAY Diffraction method and includes a built-in N3 inhibitor. Furthermore, several studies have previously utilized this PDB ID. For instance, Sisakht, M., Mahmoodzadeh, A., & Darabian, M. (2021). Plant‐derived chemicals as potential inhibitors of SARS‐CoV‐2 main protease (6LU7), a virtual screening study. Phytotherapy Research, 35(6), 3262-3274. Chhetri, A., Chettri, S., Rai, P., Mishra, D. K., Sinha, B., & Brahman, D. (2021). Synthesis, characterization and computational study on potential inhibitory action of novel azo imidazole derivatives against COVID-19 main protease (Mpro: 6LU7). Journal of molecular structure, 1225, 129230. Peele, K. A., Durthi, C. P., Srihansa, T., Krupanidhi, S., Ayyagari, V. S., Babu, D. J., ... & Venkateswarulu, T. C. (2020). Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study. Informatics in medicine unlocked, 19, 100345. Moreover, the resolution of the main protease structure of PDB ID 6LU7 is 2.16 Å, indicating the high quality of the structure. For these reasons, we choose the PDB ID 6LU7 for retrieving the main protease structure. Comment 2: Physicochemical properties, pharmacokinetics, lipophilicity, water-solubility, and medicinal chemistry are some of the ADME properties estimated to analyze drug profiles of top drug candidates. Rewrite the sentence like this. Response: We appreciate your feedback. We have rewritten the sentence. Comment 3: 'Despite considering polarization, the SPC water model is one the most reliable three-center waters models.' Fix the typological error in this sentence. Response: Thanks for your concern. We already have fixed the typological error in the latest version of the manuscript. Comment 4: The propensity of a drug to acquire pharmacologically active concentration at targeted therapies can be evaluated by a set of ADME parameters”- please add at least two recent references. Response: Thanks for your valuable feedback. We have added two recent references accordingly. Comment 5: “The protocol of new drug development is complicated, time-intensive, costly, and involves both preclinical and clinical stages”- please add references. Response: We appreciate your effort. Two new references have been added to the new version of the article. Comment 6: There are some spelling mistakes in the manuscript. And please avoid acronyms in the abstract. Please check and correct. Response: Thanks for your concern. We have checked and fixed all the spelling mistakes in the previous version of the manuscript and all the acronyms are avoided in the abstract section of the latest manuscript." } ] } ]	1	https://f1000research.com/articles/10-1313
https://f1000research.com/articles/13-930/v1	15 Aug 24	{ "type": "Systematic Review", "title": "Centering Social Justice and Equity in Research on Accessibility to Public Buildings for Individuals with Mobility Disabilities: A scoping review", "authors": [ "Sidhiprada Mohapatra", "G. Arun Maiya", "Ullas U Nayak", "Leno Benny", "Joanne Watson", "Amit Kinjawadekar", "Rama Devi Nandineni", "Sidhiprada Mohapatra", "G. Arun Maiya", "Ullas U Nayak", "Leno Benny", "Joanne Watson", "Amit Kinjawadekar" ], "abstract": "Purpose To explore how principles of social justice and equity are integrated into research concerning accessibility to public buildings for individuals with mobility disabilities.\n\nMethods Utilising a scoping review methodology to assess literature based on the criteria set by the Joanna Briggs Institute, seven databases were screened. Studies were selected using the framework: “persons with mobility disabilities” AND “accessibility” AND “public buildings”. A theoretical framework helped to extract codes and develop themes through an inductive-deductive analysis method. The results are presented descriptively.\n\nResults The examination of 84 studies uncovered a complex interplay between agencies, systemic challenges, discriminatory practices, and societal attitudes perpetuating marginalisation of individuals with mobility disabilities in their access to public buildings. The recommendations emphasize importance of practical measures, research imperatives, and policy developments to promote inclusivity. We present a ‘Ten-step approach’ to integrate social justice and equity into research on accessibility in public buildings for people with mobility disabilities.\n\nConclusion Integrating diversity, active participation, and inclusive methodologies are essential to address systemic issues, discriminatory practices, and societal attitudes that hinder accessibility and inclusion. Collaborations with diverse stakeholders are crucial for policy changes, resource allocation, and advancing social justice and equity in accessibility research and practice.", "keywords": [ "agencies", "Capability Approach", "de-discrimination", "human rights", "intersectionality", "self-categorisation" ], "content": "Introduction\n\nIndividuals with mobility disabilities face deeply rooted systemic barriers that hinder their complete engagement in society. The onset of disability, coupled with pre-existing disadvantages referred to as the ‘selection effect’, worsens existing challenges and disparities.1 Discrimination, stigma, and negative societal standards lead to further marginalisation. The resulting inequality affects access to essential services like healthcare, rehabilitation, and public facilities.2–4 These barriers hinder mobility, perpetuating poor education, joblessness, poverty, social isolation, and restricted social engagement among individuals with mobility disabilities.5–9 The social model of disability explains these difficulties within societal frameworks, demonstrating their role in continuing oppression and marginalisation.10 This oppression materialises through exploitation, marginalisation, powerlessness, cultural imperialism, and violence.11\n\nImportantly, these challenges may stem from inaccessible public and private facilities.12 Inaccessible public buildings not only limit physical entry but also reinforce social injustice and inequality, reflecting epistemic injustice where individuals’ knowledge and experiences are devalued due to their disability.13,14 This cascading effect initiates a vicious cycle characterized by a lack of accessibility, discrimination, systemic inequality, and limited social participation.15,16 Barriers in one domain frequently create a ripple effect, limiting opportunities and perpetuating cycles of exclusion and marginalisation. Despite legislative efforts persistent barriers remain, disproportionately affecting socially and economically disadvantaged individuals and violating their human rights.17,18\n\nThe socio-ecological model and the International Classification of Functioning, Disability, and Health (ICF) underscore the importance of access to public infrastructure as the social determinants of health in enabling function, activity, and participation, contributing to better health outcomes.19–21 Further, research and academic bodies including urban planners, and public health researchers have emphasized the need for inclusive infrastructure. For example, Kevin Lynch’s concept stresses the significance of visibility for individuals with disabilities in public spaces to promote a sense of belonging and safety.22,23\n\nLynch states, “people feel a sense of safety and security when they see people similar to them already occupying that space in a relaxed way”.\n\nWhile significant strides have been made through reviews on accessibility to public buildings,24–28 there remains a notable gap in understanding how research on accessibility addresses systemic challenges. Addressing the systemic challenges due to inaccessible public buildings requires a comprehensive understanding of social justice and equity within accessibility research. Thus, this study aims to bridge this gap by employing a multipronged theoretical approach, including the Capability Approach (CA), intersectionality lens, and Social Justice lens to investigate how concepts of social justice and equity are addressed in research on accessibility for individuals with mobility disabilities. By doing this, the study aims to uncover vital insights to inform advocacy efforts and policy reforms to foster greater equity and inclusion. Therefore, there is a clear need for a scoping review to understand how research on accessibility reports the challenges to social justice and equity encountered by individuals with mobility disabilities.\n\nThe question we took to the literature was: how are concepts of social justice and equity addressed or reported in research relating to accessibility in public buildings for people with mobility disabilities?\n\nSocial justice is a multifaceted approach to identifying social, economic, and political disparities that affect equal access to resources, opportunities, and rights.29 We used a multipronged theoretical approach to understand this complex phenomenon of social justice within accessibility research.30 The theoretical framework is illustrated in Figure 1.\n\nThe Capability Approach (CA) emphasizes agencies, encompassing personal, social, and environmental dimensions. It extends beyond resource availability, focusing on freedom of choice in decision-making and integrates concepts of dignity and personhood. The intersectionality lens highlights how social identities intersect to shape experiences and opportunities. The Social Justice lens examines systemic inequalities and discriminations. Employing these frameworks in accessibility research offers a comprehensive approach to understanding and addressing social injustices and disability rights. Understanding accessibility using this framework may help shift focus from mere physical entry to public buildings to individuals’ liberty to engage in society beyond.\n\n\nMethods\n\nTo explore the concepts of social justice and equity within research on accessibility, it was necessary to adopt a scoping review (ScR) methodology. The ScR was carried out using the updated methodological guidelines by the Joanna Briggs Institute (JBI). The study is registered at Open Science Framework, refer to the link: https://doi.org/10.17605/OSF.IO/4NMSV.\n\nUsing predetermined inclusion and exclusion criteria, shown in Table 1, the search was conducted in seven databases namely, Scopus, PubMed, Ebsco Cumulative Index to Nursing and Allied Health Literature (CINAHL) Complete, EMBASE, Ovid Medline, Web of Science, and Cochrane Library. The person-concept-context framework was used under “persons with mobility disabilities” AND “accessibility” AND “public buildings” for search string [Extended data file 1]. The terms accessibility and public buildings were defined using established Acts and codes.31,32 The term social justice and equity were intentionally omitted from the search term list to capture studies on accessibility to public buildings that did not explicitly target these concepts but may indirectly contribute to the overall understanding of these issues. The search was carried out with the English language and peer-reviewed original articles as the limits. If the database did not have original articles as a limit, articles on secondary data were removed during the screening process. The search was conducted for all peer-reviewed articles published until 15th August 2023, the date on which the search was carried out. The articles from databases were exported to Rayyan software® for screening.33\n\n\n\n• Studies on persons with visual, hearing, or cognitive impairments\n\n• Studies with assessments or interventions focusing primarily on medical care.\n\n• Population with health conditions and chronic illnesses like obesity, infections like human immune-deficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), cancer, asthma, respiratory or cardiometabolic conditions, psychological conditions, and medical issues primarily requiring medical care\n\n• Health conditions that cause temporary and reversible forms of disabilities like fractures, depression, sprains, and back pain.\n\n\n\n• Accessibility components not catering to public buildings like access to information, webpages, technology\n\n• Buildings catering to specific groups of users where public access is limited like private office spaces, residential buildings, classrooms, nursing facilities, etc.\n\nPotentially relevant articles were identified by the title and abstract through a blinded screening by LB, and UN using the criteria for study selection. The reviewers were trained by the primary author, SM [Extended data file 2]. Using an iterative approach, to ensure similar understanding by the reviewers, meetings were regularly organized to ensure the inter-rater reliability remained above 0.7. Differences of opinion regarding eligibility were resolved through consensus adjudication by SM. The full text of all the selected studies was imported into the Rayyan® platform for screening.33 Subsequently, full texts of articles were screened independently by LB, and UN. Exclusion criteria was applied, and reasons for exclusion were documented. Articles not addressing physical accessibility, such as those focusing solely on theoretical measurements using mathematical algorithms, were excluded from the review. Conflict resolution through meetings and further deliberations by SM ensured an IRR of 0.7 between LB’s and UN’s decisions. The final set of selected articles was exported to start data extraction. Since it is a ScR, a critical appraisal of the studies was not undertaken.34\n\nA data extraction sheet was prepared by SM using Microsoft Excel 2016. The articles were divided across SM, LB, and UN for extraction. Given the interdisciplinary nature of the research, each variable in the extraction sheet was pre-defined. Further, training on data retrieval, regular meetings, and instruction or explanation of each item on the sheet helped to ensure data reliability and the extraction process’s feasibility and comprehensiveness [Extended data file 2].\n\nThe extensive dataset underwent qualitative content analysis using an inductive-deductive hybrid thematic method.35,36 Extraction encompassed three domains: article information, detailed methodology, and extraction of social justice elements within the articles. Following extraction, themes were developed using an inductive-deductive hybrid thematic analysis to enable the convergence of methods and the generation of new theories in the review.35 The thematic analysis was carried out by SM, JW, and verified by NRD in consultation with subject experts, AGM, and AK. This ensured the adequacy of the themes. These themes underwent thorough discussion with reviewers LB and UN, with finalization achieved through complete consensus. To ensure standardized reporting, we adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) checklist.37\n\n\nResults\n\nInitially, 3,474 articles were retrieved from the databases. The detailed screening steps using the PRISMA flow-diagram38 is shown in Figure 2. A total of 84 articles deemed suitable for inclusion in the review [Extended data file 3]. Excluded articles with reasons for exclusion were documented [Extended data file 4]. In the following sections, we present the findings from these 84 articles, using the structure recommended by the JBI, participant characteristics, the context of public buildings, and the concept of accessibility. Subsequently, we present the influence of various agencies and the role of intersectionality on accessibility in public buildings. This is followed by the role of accessibility in uplifting social justice, equity and human rights and fostering opportunities for individuals with mobility disabilities. Lastly, a summary of the recommendations outlined in the research studies is furnished.\n\nAmong the 84 studies, 42 employed quantitative methodologies, whereas26 studies utilized qualitative approaches, delving into narratives to understand the experiences and perceptions of participants regarding accessibility. A summary of methods is given in Table 2. Additionally, 16 studies were classified as mixed methods or multiple methods. While these studies may or may not strictly adhere to mixed methods methodology, they incorporated more than one method that complemented each other, allowing for a comprehensive exploration of accessibility issues in public buildings.\n\n* Authors used multiple methods for data collection.\n\n** Study ID: The details of the articles can be found in extended data file 3.115\n\nCountries\n\nUsing the World Bank classification,39 studies were grouped into income categories as shown in Figure 3. Countries such as United States of America and the United Kingdom, had numerous studies, while upper-middle and lower-middle-income countries had varying representation.\n\nPublic buildings\n\nBuildings assessed in the articles, include educational commercial, recreational, hotels/restaurants, transportation, workplaces/business centers, basic amenities, historical sites, religious buildings, and refugee/sheltered structures. A significant number of articles encompassed evaluations of multiple building types. Over 19 articles did not involve building evaluation but included usage perspectives. Summary of the building typologies is given in Table 3. The spatial features assessed in these studies included exterior and interior circulation spaces, basic amenities such as dressing and fitting rooms in malls,40 and ablution areas in mosques.41–43 Some studies also delved into broader aspects of accessibility, encompassing factors such as transportation,44 availability of assistive technology,45 environmental adaptations, and daily activity spaces.46\n\n* Study ID: The details of the articles can be found in the extended data file 3.115\n\nParticipant numbers, ranged from 4 to 455 individuals, aged between 18 to 64 years. While most studies included males and females, exceptions were noted in three studies that only included a single-sex group.40,42,47 A study conducted in Riyadh mosque, excluded females due to sociocultural and religious norms.42 Details of participants are presented in Table 4.\n\n* Study ID: The details of the articles can be found in the extended data file 3.115\n\nFew studies reported on chronic orthopedic and neurological conditions like, osteoarthritis, juvenile rheumatic arthritis, amputation, club foot, stroke, multiple sclerosis, Guillain–Barré syndrome (GBS), and traumatic brain injury affecting the motor system. Sixty-nine studies assessed accessibility by people with mobility disabilities without specifying the health conditions. However, one study reported the inclusion of users with mobility aids in a historical building based on observation rather than their health conditions.48\n\nWheelchair was the most common mobility device. Calipers, prostheses, and skateboards were mentioned in three studies. Over 30 studies reported involving other stakeholders to gather their perspectives.\n\nTo understand how research conceptualized accessibility, data was extracted on accessibility including definition, tools for evaluation, and legislative underpinnings. Among these articles, only 17 provided a range of definitions for accessibility. Notably, only five studies by Pretto,49 Iwarsson,50 Evcil,51 Andrade52 and Arbour-Nicitopoulos53 went beyond defining accessibility as mere usability or reaching a destination, grounding it within the holistic need for the realization of freedom and enhancing quality of life of individuals with disabilities.\n\nTo assess accessibility quantitative methods were employed in 63 articles, while qualitative tools were utilized in 30 articles. Among the four studies that employed technology or devices for assessment, include Geographical Information System,54 and two used the ADA Accessibility Stick (Access, Lawrence, KS, USA),55,56 a measurement device designed to assess spatial dimensions in public buildings. Additionally, another study utilized a door pressure gauge and the ADA Accessibility Stick.57 Commonly used quantitative tools included the McClain and Todd questionnaire (n=5), Accessibility Instruments Measuring Fitness and Recreation Environments (n=3), and the Americans with Disabilities Act checklist (n=6). Additionally, over 20 articles utilized checklists derived from building codes or guidelines. Several studies (n=27) based their assessments on country-specific guidelines, codes, or Acts. The tools and guidelines utilised are summarized in Tables 5 and 6, respectively. Studies employing multiple methods typically utilised a combination of qualitative and quantitative tools.\n\n* Study ID: The details of the articles can be found in the extended data file 3.115\n\n* Study ID: The details of the articles can be found in the extended data file 3.115\n\nIn this section, we summarise the data extracted on accessibility using the theoretical framework, refer to Table 7 [details given in Extended Data Table 1]. The data aims to give a deeper understanding of intersection between individuals’ capabilities, resources, identities, and experiences on their ability to act and make life choices.\n\nPersonal Agencies in the realisation of opportunities\n\nThough the studies have sparingly analysed the impact of personal agencies on accessibility, qualitative reports have highlighted that access to public buildings is an individualistic experience for example individuals with mild disabilities, better health conditions, skills in wheelchair transfers, and access to power mobility demonstrated the ability to independently access public spaces Also, emphasizing the variability of abilities within the disabled community.\n\nAnthropometry can typically intersect with design dimensions impacting the usage of a space. For instance, two studies report body weight of the individual and short stature are two anthropometric factors affecting accessibility.58,59 Psychological reactions from previous experiences such as fear and anxiety played a crucial role in mobility decisions. Financial constraints led some participants to opt for home confinement to evade disappointment or feelings of burden on family caregivers.60,61 Additionally, studies reported that changing abilities over time and varying assistive device skills presented new challenges,62–64 such as access to toileting65 and work-related issues.66 This highlights the dynamic nature and diversity within disability.\n\nSocial Agencies in the realisation of opportunities\n\nThe section focuses on the role of individuals within social structures in shaping accessibility outcomes. Individual’s social relationships, societal norms, cultural and religious beliefs, and practices influence their ability to assert their rights and realise accessibility. The key themes, gleaned from the reviewed studies, included social relationships, advocacy, and socio-cultural norms and stereotypes.\n\nSocial relationships play a crucial role, with some studies emphasizing the role of service providers and peer groups in engaging and understanding the needs of individuals with mobility disabilities.67–69 Access as a right rather than charity,48,61 self-advocacy,60 involvement of health professionals in advocacy for access,50,69 and the process of advocacy56 have been reported widely in the studies.\n\nIt was noted that traditional roles and beliefs may limit opportunities for individuals with disabilities. Similarly, cultural beliefs may hinder the implementation of accessibility measures, especially in religious and heritage buildings.64,70 Deep-rooted cultural beliefs about disability as punishment or defectiveness further contribute to barriers to access and inclusion.71\n\nEnvironmental Agencies in the realisation of opportunities\n\nThe agencies emphasize the dynamic role of environmental factors in influencing accessibility. Key themes include Physical and Environmental Access; Administrative and Bureaucratic Factors; Societal Factors; and Policy and Economic Factors.\n\nAll studies reported physical structures positively or negatively on access. Challenges in physical access are evident, with issues such as steep terrain and snow-covered paths hindering mobility. Lack of coordination among responsible departments, societal attitudes and lack of awareness, with instances of ableist attitudes and insensitivity toward disability parking spaces also pose challenges. Policies and frameworks often lack consistent implementation, with enforcement relying heavily on vigilance from access groups. Additionally, economic constraints limit resource availability, leading to a shortage of well-trained professionals and inadequate investment in accessibility measures.\n\nIntersectionality\n\nEach of the agencies serve primarily as contextual factors that intersect with other dimensions of identity to produce unique experiences of marginalisation or privilege. In this study, the terms “personal agency” and “intersectionality” are distinct. While the first focuses on individuals’ capabilities, the second explores the intersections of social identities and power dynamics within broader social structures. Therefore, we further explored the intersecting identities as summarised in Table 8 [details given in Extended Data Table 2].\n\nMany studies have overlooked intersectionality beyond gender and age, with even these identities not analysed in depth. Among quantitative studies, only Gray et al. 2014 analyzed how age, income, and race interact with access to physical space at work.72 Only one study reported a statistical comparison between user satisfaction based on age, educational level, and gender.73 While two studies, Tijm et al. 2011 and Waenlor et al. 2002 mention racial and ethnic backgrounds, with no further exploration to understand their impact on accessibility.74,75\n\nIntersectionality also concerns the caregivers of individuals with mobility disabilities like inaccessible public buildings create added responsibilities to escort a family member with disabilities, as demonstrated in a study by Bhuiya et al.76 This study explores age and gendered roles of caregivers get affected due to inaccessibility. For example, an elderly respondent mentioned the physical strain of carrying heavy bags for extended periods while assisting her son with disabilities at bazaars. Similarly, a woman respondent assists her husband due to lack of accessibility have added responsibilities to her daily chores. Our findings underscore the broader societal implications of inaccessible environments, revealing restricted physical access imposes additional burdens on caregivers, often exacerbating existing social inequalities.\n\nThough studies highlight the complex interplay between occupation, finances, and accessibility, these have been often overlooked during analysis. Moreover, insights from studies like Salie et al.77 and Bhuiya et al.,76 underscore the bidirectional relationship between occupation and accessibility, illustrating how limited access can both result from and perpetuate occupational limitations. This summary aims to inform accessibility stakeholders that multiple identities intersect to produce unique experiences among people with mobility disabilities in public buildings, rather than indicating one group’s greater marginalisation.\n\nThe studies reveal three themes namely, Structural (in) equality, Empowerment and Autonomy, and Human Rights violations showcasing the intersection of social justice, equity, and human rights within accessibility research. Systemic challenges within society, where ad hoc approaches to accessibility prevail,78 often lack the political will and proper funding for modifications.79–81 Similarly, violations of fundamental human rights to dignity, autonomy, safety, basic needs, privacy and safety were reported in the studies. Violations perpetuated due to discriminatory practices, paternalization, and ableist attitudes, contribute to the reduced access to public buildings and marginalisation of people with mobility disabilities.\n\nA growing trend of including stakeholders in research is noted. However, the instrumentalisation of participants within research still persists. This further leads to a lack of understanding of the diverse and changing needs of people with mobility disabilities and perpetuates imbalanced power dynamics. It can be noted through participant reports that accessible environments are not just about physical access; it is about freedom, autonomy, and the realization of fundamental human rights.\n\nThe social outcomes discussed in the studies include basic functioning, engaging in paid and unpaid activities, social engagements, safety and health. These outcomes are critical as they directly impact the inclusion of individuals with mobility disabilities in society. Thirty-one studies did not report on social outcomes. However, some studies, although not directly assessing these outcomes, highlighted the impact of accessibility on aspects such as access to pensions,82 risk of injuries,83 lack of political participation, and risk of homelessness.74 Summary of sample codes, and themes on social justice and social outcomes reported in the studies is given in Table 9 [details given in Extended Data Table 3 and 4].\n\nRecommendations across the studies were categorized into practical measures (n=41), research initiatives (n=19), and policy developments (n=13) [Extended Data Table 5]. Under the practice category, suggestions involve securing finances, ensuring equipment availability, conducting awareness campaigns, providing incentives for accessibility to constructors, regular monitoring, and engaging multidisciplinary teams. Moreover, studies propose organising training and awareness sessions, promoting partnerships, documenting advancements, and advocating for accessibility by both healthcare professionals and individuals with disabilities themselves.\n\nWithin the realm of research, recommendations concentrate on creating dependable evaluation instruments, conducting qualitative research to comprehend requirements, guaranteeing broad geographical inclusivity, performing comprehensive field investigations, establishing databases, creating innovative low-technology gadgets, and utilizing broader and larger sample sizes for research purposes. Finally, policy recommendation includes developing context-specific regulations for historic or cultural structures, involving individuals with disabilities in decision-making procedures, ensuring the ethical execution of regulations, and facilitating their enforcement.\n\n\nDiscussion\n\nThis review includes a diverse array of study designs capturing multiple perspectives from 84 studies. Thus, contributing to a holistic understanding of accessibility to public buildings and their implications on a complex social phenomenon called social justice.\n\nHowever, studies concentrated from high-income countries like United States and the United Kingdom indicating a global imbalance in research distribution. This geographical bias may overlook unique challenges individuals face in diverse socio-economic contexts. Thus, limiting the generalizability of findings. Also, studies in high-income countries encompass a broader range of bio-psychosocial factors, while research from LMICs predominantly focuses on environmental factors.84 However, it was noted that there is a shift in trend in recent studies like studies from Botswana, Bangladesh, Mongolia, and other low-middle-income countries highlighted accessibility from a rights perspective.45,54,85 The imbalance in research distribution may be attributed to resource availability, funding opportunities, and infrastructure for research in high-income countries compared to LMICs.84,86 Despite the majority of the global population living in LMICs a bulk of disability research is conducted in high-income countries due to the above reasons.86\n\nWide range of public buildings were assessed, demonstrating the extensive scope of the research. However, there were notable gaps in the representation of specific building typologies like heritage, religious, and emergency buildings. Accessibility research traditionally focuses on educational institutions, public facilities, and recreational spaces, but there has been a lack of attention given to accessibility in religious and heritage buildings. Challenges in retrofitting historical structures with modern accessibility standards while preserving architectural integrity have hindered progress in this area.81,87,88\n\nParticipant represented in the studies have diverse demographic mobility disabilities profiles. However, men, and wheelchair users are overrepresented, potentially limiting diversity of perspectives within the research. This disparity exists in other areas of disability studies, such as the distribution of electric wheelchairs, with more men than women being prescribed these mobility aids.89 Addressing this “Boys Club” challenge can be accomplished through more equitable recruitment practices. Additionally, the visible nature of infrastructure-related barriers encounter by wheelchair users leads to their overrepresentation.90\n\nAccessibility inquiry within the articles though multifaceted, only a subset used a comprehensive approach beyond mere usability or reaching a destination as definition. Also, due to the multifaceted nature the tools concentrating on infrastructure pose a challenge to the validity and dependability of results. None of the studies used statistical inferences to understand the multifaceted relationship between agencies and accessibility. Thus, there is a need to expand the range of accessibility inquiry to encompass other facets beyond infrastructure, such as societal attitudes, cultural convictions, policy frameworks, and service provision.2,91 This will help advocating fora holistic stance to accessibility that goes beyond physical infrastructure considerations.\n\nIn general, although the scrutinized articles present valuable perspectives, there is space for enhancement in delineating accessibility, standardizing evaluation methodologies, and integrating innovative mechanisms to progress the comprehension of accessibility predicaments in public buildings.\n\nStudies have highlighted the significant influence of personal agency or capabilities on individual autonomy on movement and accessibility. Persons with mild impairments displayed varying levels of self-sufficiency in accessing public buildings. Illustrating the diversity within disability Financial restrictions often compelled some participants to select home confinement, demonstrating the intricate interplay between economic factors and accessibility. Emotional factors like apprehension and unease also impacted movement choices, underscoring the significance of safe and comfortable mobility on mental well-being. In a recent study by Okezue, 2024, participants especially women with disabilities reported higher levels of anxiety when using public buildings.92 Social structures additionally molded movement decisions, with demographic factors affecting individuals’ placements within their surroundings. Understanding the multifaceted nature of personal agency is crucial for developing inclusive policies and environments that cater to the diverse needs of individuals with disabilities.93\n\nIntersectionality intersects with accessibility research by highlighting the complex interplay of various social identities and power dynamics in shaping the experiences of individuals with mobility disabilities. The intersection of inherent vulnerabilities can create complex challenges for these individuals, affecting their choices and movement decisions.94 While many studies acknowledged that intersecting identities impact accessibility, there is a lack of statistical inference due to thinly stratified sampling.95,96 Most studies recognize overlapping identities such as age, sex, race, ethnicity, income, and education intersected with access to physical spaces. However, there are difficulties to generate inferences. Research in this area often lacks comprehensive assessments due to methodological constraints and limited focus on specific identity dimensions. This limits the practical application of the intersectional lens.\n\nDespite these constraints, some studies exhibited the interconnectedness of multiple identities in shaping accessibility experiences like occupation, finances, and accessibility were intricately related,72,97 Thus, illustrating the bidirectional relationship between limited access and opportunity constraints. Nonetheless, these gaps suggest avenues for future research. Moreover, the impact of intersectionality on accessibility experiences for caregivers of individuals with mobility disabilities was relatively underexplored. Additionally, while anthropometry was not typically considered under intersectionality, it intersected with other dimensions of identity within this framework, influencing accessibility experiences.\n\nAdditionally, future research should employ more robust methodologies to capture the nuanced intersections of identity and power dynamics, involving mixed-methods approaches, longitudinal studies, and participatory research methods.95\n\nThe examination of social agency highlights the noteworthy impact of relationships, advocacy efforts, and socio-cultural norms on accessibility. Societal connections are pivotal in the realization of access like staff’s involvement in planning lectures for students with disabilities to reduce travel time. Advocacy efforts range from promoting disability access as a right to challenging discriminatory practices, making their voices matter, and societal attitudes. Nonetheless, socio-cultural norms and stereotypes can obstruct availability measures by reinforcing traditional roles and cultural beliefs. Relatives, companions, and community participants either empower or impede access to amenities by individuals with disabilities.98 Dealing with these dynamics is crucial for fostering inclusive environments and advocating for the rights of individuals with disabilities.99 Promotion campaigns, driven by establishments backing individuals with disabilities, can help change policies and promote inclusive practices.\n\nSocio-cultural norms contribute to creating challenges like shame, employment difficulties, and social participation.100 These negative perceptions create barriers to accessing essential services and support, exacerbating challenges faced by people with mobility disabilities. Addressing these norms requires challenging harmful beliefs, promoting awareness, and education, and advocating for inclusive policies and practices to create a more accessible and equitable environment for individuals with mobility disabilities.\n\nWhile physical access was reported across all the studies, societal attitudes also posed a significant barrier. Ableism, characterized by prejudice and discrimination against individuals with disabilities, manifests in societal norms and behaviors, limiting access to essential services and social inclusion. Economic constraints further hinder resource availability, emphasizing the need for increased investment in accessibility measures.101 Collaborative efforts prioritizing awareness-raising, policy implementation, and resource allocation are essential to ensure equal access and opportunities for individuals with disabilities.102,103 Addressing ableist attitudes and investing in comprehensive accessibility measures are vital to enhancing the quality of life and independence of individuals with disabilities.104,105 The studies highlight the complex interplay of personal, social, and environmental factors, emphasizing the importance of addressing multifaceted challenges to create inclusive and accessible public spaces for individuals with mobility disabilities.\n\nThe studies highlight the complex interplay of personal, social, and environmental factors, emphasizing the importance of addressing multifaceted challenges to create inclusive and accessible public spaces for individuals with mobility disabilities. By leveraging the strengths of various agencies, stakeholders can work towards creating more inclusive and accessible public spaces for individuals with mobility disabilities.\n\nThe intersection of social justice, equity, and human rights in accessibility research reveals systemic issues and discriminatory practices that marginalise individuals with disabilities in accessing public buildings and services. Social justice principles emphasize access, participation, equity, and human rights for all individuals, including those with disabilities,106 while equity in accessibility research ensures equal opportunities and resources for full societal engagement.107 Human rights frameworks advocate for the fundamental rights of inclusion and protection of individuals with disabilities from discrimination.\n\nSystemic issues such as ad hoc approaches to accessibility and lack of political will and funding hinder progress in making buildings inclusive and accessible.108 Discriminatory practices exacerbate marginalisation, perpetuating power imbalances where individuals with disabilities are objectified in decision-making processes. Additionally, the absence of proper funding for retrofitting and accessibility modifications can hinder progress in making buildings inclusive and accessible for individuals with disabilities.108\n\nSocietal attitudes, including cultural beliefs and ableist norms, create barriers to access and perpetuate inequalities for individuals with disabilities. Lack of involvement in decision-making processes regarding facility development, reflects on the structural inequalities. For instance, the instrumentalization of participants perpetuates power dynamics, where individuals with disabilities are treated as objects of study rather than active agents in decision-making processes.\n\nAddressing these issues requires comprehensive strategies that prioritize collaboration, awareness, and policy implementation to ensure equal access and opportunities for all individuals, irrespective of abilities. Accessible environments encompass more than mere physical access; they embody principles of freedom, autonomy, and the realization of fundamental human rights. Thus, promoting social justice, equity, and human rights within accessibility research is crucial for advancing towards a more inclusive and accessible future.\n\nThe studies recommend use of pragmatic steps, research initiatives, and policy advancements, offering ways to tackle accessibility issues in future. Research recommendations are essential in both academia and public realms. In academia, they help pinpointing gaps in current literature and propose pathways and sets agendas for future studies.109 Thus, these suggestions contribute to the progression of knowledge and the formulation of novel theories and concepts and help bridge the gap between research and practice, ensuring that evidence-based approaches are effectively implemented in real-world settings.110\n\nResearch recommendations are crucial for policy decisions and practice. Suggestions derived from research contribute to evidence-based policies and interventions aimed at addressing societal challenges like accessibility.111 For example, the review studies recommend need for health professional engagement in accessibility to public buildings, thus encouraging interdisciplinary research through multidisciplinary collaborations.\n\nCentering the review on human agency and freedoms, and realization of human rights, the framework explains the social model of disability. A versatile and interdisciplinary, framework helped in examining complex social issues like accessibility challenges. This framework enriched the research by providing a theoretical foundation and was instrumental in providing a comprehensive analysis within a broader social justice and equity framework.\n\nWith the social justice and capabilities as guiding principles, the review not only enhances the relevance and applicability of the findings but also underscores the importance of addressing systemic inequalities and promoting human rights in accessibility initiatives. The review is centered around advocating for a rights-based and person-centered approach to accessibility, thus highlights the ethical imperative of ensuring equal access and opportunities for all members of society, regardless of their abilities.\n\nOne significant limitation is the likelihood of publication bias, as we concentrated mainly on peer-reviewed articles obtained from databases. This strategy might have excluded articles available in alternative forms, like grey literature or symposium proceedings, which might have offered extra perspectives into accessibility investigation. Furthermore, while attempts were made to include research from various geographical areas, there might be poor representation from LMICs. This might impact the generalizability of the results and might neglect distinctive viewpoints and obstacles encountered by people with mobility disabilities in these settings. The review did not carry out methodological appraisals of the studies.\n\nWe propose a “Ten-step approach” to prioritize social justice and equity within accessibility research as illustrated in Figure 4. These steps encompass stages of a project, from pre-initiation to knowledge dissemination. Step 1 emphasizes the formation of a diverse research team, as exemplified by Nijs,112 where team members with disabilities significantly influenced the authors. Step 2 focuses on integrating opportunities within the methodology to capture intersectional identities such as age, sex, socio-economic status, and sexuality. Step 3 underscores active participation by individuals with disabilities, including the use of photovoice. Step 4 highlights involving stakeholders—family, professionals, public officials, and community members—as they all contribute to realizing opportunities through accessible buildings. Steps 5 & 6 encourage de-differentiation and self-categorization by participants to prevent the creation of distinctions between individuals with and without disabilities, allowing participants to choose their participation category and avoid socially constructed categorization. In the analysis phase, Step 7 suggests using an intersectionality lens to understand the impact of diverse identities on accessibility to public buildings, while Step 8 emphasizes researcher and participant reflexivity. Step 9 involves disseminating findings locally and globally, followed by continued follow-up in Step 10 to explore how accessibility impacts the realization of opportunities over time as disability changes.\n\n\nConclusion\n\nBased on the objective of centering social justice and equity within accessibility research on public buildings for people with mobility disabilities, the study underscores the necessity of integrating diverse perspectives, promoting active participation, and adopting inclusive methodologies. The findings emphasize the importance of addressing systemic issues, discriminatory practices, and societal attitudes that hinder accessibility and inclusion. It concludes that collaborative efforts involving diverse stakeholders are crucial for implementing policy changes, resource allocation, and comprehensive strategies to advance social justice and equity in accessibility research and practice.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: Extended data file 1: Search string, https://doi.org/10.6084/m9.figshare.26143822 113\n\nFigshare: Extended data file 2: Instruction for data extraction, https://doi.org/10.6084/m9.figshare.26143861 114\n\nFigshare: Extended data file 3: List of included articles, https://doi.org/10.6084/m9.figshare.26143894 115\n\nFigshare: Extended data file 4: Excluded articles with reasons, https://doi.org/10.6084/m9.figshare.26143891 116\n\nFigshare: Extended Data Table 1. Themes, sub-themes, and codes for agencies, https://doi.org/10.6084/m9.figshare.26147596 117\n\nFigshare: Extended Data Table 2. Sub-themes, and codes for the theme intersectionality (n=84), https://doi.org/10.6084/m9.figshare.26147791 118\n\nFigshare: Extended Data Table 3. Themes, sub-themes, and codes on social justice, equity, and human rights (n=84), https://doi.org/10.6084/m9.figshare.26148070 119\n\nFigshare: Extended Data Table 4. Social and functional outcomes reported in the studies (n=84), https://doi.org/10.6084/m9.figshare.26148148 120\n\nFigshare: Extended Data Table 5. Summary of recommendations given in accessibility research, https://doi.org/10.6084/m9.figshare.26148247 121\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Reporting guidelines PRISMA Extension for Scoping Reviews (PRISMA-ScR). figshare. Dataset. https://doi.org/10.6084/m9.figshare.26143873 37\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 acknowledge the Chief Librarian, Department of Library, Kasturba Medical College to help retrieve the full text of irretrievable articles.\n\n\nReferences\n\nJenkins SP, Rigg JA: Disability and Disadvantage: Selection, Onset, and Duration Effects. J. Soc. Policy. 2004 Jul; 33(3): 479–501. Publisher Full Text\n\nOkoro CA, Hollis ND, Cyrus AC, et al.: Prevalence of Disabilities and Health Care Access by Disability Status and Type Among Adults — United States, 2016. MMWR Morb. Mortal Wkly. Rep. 2018 Aug; 67(32): 882–887. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSenjam S: Impact of COVID-19 pandemic on people living with visual disability. Indian J. Ophthalmol. 2020 Jul; 68(7): 1367–1370. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan Biljon HM, Salie B, Van Wyk JC, et al.: Access to Public Healthcare Rehabilitation Services by Persons with Disabilities in South Africa: a Scoping Review. Disability, CBR & Inclusive Development. 2022 Nov; 33(3): 41. Publisher Full Text\n\nBlackburn CM, Spencer NJ, Read JM: Prevalence of childhood disability and the characteristics and circumstances of disabled children in the UK: secondary analysis of the Family Resources Survey. BMC Pediatr. 2010 Dec; 10(1): 21. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchwartz N, Buliung R, Wilson K: Experiences of food access among disabled adults in Toronto, Canada. Disabil. Soc. 2023 Apr; 38(4): 610–634. Publisher Full Text\n\nBigonnesse C, Mahmood A, Chaudhury H, et al.: The role of neighborhood physical environment on mobility and social participation among people using mobility assistive technology. Disabil. Soc. 2018 Jul; 33(6): 866–893. Publisher Full Text\n\nUseh, Moyo AM, Munyonga E: Wheelchair accessibility of public buildings in the central business district of Harare, Zimbabwe. Disabil. Rehabil. 2001 Jan; 23(11): 490–496. PubMed Abstract \| Publisher Full Text\n\nBotha M, Fischer Mogensen K, Ebrahim A, et al.: In search of a landing place for persons with disabilities: A critique of South Africa’s skills development programme. Int. J. Discrim. Law. 2023 Jun; 23(1–2): 163–180. Publisher Full Text\n\nBampi LN d S, Guilhem D, Alves ED: Social Model: A New Approach of the Disability Theme. Rev. Lat. Am. Enfermagem. 2010 Aug; 18(4): 816–823. PubMed Abstract \| Publisher Full Text\n\nAriz D: Disabled Population in India: A Regional Analysis. Ann. Valahia Univ. Târgovişte. Geogr. Series. 2018; 18: 136–143. Publisher Full Text\n\nvon Braun J , Gatzweiler FW: Marginality—An Overview and Implications for Policy. Marginality. Dordrecht: Springer Netherlands; 2014; pp. 35–6. Publisher Full Text\n\nKidd IJ, Carel H: Epistemic Injustice and Illness. J. Appl. Philos. 2017 Feb 8; 34(2): 172–190. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nScully JL: From “She Would Say That, Wouldn’t She?” to “Does She Take Sugar?” Epistemic Injustice and Disability. IJFAB: Int. J. Fem. Approaches Bioeth. 2018 Feb; 11(1): 106–124. Publisher Full Text\n\nShandra CL: Disability as Inequality: Social Disparities, Health Disparities, and Participation in Daily Activities. Soc. Forces. 2018 Sep; 97(1): 157–192. Publisher Full Text\n\nGréaux M, Moro MF, Kamenov K, et al.: Health equity for persons with disabilities: a global scoping review on barriers and interventions in healthcare services. Int. J. Equity Health. 2023 Nov; 22(1): 236. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMitra S, Sambamoorthi U: Disability and the Rural Labor Market in India: Evidence for Males in Tamil Nadu. World Dev. 2008 May; 36(5): 934–952. Publisher Full Text\n\nBroderick A: Of rights and obligations: the birth of accessibility. Int. J. Hum. Rights. 2020 Apr 20; 24(4): 393–413. Publisher Full Text\n\nAkoto Y, Nketsia W, Opoku MP, et al.: Applying a socio-ecological model to understand the psychosocial support services available to students with disabilities in universities. Educ. Policy Anal. Arch. 2022 Oct; 30(152): n152. Publisher Full Text\n\nBraveman P, Gottlieb L: The Social Determinants of Health: It’s Time to Consider the Causes of the Causes. Public Health Rep. 2014 Jan 1; 129(1_suppl2): 19–31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDovjak M, Kukec A: Creating healthy and sustainable buildings: an assessment of health risk factors. Springer Nature; 2019. Publisher Full Text\n\nShahraki AA: Urban planning for physically disabled people’s needs with case studies. Spat. Inf. Res. 2021 Apr 8; 29(2): 173–184. Publisher Full Text\n\nLynch K: Good City Form. Cambridge, MA: MIT press; 1981.\n\nCalder A, Sole G, Mulligan H: The accessibility of fitness centers for people with disabilities: A systematic review. Disabil. Health J. 2018 Oct; 11(4): 525–536. PubMed Abstract \| Publisher Full Text\n\nJeannis H, Joseph J, Goldberg M, et al.: Full-participation of students with physical disabilities in science and engineering laboratories. Disabil. Rehabil. Assist. Technol. 2018 Feb; 13(2): 186–193. PubMed Abstract \| Publisher Full Text\n\nWatchorn V, Hitch D, Grant C, et al.: An integrated literature review of the current discourse around universal design in the built environment – is occupation the missing link?. Disabil. Rehabil. 2021 Jan; 43(1): 1–12. PubMed Abstract \| Publisher Full Text\n\nCarlsson G, Slaug B, Schmidt SM, et al.: A scoping review of public building accessibility. Disabil. Health J. 2022 Apr; 15(2): 101227. Publisher Full Text\n\nKapsalis E, Jaeger N, Hale J: Disabled-by-design: effects of inaccessible urban public spaces on users of mobility assistive devices – a systematic review. Disabil. Rehabil. Assist. Technol. 2024 Apr; 19(3): 604–622. PubMed Abstract \| Publisher Full Text\n\nKillen M, Yee KM, Ruck MD: Social and Racial Justice as Fundamental Goals for the Field of Human Development. Hum. Dev. 2021; 65(5–6): 257–269. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSen A: Capability and Well-Being.Nussbaum S, editor. The Quality of Life. Oxford: Clarendon Press; 1993. Publisher Full Text\n\nArticle 9 - Accessibility\|Division for Inclusive Social Development (DISD).[cited 2023 Jun 22]. Reference Source\n\nNational Building Code - Bureau of Indian Standards.[cited 2023 Mar 22]. Reference Source\n\nOuzzani M, Hammady H, Fedorowicz Z, et al.: Rayyan—a web and mobile app for systematic reviews. Syst. Rev. 2016 Dec; 5(1): 210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeters MDJ, Marnie C, Colquhoun H, et al.: Scoping reviews: reinforcing and advancing the methodology and application. Syst. Rev. 2021 Dec; 10(1): 263. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nProudfoot K: Inductive/Deductive Hybrid Thematic Analysis in Mixed Methods Research. J. Mixed Methods Res. 2023 Jul; 17(3): 308–326. Publisher Full Text\n\nPollock D, Peters MDJ, Khalil H, et al.: Recommendations for the extraction, analysis, and presentation of results in scoping reviews. JBI Evid Synth. 2023; 21(3): 520–532. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Reporting guidelines PRISMA Extension for Scoping Reviews (PRISMA-ScR). Dataset. figshare. 2024. Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021 Mar 372; 372: n71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHamadeh N, Metreau E, Van Rompaey C : World Bank Group country classifications by income level for FY24 (July 1, 2023- June 30, 2024).[cited 2024 Jan 31]. Reference Source\n\nMartin A, Watchorn V, Grant C: Changing Places, Changing Lives. J. Soc. Incl. 2018 Dec 30; 9(2): 5–21. Publisher Full Text\n\nAl-Mansoor NF: Universal Mosque/Masjid Design. Stud. Health Technol. Inform. 2018; 256: 293–298. PubMed Abstract\n\nAbu Tariah H, Ghasham N, Alolayan M, et al.: Wheelchair accessibility of mosques in Riyadh. Work. 2018 Jul 31; 60(3): 385–391. PubMed Abstract \| Publisher Full Text\n\nNour MO: Satisfaction with Quality and Access to Al-Masjid Al-Haram Services Among Persons with Disabilities During Umrah Season, 1441 H (2019-2020): Cross-sectional Study. Turkiye Klinikleri J. Med. Sci. 2021; 41(3): 242–249. Publisher Full Text\n\nFarzana F: Accessibility of Public Buildings in Khulna, Bangladesh, for Wheelchair Users. Disability, CBR & Inclusive Development. 2019 May 14; 29(4): 83. Publisher Full Text\n\nDorjbal D, Prodinger B, Zanini C, et al.: Living with spinal cord injury in Mongolia: A qualitative study on perceived environmental barriers. J. Spinal Cord Med. 2020 Jul 3; 43(4): 518–531. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeyers AR, Anderson JJ, Miller DR, et al.: Barriers, facilitators, and access for wheelchair users: sbstantive and methodologic lessons from a pilot study of environmental effects. Soc Sci Med. 2002 Oct; 55(8): 1435–1446. PubMed Abstract \| Publisher Full Text\n\nTudzi E, Bugri J, Danso A: Experiences of Students with Disabilities in Inaccessible Built Environments: A Case Study of a Student with Mobility Impairment in a University in Ghana. Scand. J. Disabil. Res. 2020 Apr 16; 22(1): 116–126. Publisher Full Text\n\nLynch S, Proverbs DG: How adaption of historic listed buildings affords access. International Journal of Building Pathology and Adaptation. 2019 Sep; 38(4): 589–605. Publisher Full Text\n\nPretto A: A study on accessibility in an Old Italian City: when the past is worth more than the present. Disabil Soc. 2022 Mar; 37(3): 496–521. Publisher Full Text\n\nIwarsson S, Fänge A, Hovbrandt P, et al.: Occupational Therapy targeting Physical Environmental Barriers in Buildings with Public Facilities. Br. J. Occup. Ther. 2004 Jan; 67(1): 29–38. Publisher Full Text\n\nEvcil AN: Wheelchair accessibility to public buildings in Istanbul. Disabil. Rehabil. Assist. Technol. 2009 Jan; 4(2): 76–85. PubMed Abstract \| Publisher Full Text\n\nAndrade IF, e Ely VHMB: Assessment method of accessibility conditions: how to make public buildings accessible? Work. 2012; 41: 3774–3780. Publisher Full Text\n\nArbour-Nicitopoulos KP, Ginis KAM: Universal Accessibility of “Accessible” Fitness and Recreational Facilities for Persons With Mobility Disabilities. Adapt. Phys. Act. Q. 2011 Jan; 28(1): 1–15. PubMed Abstract \| Publisher Full Text\n\nBhuiya MM, Shao W, Jones S: Measuring accessibility of movement challenged persons during earthquake evacuation of Dhaka City, Bangladesh: A participatory GIS-Based approach. Appl. Geogr. 2023 Jul; 156: 102974. Publisher Full Text\n\nDolbow DR, Figoni SF: Accommodation of wheelchair-reliant individuals by community fitness facilities. Spinal Cord. 2015 Jul 17; 53(7): 515–519. PubMed Abstract \| Publisher Full Text\n\nNary D, Froehlich AK, White G: Accessibility of Fitness Facilities for Persons with Physical Disabilities Using Wheelchairs. Top Spinal Cord Inj. Rehabil. 2000 Jul; 6(1): 87–98. Publisher Full Text\n\nMojtahedi MC, Boblick P, Rimmer JH, et al.: Environmental Barriers to and Availability of Healthy Foods for People With Mobility Disabilities Living in Urban and Suburban Neighborhoods. Arch. Phys. Med. Rehabil. 2008 Nov; 89(11): 2174–2179. PubMed Abstract \| Publisher Full Text\n\nCrytzer TM, Cooper R, Jerome G, et al.: Identifying research needs for wheelchair transfers in the built environment. Disabil. Rehabil. Assist. Technol. 2017 Feb 17; 12(2): 121–127. PubMed Abstract \| Publisher Full Text\n\nDuignan MB, Brittain I, Hansen M, et al.: Leveraging accessible tourism development through mega-events, and the disability-attitude gap. Tour. Manag. 2023 Dec; 99: 104766. Publisher Full Text\n\nMao X, Chen L: “To go, or not to go, that is the question”: perceived inaccessibility among individuals with disabilities in Shanghai. Disabil Soc. 2022 Nov 26; 37(10): 1659–1677. Publisher Full Text\n\nKamarudin H, Abdul Kadir S, Alias R, et al.: TRANSPORTATION BARRIERS CONFRONTED BY MOBILITY-CHALLENGED TRAVELLERS IN KLANG VALLEY. PLANNING MALAYSIA. 2023 Jun; 21(26). Publisher Full Text Reference Source\n\nMcClain L: Shopping Center Wheelchair Accessibility: Ongoing Advocacy to Implement the Americans with Disabilities Act of 1990. Public Health Nurs. 2000 May 25; 17(3): 178–186. PubMed Abstract \| Publisher Full Text\n\nMojtahedi MC, Boblick P, Rimmer JH, et al.: Environmental Barriers to and Availability of Healthy Foods for People With Mobility Disabilities Living in Urban and Suburban Neighborhoods. Arch. Phys. Med. Rehabil. 2008 Nov; 89(11): 2174–2179. PubMed Abstract \| Publisher Full Text\n\nLena K, Kristin A, Staffan B, et al.: How Do People with Disabilities Consider Fire Safety and Evacuation Possibilities in Historical Buildings?—A Swedish Case Study. Fire. Technol. 2012 Jan; 48(1): 27–41. Publisher Full Text\n\nKitchin R, Law R: The Socio-spatial Construction of (In) accessible Public Toilets. Urban Stud. 2001 Feb 2; 38(2): 287–298. Publisher Full Text\n\nMcNeal DR, Somerville NJ, Wilson DJ: Work Problems and Accommodations Reported by Persons Who Are Postpolio or Have a Spinal Cord Injury. Assist. Technol. 1999 Dec 31; 11(2): 137–157. Publisher Full Text\n\nImrie RF, Wells PE: Disablism, Planning, and the Built Environment. Environ. Plann. C Gov. Policy. 1993 Jun 30; 11(2): 213–231. Publisher Full Text\n\nNelson PP: Library services for people with disabilities: results of a survey. Bull. Med. Libr. Assoc. 1996 Jul; 84(3): 397–401. PubMed Abstract\n\nPierce LL: Barriers to Access: Frustrations of People Who Use a Wheelchair for Full-Time Mobility. Rehabil. Nurs. 1998 May; 23(3): 120–125. PubMed Abstract \| Publisher Full Text\n\nSendi R, Kerbler B: Disabled people and accessibility: How successful is Slovenia in the elimination and prevention of built-environment and communication barriers? Urbani izziv. 2009; 20(1): 123–140. Publisher Full Text\n\nPașcalău-Vrabete A, Băban A: Is ‘different’ still unacceptable? Exploring the experience of mobility disability within the Romanian social and built environment. Disabil Soc. 2018 Nov 26; 33(10): 1601–1619. Publisher Full Text\n\nGray DB, Morgan KA, Gottlieb M, et al.: Person factors and work environments of workers who use mobility devices. Work. 2014; 48(3): 349–359. PubMed Abstract \| Publisher Full Text\n\nAlhusban AA, Almshaqbeh SN: Delivering an inclusive built environment for physically disabled people in public universities (Jordan as a case study). J. Eng. Des. Technol. 2023 Mar 7. Publisher Full Text\n\nTijm MM, Cornielje H, Edusei AK: ‘Welcome to My Life!’ Photovoice: Needs Assessment of, and by, Persons with Physical Disabilities in the Kumasi Metropolis, Ghana. Disability, CBR & Inclusive Development. 2011 May 2; 22(1): 55. Publisher Full Text\n\nWaenlor W, Wiwanitkit V, Suwansaksri J, et al.: Facilities for the disabled in the commercial districts of Bangkok--are they adequate? Southeast Asian J. Trop. Med. Public Health. 2002; 33 Suppl 3: 164–165. PubMed Abstract\n\nBhuiya MMR, Hasan DMMU, Jones DS: Accessibility of movement challenged persons and challenges faced by their escorting family members – A Case Study of Dhaka, Bangladesh. J. Transp. Health. 2022 Mar; 24(March 2021): 101323. Publisher Full Text\n\nSalie R, Kleintjes S, Eken MM, et al.: Exploring the unmet needs of adults with cerebral palsy living in urban South Africa. Disabil. Rehabil. 2024 Feb; 46(4): 741–749. PubMed Abstract \| Publisher Full Text\n\nChiwandire D, Vincent L: Wheelchair users, access and exclusion in South African higher education. Afr. J. Disabil. 2017 Sep 8; 6: 1–9. Publisher Full Text\n\nTudzi EP, Bugri JT, Danso AK: Human Rights of Students with Disabilities in Ghana: Accessibility of the University Built Environment. Nord. J. Hum. Rights. 2017 Jul 3; 35(3): 275–294. Publisher Full Text\n\nNaami A: Access barriers encountered by persons with mobility disabilities in Accra, Ghana. J. Soc. Incl. 2019 Dec 20; 10(2): 70–86. Publisher Full Text\n\nYarfi C, Ashigbi EYK, Nakua EK: Wheelchair accessibility to public buildings in the Kumasi metropolis, Ghana. Afr J Disabil. 2017 Sep 28; 6: 1–8. Publisher Full Text\n\nBuchanan J: Disability and the built environment. Int. J. Rehabil. Res. 1987 Dec; 10: 240–242. Publisher Full Text\n\nCrowe TK, Picchiarini S, Poffenroth T: Community Participation: Challenges for People with Disabilities Living in Oaxaca, Mexico, and New Mexico, United States. OTJR (Thorofare N J). 2004 Mar 24; 24(2): 72–80. Publisher Full Text\n\nViljoen M, Mahdi S, Shelly J, et al.: Parental perspectives of functioning in their children with autism spectrum disorder: A global scoping review. Autism. 2021 Jan 30; 25(1): 176–198. PubMed Abstract \| Publisher Full Text\n\nMafatlane GR, Fidzani LC, Gobotswang KSM: Wheelchair users as consumers: accessibility of supermarkets in Gaborone, Botswana. Int. J. Consum. Stud. 2015 Mar 28; 39(2): 94–100. Publisher Full Text\n\nBlasko AM, Morin KL, Bauer K, et al.: A Meta-Synthesis of Disability Research in Western Africa. J. Spec. Educ. 2023 Feb 2; 56(4): 208–218. Publisher Full Text\n\nAbdul Kadir S, Jamaludin M, Awang AR: Accessibility Adaptation in the Design of Heritage Boutique Hotels: Malacca case studies. Environ. Behav. Proc. J. 2020 Mar 24; 5(13): 205–211. Publisher Full Text\n\nZahari NF, Che-Ani AI, Abdul Rashid RB, et al.: Factors contribute in development of the assessment framework for wheelchair accessibility in National Heritage Buildings in Malaysia. Int. J. Build. Pathol. Adap. 2019 Sep 6; 38(2): 311–328. Publisher Full Text\n\nStenberg G, Henje C, Levi R, et al.: Living with an electric wheelchair – the user perspective. Disabil. Rehabil. Assist. Technol. 2016 Jul 3; 11(5): 385–394. PubMed Abstract \| Publisher Full Text\n\nGeilen BG, de Witte L , Norman G, et al.: Quality of wheelchair services as perceived by users in rural Bangalore district, India: a cross-sectional survey. Disabil. Rehabil. Assist. Technol. 2022 Nov 17; 17(8): 965–973. PubMed Abstract \| Publisher Full Text\n\nYuen HK, Wolf BJ, Bandyopadhyay D, et al.: Factors that limit access to dental care for adults with spinal cord injury. Spec. Care Dentist. 2010 Jul 17; 30(4): 151–156. PubMed Abstract \| Publisher Full Text\n\nOkezue OC, Uzoigwe M, Ugwu LE, et al.: Level of independence, anxiety and relevant challenges among persons with disabilities towards their use of facilities in public buildings. Facilities. 2024 Mar 12; 42(5/6): 472–484. Publisher Full Text\n\nWillis M, Bridges AJ, Jozkowski KN: Gender and racial/ethnic disparities in rates of publishing and inclusion in scientific-review processes. Transl Issues Psychol. Sci. 2021 Dec; 7(4): 451–461. Publisher Full Text\n\nSmall F, Mehmet M, Kleinschafer J: The circle of vulnerability and the myth of choice. J. Soc. Mark. 2020 May 8; 10(4): 489–506. Publisher Full Text\n\nDispenza F, Ray M, Coleman JS: Supporting LGBTQ+ college students living with disabilities.Rivera DP, Abreu RL, Gonzalez KA, editors. Affirming LGBTQ+ students in higher education. Washington: American Psychological Association; 2022; 123–40.\n\nBatastini AB, Jones ACT, Patel M, et al.: Why Correctional Service Providers and Researchers Should Focus on Intersectionality and Recommendations to Get Started. Crim. Justice Behav. 2022 Jun 12; 49(6): 930–946. Publisher Full Text\n\nSaigal N, Narayan R: Structural barriers at the workplace for employees with vision and locomotor disabilities in New Delhi, India. Work. 2014; 48(3): 329–337. PubMed Abstract \| Publisher Full Text\n\nJesus TS, Kamalakannan S, Bhattacharjya S, et al.: PREparedness, REsponse and SySTemic transformation (PRE-RE-SyST): a model for disability-inclusive pandemic responses and systemic disparities reduction derived from a scoping review and thematic analysis. Int. J. Equity Health. 2021 Dec 14; 20(1): 204. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu FY, Nittrouer C, Nguyen V, et al.: Now protected or still stigmatized? A 25-year outlook on the impact of the Americans with Disabilities Act. Equal. Divers. Incl. 2022 Apr 20; 41(3): 383–403. Publisher Full Text\n\nvan Brakel WH , Sihombing B, Djarir H, et al.: Disability in people affected by leprosy: the role of impairment, activity, social participation, stigma and discrimination. Glob. Health Action. 2012 Dec 19; 5(1): 18394. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKuper H, Hanefeld J: Debate: can we achieve universal health coverage without a focus on disability? BMC Health Serv. Res. 2018 Dec 26; 18(1): 738. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRotarou ES, Sakellariou D: Inequalities in access to health care for people with disabilities in Chile: the limits of universal health coverage. Crit. Public Health. 2017 Oct 20; 27(5): 604–616. Publisher Full Text\n\nVergunst R, Swartz L, Mji G, et al.: ‘You must carry your wheelchair’ – barriers to accessing healthcare in a South African rural area. Glob. Health Action. 2015 Dec; 8(1): 29003. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYin Mun L, Kun Xin W, Devi Rajendran S: A study on the Barriers in Accessibility for the Disabled at Bus Terminal.Fang TY, Khaletski V, editors. E3S Web Conf. 2019 Dec 10; 136: 04084. Publisher Full Text\n\nScheer J, Kroll T, Neri MT, et al.: Access Barriers for Persons with Disabilities. J. Disabil. Policy Stud. 2003 Mar 13; 13(4): 221–230. Publisher Full Text\n\nWinberry J, Bishop BW: Documenting social justice in library and information science research: a literature review. J. Doc. 2021; 77(3): 743–754. Publisher Full Text\n\nBanda-Chalwe M, Nitz JC, De Jonge D: Impact of inaccessible spaces on community participation of people with mobility limitations in Zambia. Afr. J. Disabil. 2014 Apr 1; 3(1): 1–17. Publisher Full Text\n\nBuda A, de Place Hansen EJ , Rieser A, et al.: Conservation-Compatible Retrofit Solutions in Historic Buildings: An Integrated Approach. Sustainability. 2021 Mar 8; 13(5): 2927. Publisher Full Text\n\nThorn J, Coast J, Andronis L: Interpretation of the Expected Value of Perfect Information and Research Recommendations. Med. Decis. Mak. 2016 Apr 18; 36(3): 285–295. PubMed Abstract \| Publisher Full Text\n\nCheung M, Ma AK, Thyer BA, et al.: Research–Practice Integration in Real Practice Settings. Res. Soc. Work. Pract. 2015 Jul 1; 25(4): 523–530. Publisher Full Text\n\nBrownson RC, Fielding JE, Maylahn CM: Evidence-Based Public Health: A Fundamental Concept for Public Health Practice. Annu. Rev. Public Health. 2009 Apr 1; 30(1): 175–201. Publisher Full Text\n\nNijs G, Heylighen A: Turning disability experience into expertise in assessing building accessibility: A contribution to articulating disability epistemology. Alter. 2015 Apr; 9(2): 144–156. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended data file 1 Search string. Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended data file 2 Instruction for data extraction. Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended data file 3 List of included articles. Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended data file 4 Excluded articles with reasons. Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended Data Table 1. Themes, sub-themes, and codes for agencies. Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended Data Table 2. Sub-themes, and codes for the theme intersectionality (n=84). Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended Data Table 3. Themes, sub-themes, and codes on social justice, equity, and human rights (n=84). Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended Data Table 4. Social and functional outcomes reported in the studies (n=84). Dataset. figshare. 2024. Publisher Full Text\n\nSidhiprada M, Arun MG, Nayak Ullas U, et al.: Extended Data Table 5. Summary of recommendations given in accessibility research. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "316830", "date": "29 Aug 2024", "name": "Sureshkumar Kamalakannan", "expertise": [ "Reviewer Expertise I am an academic researcher with expertise in disability", "rehabilitation in health systems and policy research as well as systematic review of interventions" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 important and complex question for inquiry. The authors have made an excellent attempt and reported it using an understandable framework. Well done.\n\nSome key feedback: Abstract: The methods in the abstract section could have details about databases and inclusion criteria. The results in the abstract are not related to the objective of this review.\nIntroduction: The introduction needs to provide a bit more detail to explain the various concepts like disability, social justice, research, and integration and how they are related to each other. The importance of doing this review is also missing. Please include.\nMethods: The criteria for inclusion lacks clarity. For example - Study designs to be included, Non-electronic searches; Criteria that talk about chronic illness or issues related to non-physical impairments that are disabling, etc. The last point is very important from a social justice perspective - You can have a building physically accessible but what if it's not accessible for someone with other kinds of disability? A clear explanation of why this criteria is required.\nResults: Very well presented and in greater detail. Well done. However, I am curious to know how many buildings or how many studies were looking at accessibility of health facilities. including available rehabilitation centres. This is a key component of this review objective. It would be great to describe this aspect particularly in LMICs at least.\nDiscussion: Implications for practice, research, and policy must be clearly reported and also as mentioned above the implication for people with disabilities and their access to government health facilities and its relevance / importance.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? 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": "12535", "date": "07 Oct 2024", "name": "Sidhiprada Mohapatra", "role": "Author Response", "response": "Suggestion 1 (Abstract): Thank you for the suggestion. We have modified and incorporated the seven databases in the abstract. We have modified the results to be specific to the objectives ensuring the social justice and equity concept is reported. Suggestion 2 (Introduction): Thank you for the suggestion. We have modified and incorporated the suggestions in the introduction. The introduction now states the integration of disability, social justice, research, and community integration. Suggestion 3 (Introduction): Thank you for the suggestion. We have modified and incorporated the suggestions in the introduction on importance of conducting the scoping review stating that the importance lies to explore of how the concepts of social justice are applied or overlooked in accessibility research thus help uncover gaps in how social justice, equity, and accessibility are interconnected and to offer a framework for integrating these principles into future research and policy development. Suggestion 4 (Methods): Thank you for the suggestion. We have modified and incorporated the suggestions in the methods. Though consideration of disability status is also integral to the concept of social justice, our focus on mobility disability decision was made to allow a focused examination, with an acknowledgment of the need for future studies to address non-visible disabilities in accessibility research. Suggestion 5 (Results): Thank you for your positive feedback on the results section. We appreciate your suggestion regarding the exploration of studies focused on health facilities and rehabilitation centres, particularly in Low- and Middle-Income Countries (LMICs). In response to this, we have revisited the analysis and identified the 14 studies that explicitly addressed accessibility of health facilities and rehabilitation centres. Among these, only 5 of studies were conducted in LMICs, where accessibility challenges were often compounded by resource constraints and lack of infrastructure. Detailed explanation and study details are given in results and Table 3. Suggestion 6 (Discussion and Implications): Thank you for your positive feedback. Suggestions have been added under Discussion and Future directions and implications." } ] }, { "id": "316821", "date": "06 Sep 2024", "name": "Franzina Coutinho", "expertise": [ "Reviewer Expertise early intervention", "social justice", "technology", "pediatric rehabilitation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for this valuable contribution - Methods: Increased description and clarity of inclusion criteria. ex: specifying the types of study designs considered or explaining the criteria for non-physical impairments would add depth to the analysis. - Additionally, the criteria need justification from a social justice perspective—buildings may be accessible physically but may not cater to non-visible disabilities, which should be addressed. - Discussion section could better link the findings to practice, research, and policy implications. Specifically, how people with disabilities access government health facilities and the significance of this access should be clearly outlined. - There seems to be large representation from High income countries. Did the search account for geographical representation.\nThe manuscript reads well and by addressing these issues it is good to go.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [ { "c_id": "12536", "date": "07 Oct 2024", "name": "Sidhiprada Mohapatra", "role": "Author Response", "response": "Thank you for all the suggestions provided to improve the quality of this article. Suggestion 1 (Methods): The methods section has been modified giving further details on inclusion criteria specifying the types of study designs and criteria for inclusion of physical impairments or mobility disabilities and exclusion of non-physical impairments are reported. Also, the table 1. showing the selection criteria has detailed study selection criteria. Suggestion 2 (Non-physical impairments): The suggestion has been incorporated in Methods and Limitations. \"The review specifically targeted mobility impairments to assess how accessibility barriers in public buildings impact this population. While non-physical impairments (e.g., cognitive, sensory) are equally important, they fall outside the scope of this review, which aims to provide an in-depth analysis of the physical accessibility challenges and systemic inequities faced by individuals with mobility disabilities. This decision was made to allow a focused examination, with an acknowledgment of the need for future studies to address non-visible disabilities in accessibility research.\" Suggestion 3 (Discussion): The link of findings to practice, research, and policy implications are incorporated into Discussion and Future directions and implications. Suggestion 4 (Discussion on studies from High-income countries): The modification is incorporated in the Discussion section. While this review included a significant number of studies from high-income countries (HICs), the search was not limited to any specific geographic location. The large representation from HICs may reflect the availability of research in these regions rather than a lack of focus on LMICs. The imbalance in geographical representation highlights a gap in research from LMICs, where accessibility challenges may differ significantly due to economic, infrastructural, and social factors. More research is required to understand the unique barriers faced by people with disabilities in LMICs and to inform policies that ensure equitable access to public buildings, including healthcare facilities. This gap is critical, as LMICs often lack resources to enforce accessibility laws or develop accessible infrastructures." } ] } ]	1	https://f1000research.com/articles/13-930
https://f1000research.com/articles/13-629/v1	13 Jun 24	{ "type": "Systematic Review", "title": "Optimization of timing for maternal immunization to protect newborns from influenza infection", "authors": [ "Eyad Rabih Abdul Wahab", "Ahmad Khalifa", "Alexander Warren Alessi", "Mohammed Saeed", "Owais Tahhan", "Sidra Bukhtiar Khan", "Hamza Khalifa", "Eyad Rabih Abdul Wahab", "Ahmad Khalifa", "Alexander Warren Alessi", "Mohammed Saeed", "Owais Tahhan", "Sidra Bukhtiar Khan" ], "abstract": "Objectives The primary objective of this systematic review was to identify the optimal timing for immunizing pregnant women to confer the most protection by reducing the incidence of laboratory-confirmed influenza or influenza-like illness in infants less than 6 months of age. Currently, there are gaps in research regarding the timing of administration during the gestational period to provide maximum immunogenicity to the infant. The research question being addressed is: ‘When considering immunization of pregnant mothers with the influenza vaccine, implementing a vaccination program during which trimester in pregnancy would optimize benefits for infants less than 6 months of age in terms of the incidence of laboratory-confirmed influenza and influenza-like illness?’\n\nDesign Systematic review/Meta-analysis\n\nMethods Randomized controlled trials (RCT’s) and observational studies comparing health outcomes of infants and children up to 6 months of age born to women who received inactivated influenza vaccine during pregnancy with mothers who did not receive the vaccine or received a control vaccine. The primary outcome was laboratory-confirmed influenza infection in infants. Secondary outcome measures included influenza –like illness diagnosed by a clinician and acute respiratory illness.\n\nResults 7 studies were included: 2 primary RCT’s and 5 observational studies (prospective and retrospective cohort studies).5 of the 7 studies were suitable to be included in the quantitative synthesis part and and were compared. Forrest plot analysis revealed that vaccinating pregnant mothers in the second and third trimester when compared with any trimester (1,2 and 3) (OR 0.18 vs. 0.65) conferred less protection, promoting vaccination in the first trimester.\n\nConclusions Vaccinating pregnant mothers in the first trimester conferred greater protection to infants than any other trimester.", "keywords": [ "Influenza", "vaccination", "immunisation", "infants" ], "content": "1. Rationale\n\nInfluenza viruses belong to the Orthomyxoviridae family and are classified into three types: A, B, and C. In humans, types A and B are the most prevalent and cause infection of the upper respiratory tract, leading to mild symptoms such as low-grade fever, sore throat, fatigue, and muscle aches.1 However, serious complications can occur in clinically high-risk groups, such as people with a weakened immune system, over 65-year-olds, pregnant women, and children under the age of 2. Complications include myocarditis, bacterial pneumonia, sepsis, and multi-organ failure, which can be fatal.2 During pregnancy, many natural changes in the body, such as a decrease in respiratory volumes and urinary stasis due to an enlarging fetus, can lead to a heightened risk of these complications, often leading to hospitalization, and can even cause death of the mother and fetus.3 In pregnant women, complications may include miscarriages and preterm deliveries. Newborns born when a woman is infected during pregnancy may have congenital anomalies such as leukemia, Parkinson’s disease, schizophrenia, congenital heart defects, and neural tube defects.4 This group of viruses are the most commonly known viruses causing respiratory infections that lead to high rates of mortality worldwide, affecting 11% of pregnant women worldwide.5\n\nIn 2012, the World Health Organization published a position paper stating that influenza vaccination during pregnancy provides protection to both mothers and infants. Evidence suggests that immunization at an earlier stage provides better protection to the woman, and during the later stages, it provides a longer duration of protection for the infant.6 Various studies have been conducted on maternal immunization for influenza virus, discussing the protection it provides for the mother and child. Infants under 6 months of age produce a weak antibody and T-cell response to viruses such as influenza due to an immature innate immune system. The adaptive immune system also produces an inadequate response to T cell-dependent antigens encountered upon exposure to the virus. The lack of a sufficient immune response as a result of the inability to produce antibodies on their owncan cause serious ramifications for an infant’s health. This shows that active immunity, and therefore vaccination, does not confer effective protection for infants.7 However, immunity against influenza is essential for infants to avert potential life-threatening consequences and to survive possible infections. Maternal vaccination is administered to achieve immunity without needing an immune response, that is, not via direct vaccination, and to reduce the rate of mortality due to influenza in the age group.8 Passive immunity is attained via transplacental transmission of antibodies and breastfeeding from the mother to the child without direct vaccination of the infant.9 It is the most effective method of protection as a child cannot be vaccinated directly since studies proving the safety of direct vaccination for influenza in under 6-month-old children have not yet been conducted.\n\nHowever, misconceptions about vaccination leading to stillbirth have affected the number of people willing to take it.10 Safety concerns regarding possible teratogenic effects during organogenesis in the embryonic stage of development in the first trimester have led to low uptake within the subgroup.11 Despite scientific evidence suggesting that the vaccine is safe for pregnant women, only 45% received the vaccine during the 2018/2019 flu season in the UK.12 The low uptake results from a lack of awareness regarding the risks associated with influenza for the infant and mother, as well as the misconceptions previously mentioned. In addition, in the UK, guidelines suggest vaccination during any trimester, whereas Australian recommendations suggest vaccination during the second or third trimester.13 This shows that due to limited data availability, national policies differ greatly across the world. However, we must keep in mind that vaccinating pregnant women is often opportunistic, and the timing is related to the timing of the flu season and availability of vaccines.\n\nThe most recent systematic review and meta-analysis, conducted by Jarvis et al. in 2020, investigated the efficacy of maternal immunization for influenza on infant health. It was concluded that vaccination prevents lab-confirmed influenza in infants aged < 6 months.14 As well as that, the results showed that the immunity provided by the maternal vaccination decreased over time as the infant grew older. However, there are gaps in research regarding the timing of administration during the gestational period to provide maximum immunogenicity. Vaccination at the optimal time would offer the highest level of protection to mothers and infants. Our review aims to combine the evidence from previously conducted studies and use it to help determine the time for providing maternal influenza vaccination to confer optimal benefits to the infant until 6 months of age.\n\n\n2. Objectives\n\nThe primary objective of this systematic review was to identify the optimal timing for immunizing pregnant women to confer the most protection by reducing the incidence of laboratory-confirmed influenza or influenza-like illness in infants less than 6 months of age.\n\n\n3. Methods\n\nThis meta-analysis was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist. The completed PRISMA checklist is available as extended data.31 The study protocol was not registered; however, registration of the study can be found at https://www.crd.york.ac.uk/prospero/display_record.php?IDCRD42021202624.\n\nThe search several electronic databases, however after applying similar strategies to other electronic databases such as Embase and Medline, no studies were found. The studies selected and screened by title and abstract only came from PubMed and not any of the other sources. Published studies ranged from the earliest known date of 17th of April 17, 1996, to the most recent date of January 21st 2021. The full search strategy is shown below. Manual searching of the reference lists was also undertaken by two peer reviewers on separate occasions.\n\n(Pregnant women) AND (Influenza vaccination OR Influenza vaccine OR Influenza immunization) AND (Unvaccinated Pregnant women OR Control OR meningococcal vaccine OR pneumococcal vaccine) AND (laboratory confirmed influenza OR influenza-like illness OR Respiratory illness OR Respiratory infection OR influenza antibodies) AND (Newborns OR children less than six months OR Neonates OR Infants) AND (Randomized Controlled Trial OR Cohort Study OR Prospective Observational Study OR Case-Control study OR Cross-sectional study).\n\nFull-text articles published as RCT’s or observational studies in the English language were included in our review. Keywords used to identify studies to be included in the study consisted of terms relating to the population of pregnant women and interventions such as influenza vaccination or immunization. Furthermore, studies that measured outcomes specifically related to laboratory-confirmed influenza or influenza-like illnesses in infants or newborns less than 6 months of age were included. Studies must also have a control group that includes either unvaccinated pregnant women, a control group, a meningococcal vaccine, or a pneumococcal vaccine. The length of follow-up of infants until an endpoint of 6 months of age was an important confounder to control; therefore, the duration of the study did not impact the outcome measures. Studies that did not have more specific outcome measures such as hospitalization rates, outpatient visits, or acute respiratory illness were excluded. Studies that had the outcome measure of serology only or hemagglutinin inhibition titers were excluded. The study designs varied from randomized controlled trials to case-control studies. Studies in the form of case series, case reports, clinical practice guidelines, commentaries, conference abstracts, editorials, meta-analyses, narrative reviews, studies reporting estimated influenza rates based on ecological approaches, statistical modelling, or systematic reviews. The following PICO keywords were used in the search:\n\nPopulation: Pregnant Women\n\nIntervention(s): Influenza vaccination OR Influenza immunization\n\nComparator (control): Unvaccinated Pregnant women OR Control group OR meningococcal vaccine OR pneumococcal vaccine\n\nOutcome(s): laboratory-confirmed influenza OR influenza-like illness OR Respiratory illness OR Respiratory infection OR influenza antibody AND Newborns OR children younger than 6 months OR Neonates OR Infants\n\nStudy design: Randomized Controlled Trial OR Cohort Study OR Prospective Observational Study OR Case-Control study OR Cross-sectional study.\n\nData extraction was undertaken by one author, but then simulated again by another author to improve reliability using a Cochrane data extraction form for both RCT’s and observational studies. A meeting was then conducted with the project supervisor to improve inter-rater reliability. Key summary statistics included odds ratios, relative risk, risk ratios, and rate ratios.\n\nThe SIGN checklist by healthcare improvement Scotland was used to evaluate the risk of bias from the methodology of both Randomized controlled trials and observational studies.15 The overall quality rating of unacceptable, low quality, acceptable, and high quality was used to rate the studies for bias. Quality assessments for both RCT’s and observational studies were performed by two independent blinded reviewers. For unblinding, a decision was made on each quality assessment and overall ranking. If no agreement was reached, the third author decided the final rating.\n\nWe performed a preliminary analysis from initial searches using six studies that tested the efficacy of maternal immunization of infants with inactivated influenza vaccine on the incidence of laboratory-confirmed influenza episodes in infants in the first six months of life. The outcomes of the individual studies are presented in quantitative tables, and the studies had similar parameters. The meta-Analysis was performed using RevMan software (version 5.4 2020) requiring a minimum of two studies, with heterogeneity I2= 90%, which is greater than 55%; however, due to the sparse data sets, it was decided that a fixed-effects model was performed despite high heterogeneity. A plot was used to test the heterogeneity between studies. The analysis included only studies that reported outcomes using a polymerase chain reaction (PCR) test to confirm influenza infection; hence, studies that used a serology test to confirm influenza infection were excluded.\n\nThe studies included both prospective and retrospective randomized controlled trials and cohort studies. The studies assessed the efficacy of influenza vaccination in exposed groups to unexposed groups as a control. The total population size varied between studies; therefore, studies were weighted according to their population size to have a greater effect on outcomes. The odds ratio was calculated using the number of influenza events in the exposed group out of the total population of the exposed group compared to the number of influenza events in the unexposed group out of the total population of the unexposed group. Odds ratios was calculated for each of the six studies. No additional analyses, such as subgroup or sensitivity analyses, were deemed necessary when discussed with the supervisor, as most studies were credible and similar in study characteristics.\n\n\n4. Results\n\nA preliminary search using the search strategy on the 21stof May 2020 revealed 153 search results. However, an updated search was undertaken on the 7thof February 2022 which revealed that there were an additional 35 studies published, increasing the total to 188 search results from PubMed. After deduplication, 186 studies were finally included. After the first screening of titles and abstracts, 153 studies were excluded, and 37 full-text articles were assessed for eligibility. A total of 30 studies were excluded for three main reasons: not specifying the trimester of the intervention (9), wrong outcome measures (17), and wrong intervention (10). This resulted in seven studies being used for the qualitative synthesis of this review. However, only five of these studies were included in the quantitative analysis. The PRISMA flowchart provides a visual illustration of the following:32\n\nThe key study characteristics are shown in Table 133 in the supplementary material according to the quality assessment value and study design.\n\nTwo randomized controlled trials with a total of 4,533 participants were included in both the quantitative and qualitative analyses. Both studies had a similar proportion of vaccinated and unvaccinated participants, considerable randomization and blinding of participants, and similar exclusion criteria for participants, including characteristics such as previous complicated pregnancy or pre-term labor, recent administration of any study vaccines, and any systemic disease. Therefore, this allows for the control of any potential confounders that can affect the baseline characteristics of participants. One of the studies was conducted In Mali, where influenza occurs in a seasonal fashion, whereas the other was conducted in Bangladesh where Influenza occurs in a perennial fashion.\n\nFive observational studies with a total of 10,625 participants were included in the quantitative analysis, and two additional studies with a total of 1,474 participants were included in the qualitative analysis. Of the studies included in the quantitative analysis, two were prospective and one was a retrospective study. Of the two additional studies included in the qualitative analysis, one was a case-control study, and the other was a matched cohort study. All studies had a similar proportion of vaccinated and control participants, the desired outcome and intervention, and similar exclusion criteria, including seasonal variation in influenza infection rates and pre-term labor. Studies were conducted in many different countries and continents, and in all of them, influenza occurred seasonally rather than perennially.\n\nAfter assessing the quality of the studies for their respective methodologies, six of the seven studies were rated as high-quality, suggesting that most of the studies were rated as highly internally valid and had a relatively low risk of bias. Only one study (Singh et al.) was rated as acceptable quality and was one of the studies included in the quantitative synthesis as well despite this. Only studies rated as acceptable or of high quality were included in the final quantitative synthesis.\n\nAll studies reported a lower incidence of influenza in infants born to vaccinated mothers than in those born to unvaccinated mothers. A study by Zaman et al.,16 Benowitz et al.,17 and Tapia et al.18 reported vaccine efficacies of 63%, 91.5%, and 31%, respectively, in a study by Eick et al.19 reported a risk reduction of 41% and Singh et al.,20 Maltezou et al.21 and Omer et al.22 compared the prevalence of influenza in infants born to vaccinated and unvaccinated mothers, and found a lower prevalence in those who were vaccinated. A general trend was observed where studies that vaccinated mothers in the first two trimesters reported a higher vaccine efficacy than those that either vaccinated mothers in any of the trimesters or in the second and third trimesters, possibly indicating that vaccination in the first trimester is responsible for the higher reported vaccine efficacy.\n\nThe RevMan software, which was used for Quantitative Analysis, could not compute the results of case-control studies, and so studies by Eick et al.19 and Benowitz et al.,17 were excluded. Therefore, the studies included in the quantitative analysis were those conducted by Zaman et al.,16 Tapia et al.,18 Maltezou et al.,21 Singh et al.,20 and Omer et al.22 Omer et al.22 was then further divided as it included trials in three different countries: Mali, where pregnant women were vaccinated in the third trimester; Nepal; and South Africa, where they were vaccinated in the second or third trimester.\n\nThe five studies consisted of 15,046 participants, including a range of trimesters during which the influenza vaccine was administered. In 2 studies,16,18 administered the vaccine in the third trimester in two studies20,21 administered the vaccine in one of all trimesters, and in one study,22 the vaccine was administered in either the second or the third trimester. The combined forest plots for each study group are shown in Figure 1.1, 1.2, and 1.3.\n\nTo determine the vaccination in which the trimesters provided the greatest protection against influenza infection, we used an elimination-based approach by grouping studies according to trimester and created forest plots comparing the two groups of studies at a time. The forest plot results were used to determine whether a difference in the trimesters correlated with a lower occurrence of influenza infection.\n\n4.6.1 Influenza vaccination in any trimester of pregnancy\n\nThe forest plot with all the studies showed that maternal influenza vaccination was effective and consistently showed a lower occurrence of influenza infection in children less than 6 months of age, where an Odds Ratio<1 correlated with a lower rate of influenza infection, and all the studies showed a negative effect size in relation to the line (Pooled OR 0.87, 95%CI (0.87, 0.93)). There was no significant heterogeneity between the studies, as found in the forest plot (χ2=21.54, df=6(P=0.001); I2=72%, Z=6.63(P<0.00001)), allowing us to disregard the null hypothesis.\n\n4.6.2 Influenza vaccination in Third trimester compared to Second or Third trimester of pregnancy\n\nThe forest plot shown in Figure 1.2 compares studies in which the vaccine was administered in the second and third trimesters and those in which it was administered in the third trimester only. The Pooled Odds Ratio was 0.64, and the test for heterogeneity found χ2=1.63 df=2 (P=0.44) I2=0%) and test for overall effect Z=4.83 (P<0.00001). The comparison shows that the pooled Odds Ratio is less than that reported by the second- and third-trimester studies depicted in Figure. 1.2. This allows us to conclude that there is no difference in efficacy between vaccinations in the second or third trimester.\n\n4.6.3 Influenza vaccination in Third trimester compared to Any Trimester of pregnancy\n\nA forest plot was created using studies in which the vaccine was delivered in the third trimester and those in which it was delivered in any of the trimesters had a pooled Odds Ratio of 0.47[0.33,0.58], which is greater than the pooled Odds Ratio for only the latter group of studies shown in Figure 1.1 (0.180.10,0.31]), and also depicted a more negative effect size (95%CI below the negative line) when compared to the pooled OR for the former set of studies. Assessment of the heterogeneity between the studies showed p value<0.05, which highlights statistical significance (χ2=16.06 (p=0.001), I2=81%, Z=5.80 (P<0.00001)). A comparison of the vaccine efficacies of the two groups showed a higher vaccine efficacy with the inclusion of the first and second trimesters, suggesting a correlation between the inclusion of these trimesters and a higher vaccine efficacy.\n\n4.6.4 Influenza vaccination in Second or Third trimester compared to Any Trimester of pregnancy\n\nThe test for heterogeneity showed the following results: χ2=18.91, df=2 (P<0.0001), I2=89%, Test for Overall Effect=5.96 (P<00001), allowing us to rule out the null hypothesis in this scenario as well. The pooled Odds Ratio for the comparison (0.55[0.45,0.67]) was greater than that for those that were not selective with the trimester shown in Figure. 1.1 (0.18[0.10,0.31]), indicating greater vaccine efficacy in the latter group. As both studies consisted of subjects administered the vaccine in the second and third trimesters, it can be concluded that the administration of the vaccine in the first trimester could be responsible for the increase in efficacy. These three comparisons allowed us to interpret that vaccinating pregnant mothers in the first trimester provides the greatest vaccine efficacy for protection against influenza infection in infants. However, more data are required to draw robust conclusions.\n\n\n5. Discussion\n\nThe results from the quantitative studies, five total (Zaman, Tapia, Singh, Maltezou, Omer) which were included in our final results, had a total of 15,133 pregnant women who showed maternal influenza vaccination in trimesters one, two, or three; this was protective against influenza in infants < 6 months of age. We compared the odds ratio of the studies reflecting the trimesters in which the mother received the vaccination such that we could isolate the impact of each trimester on the efficacy of influenza vaccination. Grouping the specific trimesters during which the vaccine was administered enabled a comparison through forest plots for each study and thereafter a comparison of the odds ratio. The results showed with statistical significance that maternal influenza vaccination in the first trimester conveyed the most significant efficacy in the reduction of infants aged under 6 months and laboratory-confirmed influenza. The clinical importance of our systematic review is that it allows for better protection of infants who are at greater risk of complications due to their susceptibility to infections as a result of their immature immune system. Coupled with influenza vaccinations licensed only for 6-month-old infants and above reinforces the significance of protecting young infants from complications related to influenza.\n\nThe strengths of the included studies include the collection of data on multiple outcomes. Most of the studies used laboratory-confirmed influenza as an outcome measure, which is known to be a highly sensitive and specific diagnostic test compared to other outcome measures such as ILI or serological testing.23 Tapia and Singh et al. reported the occurrence of influenza-like illnesses (ILI).18,20 Singh et al., in a retrospective study, utilized ILI cases to prevent an underestimation of the influenza burden.20 However, despite laboratory-confirmed influenza as a primary outcome measure, it would have allowed for improved internal validity.\n\nMoreover, Eick et al. observed laboratory-confirmed influenza (LCI) as well as 4 fold or greater increase in serum antibodies collected at intervals and compared with previous specimen samples, indicating an influenza infection in that interval period.24 This robust methodology improved the accuracy of the results.\n\nAll studies included in the review were considered to be of high quality according to the SIGN tool. The studies controlled for confounders using similar exclusion criteria, that is, maternal breastfeeding as a confounder, as well as the exclusion of pre-term babies from the studies (as pre-term babies lose exposure to antibodies, reducing the number of antibodies. These criteria enhance the strength of the individual studies, allowing them to be more comparable. All studies that were of low quality were excluded. The advantage of utilizing high-quality studies is that it avoids carrying out a sensitivity analysis to exclude low credible results; therefore, it allows for better comparison between studies. Study designs such as case reports, systematic reviews, and case series were also excluded in the selection process to allow for better comparison between studies.\n\nA final advantage of the selected studies was the inclusion of studies measuring a wide range of outcomes in different settings, from outpatient visits to hospitalizations, to provide a clearer understanding of the influenza burden. This would allow for greater coverage of cases, as most influenza cases are present in the outpatient department, and not all influenza-like illness cases would require hospitalization.\n\nThe limitations include the heterogeneity of the study designs, as observational studies and RCTs were used, making it difficult to compare them.25 Different tests have been used to confirm the presence of influenza, although PCR is the gold standard. Benowitz used a direct fluorescent antibody (DFA) test (the sensitivities of DFA and PCR were 82% and 95%, respectively), whereas Zaman used influenza antigen tests.26 The differences in sensitivity and specificity can cause detection bias, which reduces the accuracy of the results of the included studies. However, most studies used PCR to confirm LCI.\n\nMoreover, the outcomes measured in the studies varied such that they did not mention the definition of ILI.18 This increases the methodological heterogeneity between the studies and reduces the accuracy of the results from specific studies. Few studies, such as Eick et al., have mentioned the inclusion criteria for defining ILI. Future studies should be more specific in defining influenza-like illnesses to allow for standardization when reviewing the outcome measures for individual studies.\n\nThe strengths of this review include a range of high-quality studies ranging (from RCT and observational studies) with apparent exclusion (i.e., laboratory-confirmed influenza or influenza-like illness) and inclusion criteria. A range of health databases were used, such as PubMed, Embase, and Cochrane, for the search strategy, which yielded a large number of studies, implying that the search was comprehensive to encompass all relevant articles.\n\nAlthough the synthesis of RCTs is considered the highest level of clinical evidence, given the nature of our systematic review, we cannot control all variables due to the prospective nature of the study; hence, observational studies were the best fit. Observational studies are conducted in the natural environment; therefore, they are more reliable than RCTs owing to their higher external validity. This implies that the data can be extrapolated and applied to other similar contexts. Despite different study designs, strict inclusion criteria were implemented through the inclusion of studies that only measured laboratory-confirmed influenza or influenza-like illnesses as outcome measures. Therefore, making the studies even more comparable and reducing reporting bias.\n\nThe weighting for the meta-analysis was based on population size rather than study design.25 Since all studies were acceptable and of high quality when assessed for the risk of bias, a sensitivity analysis was not needed. The studies used in this systematic review all had a similar methodology in terms of outcomes measured, confounders, and measurements. An example of this is illustrated by the majority of studies using PCR to measure influenza cases and implementing regression models to control for variables such as breastfeeding.\n\nImplementing internationally renowned quality assessment tools such as the SIGN tool allows for rating of the quality of evidence. However, in the future, it would be worth implementing a supplementary tool known as the grading of recommendations. The significance of this is to further rate the credibility of the findings from the perspective of a guideline author, who will extrapolate these recommendations and implement them in a clinical setting.\n\nOne Limitation of this review was the use of a combination of RCTs and Observational studies. Observational studies used for meta-analyses are generally considered suboptimal compared to those using only randomized control trials. This is a result of methodological heterogeneity, which could be present, as well as an increased risk of bias in observational studies.25 This may pose challenges in interpreting the results and exaggerating the effects of the study. The primary endpoint of all the studies was 6 months of follow-up with infants, which controlled for differences in the study periods.\n\nFurthermore, observational studies have confounders that cannot be completely addressed, which increases the difficulty of comparing them with RCTs. A confounder between the studies was the variable timing of influenza seasons, that is, in Bangladesh, influenza is perennial, while in the USA, it is seasonal.16 This could have been controlled by carrying out a subgroup analysis and comparing the perennial and seasonal study outcomes separately. However, the limited number of perennial studies and the difficulty in classifying studies as either perennial or seasonal makes it difficult to carry out such an analysis.\n\nAfter conducting extensive searches, it was difficult to find studies that compared the timing of maternal immunization for influenza among individual studies in the form of a meta-analysis, nor did any study aim to carry this out. A study carried out by Jarvis et al. in 2019 aimed to determine the effectiveness of influenza vaccination during pregnancy on child health outcomes.14 The systematic review concluded that maternal influenza vaccination is inversely correlated with infant hospitalization due to LCI. The meta-analysis, which included 19 studies, also reported that vaccine efficacy did not vary when administered in the third or second trimester. This supports the findings of our meta-analysis, as well as studies that investigated vaccine efficacy at different trimesters by measuring transplacental antibody transfer, suggesting that vaccine efficacy did not vary by gestational age at vaccination.27 This suggests that implementing maternal immunization programs is easier when women present for care later in pregnancy. Only one randomized controlled trial investigated the trimester of maternal vaccination with respect to infant outcomes.27 However, vaccination during the first trimester was not included in this study. They concluded that the results were too narrow to detect any differences in vaccination timing. Current research supports the idea that antibody transfer occurs during the second trimester of pregnancy. However, Katz et al. (2018) found higher antibody levels in women vaccinated later in pregnancy, but this was not considered statistically significant.28 Despite these studies’ findings, there is some indication that vaccinating earlier in pregnancy would elicit a more mature antibody response, which is consistent with the results of this analysis.14 Further to that, vaccinating earlier would also protect the mother and ensure protection throughout gestation.\n\nAn updated WHO position paper published in May 2022 on vaccines against influenza suggests that pregnant women are a high-risk group and should be vaccinated in any trimester of pregnancy.29 This recommendation is based on the evidence of a significant risk of severe disease in this group. Some studies have expanded on this point by emphasizing that mothers are at the greatest risk of severe infection in the third trimester, so vaccinating earlier yields greater benefit to the mother.29 Despite theoretical evidence that vaccination in later trimesters would increase antibody titers and provide longer-lasting immunity to infants, this is not currently recommended. Our review focused on outcomes for infants and suggested that studies that included infants born to mothers vaccinated in the first trimester had a reduced incidence of influenza infection until 6 months of age. This would be useful in recommending a future policy whereby earlier vaccination of pregnant mothers would benefit not only the infant but also the mother by preventing severe disease.\n\nIn our study, we attempted to answer a question regarding the gestational timing of maternal vaccination, which optimizes infant outcomes. We aimed to carry out a multicenter prospective cohort study in which pregnant mothers were vaccinated when they were confirmed to be pregnant. Infants were followed up for outpatient visits and hospitalizations, and influenza infection was confirmed using polymerase chain reaction (PCR). This would allow for a study that aims to compare the outcomes of infants born to mothers vaccinated in different trimesters of gestation to assess the reliability of our current findings. The current meta-analysis combines the outcomes of five studies that were comparable in terms of methodology and outcome measures, and a future meta-analysis that utilized the findings of more studies would also be useful, as meta-analyses are at the highest rank in the hierarchy of evidence. It is difficult to establish a cause-effect relationship as a very low number of studies actually isolated the variable of trimester vaccination, thereby exemplifying the need for more studies investigating optimization of the timing of influenza vaccination.\n\n\n6. Conclusion\n\nOur meta-analysis showed that studies that included mothers vaccinated in the first trimester of pregnancy conferred greater protection to infants less than 6 months of age compared to mothers vaccinated in the second or third trimester by almost three times. It also showed that there was no difference in effectiveness when including mothers vaccinated in the second or third trimesters of pregnancy on infant outcomes. This supports the view that vaccinating pregnant mothers in the first trimester of pregnancy may confer greater protection to infants less than six months of age than vaccinating in the second or third trimester. Further research is needed; however, to isolate the variable as in this meta-analysis, we were not able to successfully isolate the variable; therefore, our findings only provide correlative findings and it is difficult to establish a causal relationship.", "appendix": "Data availability statement\n\nNo data are associated with this article\n\nData was made publically available on Fig share and licensed. Respective citations have been included in the bibliography and with the data set.\n\n1. Figshare, PRISMA Checklist. https://doi.org/10.6084/m9.figshare.25907518.v1 31\n\n2. Figshare PRSIMA Flow Diagram. figshare. https://doi.org/10.6084/m9.figshare.25907527.v1 32\n\n3. Figshare Table 1 F1000.docx. https://doi.org/10.6084/m9.figshare.25907551.v1 33\n\n\nBibliography\n\nFlood EM, Block SL, Hall MC, et al.: Children’s Perceptions of Influenza Illness and Preferences for Influenza Vaccine. J. Pediatr. Health Care. 2011; 25(3): 171–179. PubMed Abstract \| Publisher Full Text\n\nDawood FS, Chaves SS, Pérez A, et al.: Complications and Associated Bacterial Coinfections Among Children Hospitalized with Seasonal or Pandemic Influenza, United States, 2003–2010. J. Infect. Dis. 2014; 209(5): 686–694. PubMed Abstract \| Publisher Full Text\n\nhttp\n\nRasmussen SA, Jamieson DJ, Uyeki TM: Effects of Influenza on Pregnant Women and Infants. Am. J. Obstet. Gynecol. 2012; 207(3): S3–S8. Publisher Full Text\n\nTaubenberger JK, Morens DM: The Pathology of Influenza Virus Infections. Annu. Rev. Pathol. 2008; 3(1): 499–522. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Vaccines against influenza WHO position paper-November 2012. Wkly Epidemiol. Rec. 2012; 87(47): 461–476. Reference Source\n\nSimon AK, Hollander GA, McMichael A: Evolution of the Immune System in Humans from Infancy to Old Age. Proc. R. Soc. B Biol. Sci. 2015; 282(1821): 20143085. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlexander-Miller MA: Challenges for the Newborn Following Influenza Virus Infection and Prospects for an Effective Vaccine. Front. Immunol. 2020; 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCuningham W, Geard N, Fielding JE, et al.: Optimal Timing of Influenza Vaccine during Pregnancy: A Systematic Review and Meta-analysis. Influenza Other Respir. Viruses. 2019; 13(5): 438–452. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDonahue JG, Kieke BA, King JP, et al.: Association of Spontaneous Abortion with Receipt of Inactivated Influenza Vaccine Containing H1N1pdm09 in 2010–11 and 2011–12. Vaccine. 2017; 35(40): 5314–5322. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBednarczyk RA, Adjaye-Gbewonyo D, Omer SB: Safety of Influenza Immunization during Pregnancy for the Fetus and the Neonate. Am. J. Obstet. Gynecol. 2012; 207(3): S38–S46. Publisher Full Text\n\nVaccine Knowledge Group: Flu Vaccine in Pregnancy.2018. Reference Source\n\nMak TK, Mangtani P, Leese J, et al.: Influenza Vaccination in Pregnancy: Current Evidence and Selected National Policies. Lancet Infect. Dis. 2008; 8(1): 44–52. PubMed Abstract \| Publisher Full Text\n\nJarvis JR, et al.: The effectiveness of influenza vaccination in pregnancy in relation to child health outcomes: Systematic review and meta-analysis. Vaccine. 2020; 38(7): 1601–1613. PubMed Abstract \| Publisher Full Text\n\nChecklists: SIGN.no date. (Accessed: September 17, 2022). Reference Source\n\nZaman K, et al.: Effectiveness of maternal influenza immunization in mothers and infants. N. Engl. J. Med. 2008; 359(15): 1555–1564. Publisher Full Text\n\nBenowitz I, et al.: Influenza vaccine given to pregnant women reduces hospitalization due to influenza in their infants. Clin. Infect. Dis. 2010; 51(12): 1355–1361. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTapia MD, et al.: Maternal immunisation with trivalent inactivated influenza vaccine for prevention of influenza in infants in Mali: a prospective, active-controlled, observer-blind, randomised phase 4 trial. Lancet Infect. Dis. 2016; 16(9): 1026–1035. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEick AA, et al.: Maternal influenza vaccination and effect on influenza virus infection in young infants. Obstet. Gynecol. Surv. 2011; 66(6): 333–334. Publisher Full Text\n\nSingh M, et al.: Influenza vaccine: A viable option to protect pregnant women and infants from seasonal flu: A retrospective hospital-based study in India. Int. J. Clin. Pract. 2019; 73(7): e13361. PubMed Abstract \| Publisher Full Text\n\nMaltezou HC, et al.: Effectiveness of quadrivalent influenza vaccine in pregnant women and infants, 2018–2019. Vaccine. 2020; 38(29): 4625–4631. PubMed Abstract \| Publisher Full Text\n\nOmer SB, et al.: Efficacy, duration of protection, birth outcomes, and infant growth associated with influenza vaccination in pregnancy: a pooled analysis of three randomised controlled trials. Lancet Respir. Med. 2020; 8(6): 597–608. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOverview of influenza testing methods: 2021. (Accessed: September 17, 2022). Reference SourceReference Source\n\nEick AA, et al.: Maternal influenza vaccination and effect on influenza virus infection in young infants. Arch. Pediatr. Adolesc. Med. 2011; 165(2): 104–111. Publisher Full Text\n\nMetelli S, Chaimani A: Challenges in meta-analyses with observational studies. Evid. Based Ment. Health. 2020; 23(2): 83–87. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCaliendo AM, et al.: Performance of a PCR assay for detection of Pneumocystis carinii from respiratory specimens. J. Clin. Microbiol. 1998; 36(4): 979–982. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSteinhoff MC, et al.: Year-round influenza immunisation during pregnancy in Nepal: a phase 4, randomised, placebo-controlled trial. Lancet Infect. Dis. 2017; 17(9): 981–989. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKatz J, et al.: Impact of timing of influenza vaccination in pregnancy on transplacental antibody transfer, influenza incidence, and birth outcomes: A randomized trial in rural Nepal. Clin. Infect. Dis. 2018; 67(3): 334–340. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVaccines against influenza: WHO position paper – May 2022: Who.int.no date. (Accessed: September 17, 2022). Reference Source\n\nAbdul Wahab E: figures influenza.docx. figshare. Figure. 2024. Publisher Full Text\n\nAbdul Wahab E: PRISMA Checklist. figshare. Figure. 2024. Publisher Full Text\n\nAbdul Wahab E: PRSIMA Flow Diagram. figshare. Figure. 2024. Publisher Full Text\n\nAbdul Wahab E: Table 1 F1000.docx. figshare. Figure. Publisher Full Text" }	[ { "id": "291584", "date": "23 Jul 2024", "name": "Jeanette Dawa", "expertise": [ "Reviewer Expertise Public health", "infectious disease epidemiology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present findings from their research on the optimal timing of maternal influenza vaccination for protection of infants. This is a very interesting topic, however because of the limited data available, the conclusions drawn by the authors do not seem appropriate given that the analysis was not able to directly answer the research question. Despite the limited data, their research question is of importance and if the analysis was redone to address these concerns, it would be a very informative and useful paper.\nThere are a few areas the authors could address to improve their publication: 1. The search is outdated. It should be updated to 2024. In addition, the search terms could be more comprehensive by including truncated and wild card searches 2. The authors do not describe the indications for influenza testing in each study. As influenza can also lead to asymptomatic infection, it would be important to state whether testing was done regularly in infants or only if they presented with symptoms. 3. It would have been helpful to include information in the summary table of studies on whether the studies were considering severe influenza (hospitalised influenza), medically attended influenza at the out patient clinic or any influenza. The analysis should have considered these groups separately as vaccine effectiveness varies for each type of outcome 4. It is not clear whether these types of studies were excluded or included: \"Studies in the form of case series, case reports, clinical practice guidelines, commentaries, conference abstracts, editorials, meta-analyses, narrative reviews, studies reporting estimated influenza rates based on ecological approaches, statistical modelling, or systematic reviews.\" 5. Whether influenza is seasonal or year-round could have an effect on outcome of each study and this should have been considered in the analysis and presentation of results. It would be important to describe the analysis and results separately for areas with significant year round or seasonal influenza activity. 6. Importantly the authors set out to determine whether vaccination in the first semester provides better protection than vaccination in the second or third trimester. It would therefore be important that they include manuscripts that designed their studies to do that, or at least be able to extract data from the studies that compares outcomes among those vaccinated in each trimester. It appears that there were few if any published papers with this information, and the authors therefore compared pooled analyses of different types of groups. Because they were not able to identify and compare studies that tested outcomes across different trimesters it is not appropriate to conclude from the data available that vaccinating in the first trimester is better than vaccinating in other trimesters. It does not appear that there was enough data to reach this conclusion, and the analysis given the possibility of differences in indications for timing of testing and influenza transmission is not appropriate to answer the primary research question. In summary, the studies found do not seem able to answer the research question and so the quantitative analysis does not appear to be appropriate in reaching their conclusion.\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? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "302743", "date": "29 Jul 2024", "name": "Maggie Jing Ouyang", "expertise": [ "Reviewer Expertise Influenza virus infection", "host immune response to virus infection", "vaccine against virus infection" ], "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 focused on an important topic: what is the right time for maternal immunization to protect infants? They have searched and selected 7 studies, and performed the meta-analysis to compare the maternal vaccination efficacy against influenza virus at different trimesters. The influenza infection events detected by PCR are analyzed through Forrest plot analysis and used to evaluate the protection to the infants transferred from their vaccinated mothers during pregnancy. The authors found that infants born from mothers who took influenza vaccination in the second and third trimesters got less protection, compared with those vaccinated in any trimester (1,2, and 3). They conclude that vaccination of pregnant mothers in the first trimester confers greater protection to infants. However, the design of data analysis is incomplete and the studies selected are limited, these cause the evidence shown in the results not sufficient to make the conclusion. Major problems: 1. The conclusion that vaccination in the first trimester conferred greater protection is not convincing since no solid evidence (such as a study with vaccination in the first trimester only) is included. 2. The authors analyzed the influenza infection in infants of ages less than 6 months, compared and showed the OR calculated from the numbers of influenza events. However, this limited data is not sufficient for the assessment of vaccines. The result mentioned the vaccine efficacies and risk reduction of each separate studies (as published), but did not show the total reduction of influenza infection determined by PCR of all the studies after systemic analysis, nor the vaccine efficacy (because studies with serological tests are excluded). These are critical concerns and criteria for vaccine evaluation. The details of the influenza infection, such as the infection rate, the virus titers, and virus types/subtypes, also can support the assessment. Unfortunately, these are not analyzed or not mentioned. 3. The OR definition is confusing. \"Unexposed\" control means the unvaccinated control? Why the number or the rate of total infection events in the control group is higher than that of the vaccinated group in Figures 1.1-1.4? Pease view the table in the file found here: https://f1000research.s3.amazonaws.com/linked/666208.148519_table_1.pdf\n4. Even though Influenza-like (ILI) is the secondary outcome as mentioned in the abstract, no data linking the influenza vaccine to the ILI is shown in the result. Also, the relationship of ILI with influenza vaccination is elusive. What is the conclusion from this secondary outcome? 5. The organization of figures and results also has some problems. For example, the result description in 4.6 needs to be revised to let it easy to understand. The figure numbers should be mentioned in the corresponding place: Fig 1.1 should be cited when describing the data of the vaccination that administered in any trimesters in Result 4.6.1, and Figure 1.3 should be cited in Result 4.6.2 and 4.6.3. 6. Figure legend is needed for each figure. 7. Figure of the flow diagram should be shown in result 4.1 and the major details should be described in the manuscript. It is inconvenient for readers to dig out the figure from the cited reference or the listed extended data. Even though this figure is shared in the database, it could be a part of this paper if it is the first time used. 8. Tables of study characteristics should be shown and the major points should be described in result 4.2. These tables will provide important information that helps to evaluate the reliability of the conclusion. 9. In results 4.2, 4.3, and 4.4, When the study is mentioned in the manuscript, the corresponding reference should be cited, so readers can easily figure it out from others. 10. If applicable, the study characteristics (4.2-4.3) should include the cohort information, such as the number of pregnant women, vaccination time points, the city, sample types, virus detection method (PCR or ELISA or others), virus types/subtypes (H1N1, H3N2, B), etc. 11. Result 4.5, please use a table to summarize the extracted data, and revise the description to be concise and clear. The \"general trend\" should be supported by data. 12. \"provide maximum immunogenicity\" may be \"provide maximum protection\"? Immunogenicity is the ability of antigens to trigger immune responses in the host.\n\nMinor 1. \"This shows that active immunity, and therefore vaccination, does not confer effective protection for infants.\" It is hard to understand \"active immunity\" in this sentence. 2. Incorrect usage of some terms confuses readers. For example, \"influenza\" is a disease, when mentioning the virus, it is better to say \"influenza virus\". 3. References have some errors. For example: -Ref 3 is blank -In \"1. Rationale\", the 2nd paragraph should add Refs in appropriate places. For example, the 1st, 3rd, 4th and 5th sentences, both mentioned papers/studies, but no refs. Ref should be added to the first sentence when citing the content. -In '1. Rationale\", 4th paragraph: please add the ref for \"Jarvis et al. in 2020\" -In result 4.4, please add the ref for Singh et al. -The extended data should not be cited again as Refs (#30-33).\n4. Typos or grammar errors, for example: - \"to produce antibody on their owncan\". - The full name followed with an abbreviation: Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA). The ref should be cited after this. - \"The search several electronic databases\" - \"17th of April 17, 1996\" - In result 4.6, 2nd paragraph \"In 2 studies, administered the vaccine in the third trimester in twostudies administered the vaccine in one of all trimesters, ...\" - \"Studies in the form of case series, case reports, clinical practice guidelines, commentaries, conference abstracts, editorials, meta-analyses, narrative reviews, studies reporting estimated influenza rates based on ecological approaches, statistical modelling, or systematic reviews. \"\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? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "302742", "date": "08 Aug 2024", "name": "Chenyan Zhao", "expertise": [ "Reviewer Expertise Pathogen Biological research on influenza virus", "hepatitis E virus and evaluation of vaccine products" ], "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 article compares the health outcomes of infants born and children (<6 months) to women who received influenza vaccines and infants born to pregnant women who did not receive vaccines or control vaccines through a systematic review/META analysis. The conclusion is that mothers who received vaccines during the first trimester provided greater protection than those who received vaccines during any other trimester. However, the conclusion was not adequately supported by the results presented in the review. There are a few areas the authors could address to improve this article:\nRegarding quantitative analysis, this article only compiled the results of 5 studies (references 16, 18, 20, 21, 22), and the most recent article was indexed in 2020. Are there any relevant studies after 2022? If so, suggesting including them. Authors mentioned that Jarvis et al. (reference 14) analyzed that received vaccines at the optimal time would provide the highest level of protection for both mothers and infants. However, the mains study objective of the authors of this paper is only “to determine the time for providing maternal influenza vaccination to confer optimal benefits to the infant until 6 months of age”, not considering both mother (pregnant woman) and baby at the same time, If the optimal timing for a pregnant woman to receive a flu vaccine is not consistent with the optimal timing for the baby, what is the study significance of this article? The authors mentioned in \"Objectives\" that “to identify the optimal timing for immunizing pregnant women to confer the most protection by reducing the incidence of laboratory-confirmed influenza or influenza-like illness in infants less than 6 months of age.” As mentioned later, influenza cases are only included in the study if they are determined by PCR, but how are influenza-like cases determined? In the sentence at 3.4 Data synthesis, “The studies assessed the efficacy of influenza vaccination in exposed groups to unexposed groups as a control.” What does exposure refer to? What is the exposed group and what is the unexposed group? Suggest further clarification. influenza cases are only included in the study if they are determined by PCR, but how are influenza like cases determined? The definition and meaning of \"odds ratio\" should be clarified. Are there 6 or 5 studies included in the 'quantitative analysis'? The method and results mentioned 6 and 5 studies respectively, please verify if they are consistent?\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? 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.) Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-629
https://f1000research.com/articles/12-421/v1	19 Apr 23	{ "type": "Research Article", "title": "In vivo immunomodulatory effect and safety of MSC-derived secretome", "authors": [ "Dwi Aris Agung Nugrahaningsih", "Purwadi Purwadi", "Is Sarifin", "Indra Bachtiar", "Sunarto Sunarto", "Ubaidillah Ubaidillah", "Ines Larasati", "Pamungkas Bagus Satriyo", "Dicka Wahyu Setiasari", "Maria Nur Hasanah", "Jarir At-thobari", "Sofia Mubarika", "Purwadi Purwadi", "Is Sarifin", "Indra Bachtiar", "Sunarto Sunarto", "Ubaidillah Ubaidillah", "Ines Larasati", "Pamungkas Bagus Satriyo", "Dicka Wahyu Setiasari", "Maria Nur Hasanah", "Jarir At-thobari", "Sofia Mubarika" ], "abstract": "Background: Secretomes have been gaining interest in treating several diseases due to their pharmaceutical effects, such as the immunomodulatory effect. This study aimed to determine the immunomodulatory effect of secretomes derived from human umbilical cord mesenchymal stem cells (MSCs) and their safety. Methods: We conducted an in vivo immunomodulatory study using a carbon clearance assay. The safety of single-dose administration of secretome was done using fixed-dose methods of acute toxicity test. Results: The phagocytic index was higher in mice treated with secretome than in untreated mice. The acute toxicity study also showed that the administration of secretome derived from human umbilical cord MSCs did not change the mice’s body weight, physical examination results, organ weight, and gross anatomy examination. Conclusions: This study presents the potential of secretome derived from MSCs as a safe immunomodulatory agent.", "keywords": [ "Secretome", "Mesenchymal stem cells", "Immunomodulator", "In vivo", "Safety" ], "content": "Introduction\n\nMesenchymal stem cells (MSC) have been a potential candidate therapeutic agent for many degenerative diseases due to their ability to modulate many processes in the body, such as angiogenesis, inflammation, apoptosis, wound healing, and the immune response.1–3 Their pharmacological activities have been suggested to be the result of their ability to differentiate into cells that can perform repairs in problematic areas in the body.4 In addition, MSCs secrete substances that can repair damage in the body and maintain body homeostasis. Some of the substances produced by MSCs include growth factors, extracellular vesicles, and other soluble proteins.2,5 These materials are often called secretomes, and since they exist in the MSC medium, the medium is called “conditioned medium”.\n\nSecretomes are becoming a very attractive agent in drug development because of their several advantages over MSCs. Among them are their safety, easy administration, and easy storage. Secretomes are considered safer than MSC because they don’t contain cells, have no risk of causing an embolism, have no risk of tumor formation due to wrong cell differentiation, do not need cryopreservation, and have a low risk of carrying infectious agents as well. In addition to their advantages over MSCs, secretomes also have a pharmacological activity, including anti-inflammatory, anti-fibrosis, wound healing, and immunomodulatory effect.6\n\nStudies have shown the immunomodulatory effect of MSCs.7 However, there is a lack of information regarding the effect of secretomes derived from human umbilical cord MSCs (UCMSCs) in vivo. Therefore, this study aimed to investigate the immunomodulatory activity of secretomes. We also aimed to evaluate the safety of the secretome by conducting an acute toxicity assay.\n\n\nMethods\n\nThe experimental protocol was approved by the Medical and Health Research Ethics Committee (MHREC) Faculty of Medicine Universitas Gadjah Mada (KE/0108/01/2022) on February 23rd 2022. The collection of secretomes was approved by PT Tristem Medika Indonesia (UC-2-RMD-3) on June 15th 2021. Participants provided informed written and verbal consent prior to their participation.\n\nPT Tristem Medika Indonesia provided the MSC secretome. The MSC secretome was produced in four batches, on 17th September 2021 (Batch I), 27th January 2022 (Batch II), 10th April 2022 (Batch III), and 5th July 2022 (Batch IV), respectively. The MSC secretome production procedure followed the PT Tristem Medika Indonesia method. Briefly, the umbilical cord tissue was collected from eligible consenting donors following caesarean delivery and transported to the laboratory using a sterile bottle with DPBS (Gibco) with 2% penicillin-streptomycin (Sigma Aldrich, Germany). The tissue was rinsed and cleaned from blood using a similar solution that was used for transport. The blood vessel was removed and cut transversally into 1-cm segments. Then, it was cut longitudinally into halves. The tissues were rinsed using DPBS (Gibco, Thermo Fisher Scientific, USA), minced into 2-5 mm small pieces, and explanted to a 100 mm cell dish (Nunc, Thermo Fisher Sceintific, USA) in MEM Alpha Glutamax (Gibco) supplemented with 10% UltraGro (AventaCell Biomedical, USA) and 1% penicillin-streptomycin. The explants were incubated at 37°C, 5% CO2 and 2-8% O2. The medium was replaced every four days, and the tissues were removed once the cells were migrated. After 14 days, the cells were harvested and subcultured using the antibiotic-free complete medium with a seeding density of 8000 cells/cm2. The UCMSCs were further expanded until passage four to create a two-tier cell bank, master cell bank (passage two), and working cell bank (passage four). The working cell banks were thawed and cultured to passage six. After cells reached 90% confluency (day three), the culture medium was replaced with MEM Alpha without phenol red (Gibco) and further cultured for another three days. After three days, the conditioned medium was harvested, filtered using a 0.22 μm membrane (Nunc), and filled into cryovials (Corning) with 1.5 mL volume. The secretome products were stored at -20°C.\n\nStandard ELISA procedures using EliKineTM Human IL-10 ELISA KIT (Abbkine, China) were used to evaluate the IL-10 concentration in the secretome. The measurements of IL-10 in secretome were conducted based on the protocol provided by the kit manufacturer. The absorbance was read at 450 nm using an iMar Microplate reader (Bio-Rad, UK). The ELISA data were analyzed using Microplate Manager Software (Bio-Rad).\n\nExosomes were isolated from MSC secretome using Total Exosome Isolation from biofluids (Invitrogen, Thermo Fisher Scientific, USA). The starting volume of the secretome used was 10 mL and prepared according to the manufacturer’s instructions. The isolated exosomes were then diluted using PBS as much as 1 mL. Diluted exosomes were stored for further characterization.\n\nThe size distribution and concentration of isolated exosomes were examined using NTA. The NTA (ViewSizer 3000 – Horiba) instrumentation was equipped with multi-Laser; Blue-445 nm, Green-520 nm, and Red-635 nm, and a fluorescent detector with 450, 550, and 650 nm filters so that analysis could be done using a fluorescent marker. The volume required for the measurement process was as much as 500 μL exosome in PBS, and the observed particle sizes were limited to a 30 to 150 nm range.\n\nFor TEM analysis, as much as 200 μL of isolated exosomes were diluted using PBS to reach a volume of 1 mL exosome in PBS. Exosomes were dripped onto the 400 mesh Cu coated grid, allowed to absorb, and dried using filter paper. Negative staining was applied, using 1% uranyl acetate. The negative staining was dripped on the grid and allowed to be absorbed, then dried with filter paper. TEM visualizations were performed using JEOL 1400 Transmission Electron Microscope at 120 kV, and images were captured using a fully integrated high resolution camera system (8 million pixel CCD camera). Exosome particle size measurements were carried out using ImageJ software version 1.53K.\n\nThe miRNA profiling started by isolating the exosome using exoRNeasy Midi Kit (Qiagen) based on the manufacturer’s protocols. The total RNA calculation was done using a NanoDrop (Thermo Scientific) and the miRNA profiling was conducted using the Nanostring OID NGS-036 (NanoString Technology, USA). Then, the miRNA data analysis was conducted using nSolver Analysis Software 4.0, with which the ten highest normalized expressions of the miRNA were obtained. The endogenous housekeeping gene was beta-actin. The threshold for reading background subtraction was determined using negative control read.\n\nThe prediction of the top 10 miRNA biological activity was done using free software DIANA miRPath v3.0 tools available From DIANA Lab, supported by experimental interaction from DNA-TarBase v.7.0. TarBase v7.0 is a combination of half a million miRNAs derived from gene interactions from hundreds of publications and more than 150 CLIP-Seq libraries.8\n\nMale Swiss albino mice, 6-8 weeks old, weighing 15 to 25 g, were used in the study. The animal’s room temperature is set to 22° ± 3°C, with a relative humidity of 30–70%, 12 hours of light, and 12 hours of darkness. Animals are fed according to laboratory standards and given indefinitely (ad libitum). The animals were maintained under standard conditions according to Regulation of the Head of National Agency of Drug and Food Control (BPOM) No. 7 of 2014 concerning guidelines for in vivo tests.8 The person conducting the animal handling was not blinded to the treatment group. However, the person conducting the measurement of the carbon clearance assay was blinded to the treatment group.\n\nAfter the test was complete, all experimental animals were sacrificed using ketamine at a dose of 80 mg/kg BW. Ketamine is injected intraperitoneally. The experimental protocol was approved by the Medical and Health Research Ethics Committee (MHREC) Faculty of Medicine Universitas Gadjah Mada (KE/0108/01/2022).\n\n20 healthy male mice were randomly divided into four groups. Each group consisted of five mice, and all received an intramuscular injection of secretome or MEM-α basal medium at 0.025 mL in each thigh. The first group received 0.00625 mL of secretome intramuscularly in each thigh (dose 1). The second group received 0.0125 mL of secretome intramuscularly in each thigh (dose 2). The third group received 0.025 mL of secretome intramuscularly in each thigh (dose 3). The control group received 0.025 mL of sterile MEM-α basal medium in each thigh (negative control). After three days of treatment, all the groups received 0.1 mL of carbon ink suspension through the tail vein. Blood was collected at an interval of 0 and 15 min immediately after injection of carbon suspension. Measurement of carbon in the blood was determined using a spectrophotometer at 675 nm. The phagocytic index was calculated based on optical densities value with the following formula.\n\nNote:\n\nOD1 is the optical density at 0 minutes after carbon injection\n\nOD2 is the optical density at 15 minutes after carbon clearance injection\n\nt2 is 15 minutes\n\nt1 is 0 minutes\n\nFemale Swiss albino mice were used in this test. Healthy female mice at 8-10 weeks old were used because, generally, female animals are more sensitive to toxic substances than male animals.8 The method for conducting the acute toxicity test was modified fixed dose according to Regulation of the Head of National Agency of Drug and Food Control (BPOM) No. 7 of 2014.8 There are two parts to the fixed-dose methods: preliminary and main parts. In this preliminary part, we used two mice divided into two groups, the treatment group, and the control group. The mice received secretome or MEM-α basal medium intramuscularly with the highest possible volume that can be given intramuscularly to mice, which was 0.05 mL in each thigh or 0.1 mL per mouse. The mice were randomly assigned to receive treatment or control. Observations of their behavior and clinical signs were conducted in the first 30 minutes and every 4 hours for 24 hours. After 24 hours, the mice were observed daily until day 15. Since there was no mortality in the preliminary parts of the acute toxicity test, the main test was carried out with the same dose as the dose used in the preliminary part. In the main test, we used four mice in the secretome group and one mouse in the control group. The mice were observed in the first 30 minutes after injection, every 4 hours during 24 hours, and every 24 hours until day 15. On day 15, all mice were killed, and all vital organs were examined.\n\nAll data were presented as Mean and SEM. The phagocytic index means were analysed using one way ANOVA with Tukey’s multiple comparisons test. The statistical analysis was done using GraphPad Prism version 9.0.0 (86).\n\n\nResults and discussion\n\nThe IL-10 concentration measured by ELISA showed that the concentration of IL-10 was 0.272-1.951 pg/mL (Figure 1).\n\nThe concentration of IL-10 in the secretome varied from 0.272 to 1.95 pg/mL.\n\nThe mean particle size in secretome and water was 117 nm and 104 nm, respectively. The particles in size 30-150 nm in secretome and water were 3.1×108 and 1.5×106, respectively. Figure 2 presents the particle examination result using NTA.\n\nThe graph on the left side shows the particle distribution across the different sizes. The picture on the right side shows the particle picture in measured samples. The mean particle size (x-axis) in the secretome was larger than those in water (117 nm (B) vs104 nm (A), respectively). The count of particles (y-axis) in size 30-150 nm was also greater in secretome than in water (3.1×108 (B) vs 1.5×106 (A), respectively).\n\nThe visualization using TEM revealed that exosomes had been successfully isolated within the expected size range (30-100 nm). The analyzed particles’ morphology (Figure 3) was consistent with NTA results.\n\nThe size and morphology of the isolated exosome were varied. The size of the exosome was within the expected size range (30-100 nm).\n\nThe 10 highest reads of miRNA normalized by beta actine are presented in Table 1. The 10 miRNA with highest read were hsa-miR-23a-3p, hsa-miR-4454 + miR-7975, hsa-miR-1915-3p, hsa-miR-4488, hsa-miR-125b-5p, hsa-miR-21-5p, hsa-miR-130a-3p, hsa-miR-320e, hsa-miR-494-3p, and hsa-miR-4516.\n\nPrediction of miRNA biological activity\n\nThe predicted biological activity of the top 10 miRNA in the MSC are presented in Figure 4.\n\nThe prediction of related biological activity of the 10 highest miRNA in the secretome MSC was fatty acid biosynthesis, fatty acid metabolism, prion diseases, and hippo signalling pathway (red color).\n\nThe biological activity that were most related to the miRNA in the secretome MSCs were fatty acid biosynthesis, fatty acid metabolism, prion diseases, and hippo signalling pathway.\n\nThe phagocytic index was significantly different between those in the control and 0.025 mL group (dose 3). Figure 5 shows the phagocytic index calculation of every group.\n\nThe phagocytic index was significantly higher in dose 3 compared to those in the negative control. A negative control is without secretome treatment. * p < 0.05 vs negative control.\n\nAcute toxicity test\n\nIn the preliminary part of the acute toxicity test, the mice received secretome or MEM-α basal medium intramuscularly of the highest possible volume that can be given intramuscularly to mice which is 0.05 mL in each thigh or 0.1 mL per mice. There was no abnormality in the physical examination of the mice in the control and treatment groups. The body weight (Table 2) was also similar between the control and treatment groups. Therefore, the main study was conducted using a 0.1 mL dose per mouse.\n\nThe body weight was similar in control and treatment groups.\n\nThe relative organ weight was measured by dividing the organ weight by the mouse’s body weight. The relative organ weight was also similar between groups (Table 3).\n\nThe relative organ weight was similar in control and treatment groups.\n\n\nDiscussion\n\nOur study presents the secretome effect on phagocytic activity in mice by carbon clearance assay. Phagocytosis is part of the natural immune system, which acts as a first-line defence against the intrusion of foreign matter. The injected carbon is phagocytes by reticuloendothelial systems (RES) cells which consist of phagocytic cells. This process involves opsonization and complement activation. The faster the clearance, the better the phagocytic activity.9 The phagocytic index in mice receiving the highest dose of secretome was significantly higher than those in control groups. Thus, the phagocytic activity of the mice treated with secretome was better than that of the control group.\n\nSecretomes, as well as MSCs, have been known to have an immunomodulatory effect. MSCs contain various soluble proteins such as cytokines, chemokines, growth factors, and extracellular vesicles (EV).10 The secretome protein interacts with host cells, including endogenous stem cells and progenitor cells. It influences the function of those cells, such as regulating immune response, mediating chemokines activation, and influencing the inflammatory response.11 A study on human bone marrow stem cells (hBMSC) showed that its secretome, but not the hBMSC-self, can increase the phagocytic activity of macrophages. The increase in macrophage phagocytic activity induced by the secretome was related to the increase in macrophage CD206 expression. CD206 is a marker of M2 macrophage, an anti-inflammatory macrophage that recognizes the foreign matter as phagocyted.12 The M2 macrophage, an anti-inflammatory macrophage, has been reported to have higher phagocytic affinity than the M1 macrophage under low and high density of cell target.13\n\nThe phagocytosis ability of macrophages is diverse depending on the stimulation. Our study also examined the expression of IL-10 in the secretome. We found that the secretome contained IL-10 in the range of 0.019-1.951 pg/mL. Macrophage stimulation by IL-10 resulted in higher phagocytosis activity than unstimulated macrophages.14 Meanwhile, stimulation by IL-4 resulted in higher macrophage activity than stimulation by IFN-gamma.15 The study also showed that IL-10 and IL-4 induced human macrophage phagocytes mycobacteria faster than those on M1 macrophages.16 However, another study showed that IL-10 could increase IL-4-induced M2 polarization and increase the migration of eosinophils.17 The primary function of Il-10 is to inhibit the excessive response of the immune system.\n\nConsequently, it can impair the immune response to infection. However, IL-10 is also necessary for tackling viral and parasitic infections, depending on the course of infection.18,19 Therefore, using IL-10 for immunomodulation should consider the pathogenesis of the infection and the administration timing.\n\nThe miRNA profiling showed that some miRNA are involved in hypo signalling pathways which is gaining attention for their roles in the immune system function and homeostasis.20 However, further studies are needed to gather more evidence about the MSC secretome miRNA roles in the immune system.\n\nWe also studied the safety of secretomes in mice by conducting an acute toxicity test. After a single intramuscular injection of the secretome, there was no toxicity sign or symptom in the injected mice. The therapeutic activity of stem cells has been known as the result of its secreted product in their medium, secretomes. The secretome, the cell-free medium of stem cells, has been gaining more interest from researchers since it is more tolerable due to its cell-free nature, easier to administrate, and easier to store.21–23 Our study has shown that the secretome derived from human UCMSCs is safe when injected intramuscularly in mice. Further studies are needed to determine its safety in long-term administration and other routes of administration.\n\n\nConclusions\n\nThe secretome derived from human UCMSCs shows immunomodulatory activity by modulating phagocytosis. The study also shows the safety of single administration of secretome. One of the limitations of our study is that the carbon clearance assay was only conducted on male mice to avoid the physiological variation related to the estrus cycle in female mice.", "appendix": "Data availability\n\nfigshare: accute toxicity data. https://doi.org/10.6084/m9.figshare.22338229\n\nfigshare: Secretome carbon clearance assay dataset. https://doi.org/10.6084/m9.figshare.22217824\n\nfigshare: miRNA profiling of MSC secretome. https://doi.org/10.6084/m9.figshare.22224742\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nARRIVE checklist for ‘In vivo immunomodulatory effect and safety of MSC-derived secretome’. https://doi.org/10.6084/m9.figshare.22566628.v1\n\n\nAcknowledgments\n\nThe author acknowledges the involvement of:\n\n1. Kepolisian Republik Indonesia for funding this research.\n\n2. PT Tristem Medika Indonesia has provided the MSC secretome.\n\n3. Mrs. Sumartiningsih from Laboratorium Riset Terpadu, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, for assistance in working on the ELISA technique.\n\n4. Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, has given permission to access the TEM facilities.\n\n5. Ms. Rahmi Ayu and Mr. Suroso from Laboratorium Farmakologi dan Toksikologi, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, for assistance in handling experimental animals and conducting in vivo tests.\n\n6. Laboratorium Penelitian dan Pengujian Terpadu, Universitas Gadjah Mada that, provides whole blood check sevices for supplementary data on in vivo tests.\n\n\nReferences\n\nAsanuma H, Meldrum DR, Meldrum KK: Therapeutic applications of mesenchymal stem cells to repair kidney injury. J. Urol. 2010; 184(1): 26–33. Publisher Full Text\n\nMei SHJ, Haitsma JJ, Dos Santos CC, et al.: Mesenchymal Stem Cells Reduce Inflammation while Enhancing Bacterial Clearance and Improving Survival in Sepsis. Am. J. Respir. Crit. Care Med. 2010; 182(8): 1047–1057. PubMed Abstract \| Publisher Full Text\n\nLi D, Qu J, Yuan X, et al.: Mesenchymal Stem Cells Alleviate Renal Fibrosis and Inhibit Autophagy via Exosome Transfer of miRNA-122a. Stem Cells Int. 2022; 2022: 14. Article ID 1981798.\n\nArthur A, Zannettino A, Gronthos S: The Therapeutic Applications of Multipotential Mesenchymal/Stromal Stem Cells in Skeletal Tissue Repair. J. Cell. Physiol. 2009; 218(2): 237–245. PubMed Abstract \| Publisher Full Text\n\nFuentes P, Torres MJ, Arancibia R, et al.: Dynamic Culture of Mesenchymal Stromal/Stem Cell Spheroids and Secretion of Paracrine Factors. Front. Bioeng. Biotechnol. 2022; 10: 26. Article ID 9162291. Publisher Full Text\n\nVizoso FJ, Eiro N, Cid S, et al.: Mesenchymal Stem Cell Secretome: Toward Cell-Free Therapeutic Strategies in Regenerative Medicine. Int. J. Mol. Sci. 2017; 18(9): 1852–1876. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSari DS, Maduratna E, Bumi C, et al.: Role of mesenchymal stem cell secretome as immunomodulator in periodontal diseases. J. Dentomaxillofacial Sci. 2021; 6(3): 139–146. Publisher Full Text\n\nBadan Pengawas Obat dan Makanan Republik Indonesia: Peraturan badan pengawas obat dan makanan nomor 7 Tahun 2014 Tentang Pedoman uji toksisitas praklinik secara in vivo. BPOM RI; 2014.\n\nVlachos IS, Zagganas K, Paraskevopoulou MD, et al.: DIANA-miRPath v3. 0: deciphering microRNA function with experimental support. Nucleic Acids Res. 2015; 43: W460–W466. Publisher Full Text\n\nGaneshpurkar A, Saluja AK: Experimental animal models used for evaluation of potential immunomodulators: a mini review. Bulletin of Faculty of Pharmacy, Cairo University. 2017; 55(2): 211–216. Publisher Full Text\n\nCrivellia B, Chlapanidasa T, Perteghellaa S, et al.: Mesenchymal stem/stromal cell extracellular vesicles: From active principle to next generation drug delivery system. J. Control. Release. 2017; 262(1): 104–117. PubMed Abstract \| Publisher Full Text\n\nDi Rocco G, Baldari S, Toietta G: Towards Therapeutic Delivery of Extracellular Vesicles: Strategies for in vivo Tracking and Biodistribution Analysis. Stem Cells Int. 2016; 2016: 12. Article ID 5029619.\n\nHolopainen M, Impola U, Lehenkari P, et al.: Human Mesenchymal Stromal Cell Secretome Promotes the Immunoregulatory Phenotype and Phagocytosis Activity in Human Macrophages. Cells. 2020; 9(9): 2142–2160. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchulz D, Severin Y, Zanotelli VRT, et al.: In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay. Sci. Rep. 2019; 9: 12. Article ID 1925.\n\nGratchev A, Kzhyshkowska J, Utikal J, et al.: Interleukin-4 and Dexamethasone Counterregulate Extracellular Matrix Remodelling and Phagocytosis in Type-2 Macrophages. Scand. J. Immunol. 2005; 61(1): 10–17. PubMed Abstract \| Publisher Full Text\n\nLingnaua M, Höflicha C, Volka H, et al.: Interleukin-10 enhances the CD14-dependent phagocytosis of bacteria and apoptotic cells by human monocytes. Hum. Immunol. 2007; 68(9): 730–738. PubMed Abstract \| Publisher Full Text\n\nTeles RMB, Krutzik SR, Ochoa MT, et al.: Interleukin-4 Regulates the Expression of CD209 and Subsequent Uptake of Mycobacterium leprae by Schwann Cells in Human Leprosy. Infect. Immun. 2010; 78(11): 4634–4643. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMakita N, Hizukuri Y, Yamashiro K, et al.: IL-10 enhances the phenotype of M2 macrophages induced by IL-4 and confers the ability to increase eosinophil migration. Int. Immunol. 2014; 27(3): 131–141. PubMed Abstract \| Publisher Full Text\n\nRedpath SA, Fonseca NM, Perona-Wright G: Protection and pathology during parasite infection: IL-10 strikes the balance. Parasite Immunol. 2014; 36(6): 233–252. PubMed Abstract \| Publisher Full Text\n\nRojas JM, Avia M, Martín V, et al.: IL-10: A Multifunctional Cytokine in Viral Infections. J. Immunol. Res. 2017; 2017: 14. Article ID 6104054.\n\nHong L, Li X, Zhou D, et al.: Role of Hippo signaling in regulating immunity. Cell. Mol. Immunol. 2018; 15: 1003–1009. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhangar P, Mills SJ, Cowin AJ: Mesenchymal Stem Cell Secretome as an Emerging Cell-Free Alternative for Improving Wound Repair. Int. J. Mol. Sci. 2020; 21(19): 7038–7053. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFoo JB, Looi QH, Chong PP, et al.: Comparing the Therapeutic Potential of Stem Cells and their Secretory Products in Regenerative Medicine. Stem Cells Int. 2021; 2021: 30. Article ID 2616807." }	[ { "id": "203914", "date": "10 Oct 2023", "name": "Francesca Pischiutta", "expertise": [ "Reviewer Expertise neuroscience", "cell based therapies" ], "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\nStudies investigating the immunomodulatory properties of mesenchymal stromal cells (MSCs) have gained significant attention in the field of regenerative medicine and immunology.\nIn this work by Nurgahaningsih and colleagues, the immunomodulatory effect of secretome derived from human cord MSC is investigated. The authors provide a characterization of the secretome profile analyzing the amount of IL-10 and showing the exosomes and miRNA profile. At last an in vivo analysis is performed in order to investigate the safety profile of secretome infusion and the modulation of phagocytic activity.\nThe manuscript investigates important questions however it is not clear what novel information the analyses provide. The abstract should better summarize all the main findings of the manuscript, since it now describes only the results of the in vivo analysis and not the characterization of the in vitro profile.\nMajor criticism\nThe rational of the study and the gap of knowledge is not clear and the analyses performed in vitro and the in vivo are not described as part of the same goal. Why has IL-10 been quantified? Is there any relation between the IL-10 amount in the secretome and the immunomodulatory function? What is the link between the top 10 miR found in the secretome with the in vivo findings? Authors should also better contextualize their findings with what already published in terms of miR characterization.\n\nIn the in vivo analysis, healthy mice have been subjected to intramuscular injection of the secretome or control medium. Then they were subjected to carbon clearance assay after 3 days via intravenous injection of carbon ink suspension. What is the rational of the intramuscular injection? Why not perform the IV secretome infusion (as delivery route mostly used)? What is the rational of studying the phagocytic activity in healthy mice? Having the effect in the context of a pathological condition would increase the translational validity of the findings.\n\nA characterization of the immune profile of the circulating phagocytic cells after secretome treatment is needed.\n\nAcute toxicity test: no details of the kind of observations and measurements have been provided. In the results, it has been reported only the variance of the body weight of living mice or of post mortem organs. Please provide more details.\nMinor criticism\nIn the introduction, authors underline the MSC ability to differentiate into specialized cells as main pharmacological activity. However, the study is focused on the use of MSC-derived secretome, the a-cellular counterpart. Please modify.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "12421", "date": "07 Oct 2024", "name": "Dwi Aris AgungNugrahaningsih", "role": "Author Response", "response": "Response to reviewer Reviewer:1 The manuscript investigates important questions however it is not clear what novel information the analyses provide. The abstract should better summarize all the main findings of the manuscript, since it now describes only the results of the in vivo analysis and not the characterization of the in vitro profile. Thank you for the suggestion to improve our manuscript. We have revised the abstract of the manuscript by providing highlight of our study findings. Background: The immune system is a complex network designed to protect the body from harmful pathogen. Phagocytosis process eliminate invaders before they enter the bloodstream. Recent research has highlighted the potential of secreted materials from Mesenchymal Stem Cells (MSCs), called as secretom, as immunomodulatory agent. This study aims to evaluate MSC secretome effect on phagocytosis and its safety. Methods: Characterization of the secretome content was achieved through nanoparticle tractking analysis (NTA), Transmission Elctron Microscopy (TEM), Enzyme-linked Immunosorbent Assay (ELISA), and nanostring. The assessment of immunomodulatory activity was conducted using carbon clearance assay. Additionally, we measure spleen mRNA CD68, and CD206. Safety evaluation involved a single-dose administration of the secretome, followed by acute toxicity testing using fixed dose method. Results: The characterization revealed the presence of interleukin 10 (IL-10), exosome-sized particles, and miRNA within the secretome. Mice treated with the secretome displayed a significantly higher phagocytic index compared to untreated controls and higher CD68 mRNA expression in the spleen. Furthermore, acute toxicity testing showed no significant effects on the mice’s body weight, physical examination results, organ weight, or gross anatomy, indicating a favorable safety profile. Conclusions: This study highlights the novel insights into MSC-derived secretomes, demonstrating their potential as safe and effective immunomodulatory agents. Major criticism The rational of the study and the gap of knowledge is not clear and the analyses performed in vitro and the in vivo are not described as part of the same goal. Why has IL-10 been quantified? Is there any relation between the IL-10 amount in the secretome and the immunomodulatory function? What is the link between the top 10 miR found in the secretome with the in vivo findings? Authors should also better contextualize their findings with what already published in terms of miR characterization. Thank you for the suggestion to improve our manuscript. Our study integrates in vitro and in vivo analyses to provide a comprehensive understanding of the secretome's immunomodulatory effects. The in vitro characterization identifies the content of the secretome, including IL-10, which is known for its role in phagocytic activity and may influence immunomodulation. The in vivo study evaluates the effect of secretome on phagocytic activity. By measuring IL-10, we aim to correlate its levels with observed immunomodulatory effects. Additionally, analyzing the particles in the secretome, and miRNA content helps identify potential molecular mechanisms underlying these effects. This approach bridges the gap between secretome composition and its functional impact, offering insights into the immunomodulatory mechanisms at play. We have corrected the introduction of the manuscript: The immune system is a sophisticated network designed to protect the body from harmful pathogens. It is generally divided into two main categories: the innate immune system and the adaptive immune system [Marshall et al, 2019]. The innate immune system serves as the first line of defence mechanism against pathogens, using processes like phagocytosis to eliminate harmful invaders before they enter the bloodstream and cause further complications [Lim et al, 2017]. Macrophages in the tissue remove pathogens or foreign particles that enter the tissue, while the spleen helps remove pathogens or foreign particles that have entered the bloodstream by filtering the blood and facilitating their destruction [Lewis et al, 2019]. Maintaining homeostasis in the immune system is crucial to ensure that it is prepared to protect the body whenever pathogens or other harmful substances enter. Factors such as daily stress, lifestyle choices, and environmental hazards can weaken the immune system and increase susceptibility to illness. Therefore, it is essential to maintain and enhance immune function to prevent infections and other diseases [Thorbur et al, 2014; Marques et al, 2016] Researchers are finding that the secreted materials from mesenchymal stem cells (MSCs), known as the \"secretome,\" and the liquid containing these materials, referred to as \"conditioned medium,\" are promising as immunomodulatory agents [Muzes & Sipos, 2022; ]. The secretome includes soluble factors like immunomodulatory molecules, cytokines, and growth factors, as well as vesicular factors such as extracellular vesicles (EVs) including exosome [Rostami et al, 2018Munos-Perez et al, 2021]. Notably, MSC-derived exosomes, which are small vesicles containing proteins, nucleic acids (like mRNA and miRNA), and lipids, have shown significant potential [Asgarpour et al, 2020]. Overexpression of IL-10 in the secretome of human umbilical cord MSCs can enhance macrophage function [Jerkic et al, 2019], while MSC-derived exosomes can improve the anti-inflammatory properties of macrophages and aid in reducing inflammation [song et al, 2017]. Additionally, apoptotic bodies from MSCs can influence macrophage behavior in wound healing models, and MSC exosomes have the potential to inhibit the proliferation, activation, and cytotoxicity of natural killer cells [Tang et al, 2022]. Furthermore, miRNAs present in MSC-derived EVs play a crucial role in regulating macrophage functions during inflammation [Wu et al, 2015; Wu et al, 2017]. Although the immunomodulatory effects of the secretome are well-documented, there is limited information on how secretomes derived from human umbilical cord MSCs (UC-MSCs) support immune function in healthy or normal conditions. This study aims to address this gap by evaluating several key aspects of the UC-MSC secretome in a healthy context. We measured interleukin-10 (IL-10) to understand its role in phagocytosis, profiled the miRNA content to uncover the mechanisms behind the secretome’s effects, characterized the extracellular vesicles (EVs) to explore their therapeutic potential, and assessed the impact of the secretome on phagocytosis in vivo. Additionally, we conducted an acute toxicity assay to ensure the safety of UC-MSC-derived secretomes. Methods In the in vivo analysis, healthy mice have been subjected to intramuscular injection of the secretome or control medium. Then they were subjected to carbon clearance assay after 3 days via intravenous injection of carbon ink suspension. What is the rational of the intramuscular injection? Why not perform the IV secretome infusion (as delivery route mostly used)? What is the rational of studying the phagocytic activity in healthy mice? Having the effect in the context of a pathological condition would increase the translational validity of the findings. Thank you for the suggestion to improve our manuscript. Immunomodulatory studies are conducted in healthy animals to establish a baseline understanding of how potential treatments affect the immune system under normal conditions. Healthy animals provide a controlled environment to observe the natural immune responses and assess the impact of interventions without the complications that might arise from pre-existing health conditions. This approach ensures that any observed effects can be attributed to the treatment being studied rather than to underlying health issues. One common method used in these studies is the carbon clearance assay. This assay measures the efficiency of phagocytosis, the process by which immune cells engulf and eliminate particles such as carbon particles. By introducing carbon particles into the bloodstream and monitoring their clearance rate, researchers can evaluate how well the immune system is functioning, particularly the activity of macrophages, which play a crucial role in the immune response. The carbon clearance assay provides valuable insights into how the treatment modulates immune function and can help in understanding its potential therapeutic benefits. We appreciate your question regarding the rationale for choosing intramuscular injection over intravenous infusion of the secretome. While intravenous (IV) delivery is indeed a common method, we opted for intramuscular (IM) administration for several reasons. Firstly, IM delivery allows the secretome to be deposited directly in the muscle tissue, where it can be gradually released into the bloodstream, potentially providing a more sustained effect. Additionally, muscles have a rich blood supply, which facilitates the secretome's absorption into the circulatory system. The large surface area of the muscle also makes intramuscular administration relatively straightforward and practical. Research supports the effectiveness of intramuscular administration for achieving systemic effects. For example, studies have demonstrated that intramuscular delivery of MSCs can result in systemic benefits (Jahromi & Davis, 2019). Furthermore, research has shown that exosomes, a key component of the secretome, can reach systemic circulation even when administered intramuscularly (Rehorova et al., 2019; Fennel et al., 2024). Therefore, while IV infusion is a commonly used route, intramuscular injection offers unique advantages that align with our study's objectives. Reference: Hamidian Jahromi S, Davies JE. Concise Review: Skeletal Muscle as a Delivery Route for Mesenchymal Stromal Cells. Stem Cells Transl Med. 2019 May;8(5):456-465. doi: 10.1002/sctm.18-0208. Epub 2019 Feb 5. PMID: 30720934; PMCID: PMC6477141. Fennel, Z. J., Bourrant, P.-E., Kurian, A. S., Petrocelli, J. J., de Hart, N. M. M. P., Yee, E. M., Boudina, S., Keirstead, H. S., Nistor, G., Greilach, S. A., Berchtold, N. C., Lane, T. E., & Drummond, M. J. (2024). Stem cell secretome treatment improves whole-body metabolism, reduces adiposity, and promotes skeletal muscle function in aged mice. Aging Cell, 23, e14144. https://doi.org/10.1111/acel.14144 Řehořová M, Vargová I, Forostyak S, Vacková I, Turnovcová K, Kupcová Skalníková H, Vodička P, Kubinová Š, Syková E, Jendelová P. A Combination of Intrathecal and Intramuscular Application of Human Mesenchymal Stem Cells Partly Reduces the Activation of Necroptosis in the Spinal Cord of SOD1G93A Rats. Stem Cells Transl Med. 2019 Jun;8(6):535-547. doi: 10.1002/sctm.18-0223. Epub 2019 Feb 25. PMID: 30802001; PMCID: PMC6525562. We have revised the discussion section to include this important points. A characterization of the immune profile of the circulating phagocytic cells after secretome treatment is needed. We agree that profiling circulating phagocytic cells after secretome treatment would offer valuable insights into the mechanism of the secretome as an immunomodulator. Unfortunately, we do not have data on the phagocytic profile in the circulation. However, we do have mRNA expression data for CD68 and CD206 from the spleen. The spleen is a key organ in the immune system, responsible for filtering the blood and removing foreign materials. To assess macrophage activity, we measured the mRNA levels of CD68, a common marker for macrophages, and CD206, a marker for anti-inflammatory macrophages, in the spleen. We have revised the methods, results, and discussion sections to reflect this update. Method: Spleen CD68 mRNA Analysis Total mRNA was extracted from the spleen using the FavorPrep™ Tissue Total RNA Mini Kit (Favorgen) according to the instructions provided in the kit. The extracted mRNA was then converted into complementary DNA (cDNA) using the ReverTraAce™ qPCR RT Master Mix (Toyobo). The mRNA expression was evaluated using the RT-qPCR SensiFAST™ SYBR® Low-ROX Kit (Bioline), with Beta Actin as the housekeeping gene. The primers used were: F 5'-TCT CCA CCT TCC AGC AGA TGT-3' R 5'-GCT CAG TAA CAG TCC GCC TAGA-3'. The CD68 primers were: F 5'- CGC AGA CAA TCA ACC TA-3' R 5'-GGC ATG GTG AAG TGA GG-3'. Result: Spleen CD8 and CD206 mRNA expression The CD68 mRNA expression of the spleen is higher in dose 3 compare to those on negative control group. Figure 6 present the spleen CD68 mRNA expression. Figure 6. Spleen CD68 mRNA expression in each group of treatment. The spleen CD68 mRNA expression was significantly higher in dose 3 compare to those on negative control. A negative control is without secretome treatment. * p < 0.05 vs negative control Acute toxicity test: no details of the kind of observations and measurements have been provided. In the results, it has been reported only the variance of the body weight of living mice or of post mortem organs. Please provide more details. Thank you for the suggestion. We conducted the acute toxicity test using the fixed dose method (OECD Acute Toxicity Test No. 420 and BPOM 2014) to determine whether a single injection of the secretome at the highest dose causes toxicity in animals. This test is an internationally accepted protocol for evaluating the toxicity of single exposures to substances. Briefly, after administering the injection, we observed the animals' behavior at specific time points. We also measured their body weight and, finally, sacrificed the animals to examine the macroscopic appearance of their organs and record organ weights. We agree that our method and results sections may not have clearly described the test conducted. Here is the revised version of the method and results sections related to the acute toxicity test. Methods (acute toxicity) Female Swiss albino mice were used in this test. Healthy female 8-10 weeks mice were used because, generally, female animals are more sensitive to toxic substances than male animals [8]. The method for conducting the acute toxicity test was modified fixed dose according to Regulation of the Head of National Agency of Drug and Food Control (BPOM) No. 7 of 2014 [8]. There are two parts to the fixed-dose methods: preliminary and main parts. In this preliminary part, we used two mice divided into two groups, the treatment group, and the control group. The mice received secretome or MEM-α basal medium intramuscularly with the highest possible volume that can be given intramuscularly to mice, which was 0.05 mL in each thigh or 0.1 mL per mouse. The mice were randomly assigned to receive treatment or control. Observations of their behavior and clinical signs were conducted in the first 30 minutes and every 4 hours for 24 hours. After 24 hours, the mice were observed daily until day 15. Since there was no mortality in the preliminary parts of the acute toxicity test, the main test was carried out with the same dose as the dose used in the preliminary part. In the main test, we used four mice in the secretome group and one mouse in the control group. The mice were observed in the first 30 minutes after injection, every 4 hours during 24 hours, and every 24 hours until day 15. On day 15, all mice were killed, and all vital organs were examined. The behavioral examination includes the following assessments: skin condition, fur piloerection, corneal reflex and corneal opacity, mucous membrane color, type and rate of respiration, palpebral reflexes, digit reflexes, paralysis, seizures, torticollis, somatomotor activity, reverse walking, tremors, salivation, sleep patterns, defecation, and urination. Result (acute toxicity) In the preliminary part of the acute toxicity test, the mice received secretome or MEM-α basal medium intramuscularly of the highest possible volume that can be given intramuscularly to mice which is 0.05 mL in each thigh or 0.1 mL per mice. There was no abnormality in the following behavioral assessment: skin condition, fur piloerection, corneal reflex and corneal opacity, mucous membrane color, type and rate of respiration, palpebral reflexes, digit reflexes, paralysis, seizures, torticollis, somatomotor activity, reverse walking, tremors, salivation, sleep patterns, defecation, and urination of the mice in the control and treatment groups. Reference: OECD (2002), Test No. 420: Acute Oral Toxicity - Fixed Dose Procedure, OECD Guidelines for the Testing of Chemicals, Section 4, OECD Publishing, Paris, https://doi.org/10.1787/9789264070943-en. Minor criticism In the introduction, authors underline the MSC ability to differentiate into specialized cells as main pharmacological activity. However, the study is focused on the use of MSC-derived secretome, the a-cellular counterpart. Please modify. Thank you, we have modified the introduction. Reviewer 2 The number of studies examining the immunomodulatory effects of mesenchymal stem cells through the secretome is increasing, and the safety of the conditioned media used needs to be investigated. In this respect, the authors have drawn attention to a current issue, but essential problems need to be clarified before the article is indexed. 1. First, characterization data of the isolated cells are lacking. Authors must include characterization experiments with immunophenotypic and differentiation data for UCMSCs. Thank you for your recommendation. We have included the secretome provided by the commercial supplier, PT Tristem Indonesia. We have updated the characterization and modified the methods and results sections based on your suggestions. Method: “The characterization of MSCs was performed using flow cytometry at the commercial lab testing facility, PharmaMetricLabs®. Several parameters were measured, including CD105, CD90, CD73, CD45, CD34, CD14, HLA-DR, and CD19. “ Result: Characterization of MSCs The characterization of MSCs was performed using flow cytometry (FACS). High percentages of CD105, CD90, and CD73 were observed, while CD45, CD34, CD14, HLA-DR, and CD19 were present in low percentages. The complete results are presented in Table 1. Table 1. MSC characterization result. Parameter Result CD105 99,98% CD90 99,97% CD73 100% CD45 0,75% CD34 0,22% CD14 0,15% HLA-DR 0% CD19 0,75% 2. It is not appropriate to store the secretome at -20 °C (especially when miRNA research is involved). Thank you for your observation. In our study, we stored the secretome at -80°C for long-term preservation. However, for short-term storage, such as when preparing for studies, we stored the secretome at -20°C. Research has shown that storage at -20°C does not significantly affect miRNA levels for up to 4-5 years (Grasedieck et al., 2012). We also update the method section to include this information. Method: … The secretome was stored at -80°C for long-term preservation. However, for short-term storage, such as when preparing for studies, we stored the secretome at -20°C….. Reference Grasedieck, S., Schöler, N., Bommer, M. et al. Impact of serum storage conditions on microRNA stability. Leukemia 26, 2414–2416 (2012). https://doi.org/10.1038/leu.2012.106 3. In the introduction section, it is stated that there is limited information in the literature about the immunomodulatory effects of the secretome, and it is claimed that the immunomodulatory effects will be evaluated. There are studies in the literature investigating the immunomodulatory effects of MSC-secretome. The authors did not use these studies for their manuscripts. Additionally, it is unclear how immunomodulatory effects are evaluated. Why has only IL-10 been investigated within the secretome? Why are other cytokines, molecules, and growth factors not mentioned? It should be explained. protein concentration was very low 0.04 ug/ul and 0.45 ug/ul. Thank you for your feedback. We have addressed your concerns as follows: Introduction: We have now included references to studies on MSC-secretome and its immunomodulatory effects in the introduction. This addition highlights the existing research and aligns our work with the current literature. Evaluation of Immunomodulatory Effects: We have clarified the criteria and methods used to evaluate the immunomodulatory effects. Specifically, we have detailed why IL-10 was selected for measurement. Protein Concentration: We acknowledge that the concentration of IL-10 was indeed very low (0.04 µg/µl and 0.45 µg/µl). We have addressed this issue in the discussion section, providing an explanation and considering its implications for our findings. Revised sections, including these points, are now incorporated into the introduction and discussion. 4. In vitro experimental setup is not sufficient to examine immunomodulatory effects. It should be investigated in vivo and the results added. The results of acute toxicity testing are unclear. Why was only IM injection administered? The most common route of administration for conditioned mediums is not IM. Why other routes were not chosen should be stated. We conducted the immunomodulatory effect in vivo using carbon clearance assay. We describe the assay in the method section. In the assay the live animal was injected with carbon solution and we calculated the carbon absorbance after 15 minutes. We appreciate your question regarding the rationale for choosing intramuscular injection over intravenous infusion of the secretome. While intravenous (IV) delivery is indeed a common method, we opted for intramuscular (IM) administration for several reasons. Firstly, IM delivery allows the secretome to be deposited directly in the muscle tissue, where it can be gradually released into the bloodstream, potentially providing a more sustained effect. Additionally, muscles have a rich blood supply, which facilitates the secretome's absorption into the circulatory system. The large surface area of the muscle also makes intramuscular administration relatively straightforward and practical. Research supports the effectiveness of intramuscular administration for achieving systemic effects. For example, studies have demonstrated that intramuscular delivery of MSCs can result in systemic benefits (Jahromi & Davis, 2019). Furthermore, research has shown that exosomes, a key component of the secretome, can reach systemic circulation even when administered intramuscularly (Rehorova et al., 2019; Fennel et al., 2024). Therefore, while IV infusion is a commonly used route, intramuscular injection offers unique advantages that align with our study's objectives. We have added this in our discussion section. 5. It should be stated under which conditions diluted exosomes were stored. Thank you for the sugestion, we have added the information in method section: “Diluted exosomes were stored in -80°C for further characterization. ” 6. The morphology of the TEM images is not compatible with the exosome image. The double-membrane structure is not visible. The authors measured exosome diameters, but there is no scale bar in the TEM images. Details regarding the storage conditions of exosomes and the negative-staining method should be specified in the method section. References should be added for the methods used. Thank you for the suggestion we have added the reference for the staining protocol that we used in this study. We also have revised the exosome picture based on the reviewer suggestion. Methods: For TEM analysis, as much as 200 µL of isolated exosomes were diluted using PBS to reach a volume of 1 mL exosome in PBS. Exosomes were dripped onto the 400 mesh Cu coated grid, allowed to absorb, and dried using filter paper. Negative staining was applied based on protocol by Jung and Mun, 2018, using 1% uranyl acetate. The negative staining was dripped on the grid and allowed to be absorbed, then dried with filter paper. After that, the grid stored in an EM grid box for TEM observation. TEM visualizations were performed using JEOL 1400 Transmission Electron Microscope at 120 kV, and images were captured using a fully integrated high resolution camera system (8 million pixel CCD camera). Exosome particle size measurements were carried out using ImageJ software version 1.53K. Figure 3. Size and morphology of isolated exosomes visualization using TEM. The size and morphology of the isolated exosome were varied. The size of the exosome was within the expected size range (30-100 nm). The double membrane appearance is pointed by the black arrow. 7. Authors should indicate the number of animals used in animal experiments. It is inappropriate to perform statistical analysis with parametric tests with the small sample size. Thank you for the suggestion. We have added the information regarding the number of animals in the Methods section. We have 4 groups, with 5 animals in each group, in total 20 animals used in our study. The animal number was calculated using the resource equation method, which states that the E value should be between 10 and 20. The formula for E is: total number of animals minus the total number of groups. In our study, we have 4 groups. Therefore, to keep the E value between 10 and 20, the number of animals in each group should be between 4 and 6 (Charan & Kantharia, 2013). We also conducted statistical analyses using the Kruskal-Wallis and Mann-Whitney tests, and still found a significant difference between the negative control and the dose 3 group. Method: “Twenty male Swiss albino mice 6-8 weeks old, weighing 15 to 25 g, were used in the study. The animal's room temperature is set to 22° ± 3° C, with a relative humidity of 30–70%, 12 hours of light, and 12 hours of darkness. Animals are fed according to laboratory standards and given indefinitely (ad libitum). The animals were maintained under standard conditions according to Regulation of the Head of National Agency of Drug and Food Control (BPOM) No. 7 of 2014 concerning guidelines for in vivo tests [8]. The person conducting the animal handling was not blinded to the treatment group. However, the person conducting the measurement of the carbon clearance assay was blinded to the treatment group”. All data were presented as Mean and SEM. The phagocytic index and spleen CD68 mRNA data were analysed using the Kruskal-Wallis and Mann-Whitney tests. The statistical analysis was done using GraphPad Prism version 9.0.0 (86)." } ] }, { "id": "216932", "date": "24 Oct 2023", "name": "Basak Isildar", "expertise": [ "Reviewer Expertise In vitro and in vivo investigations of human umbilical cord mesenchymal stem cell secretome." ], "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 number of studies examining the immunomodulatory effects of mesenchymal stem cells through the secretome is increasing, and the safety of the conditioned media used needs to be investigated. In this respect, the authors have drawn attention to a current issue, but essential problems need to be clarified before the article is indexed.\n1. First, characterization data of the isolated cells are lacking. Authors must include characterization experiments with immunophenotypic and differentiation data for UCMSCs.\n2. It is not appropriate to store the secretome at -20 °C (especially when miRNA research is involved).\n3. In the introduction section, it is stated that there is limited information in the literature about the immunomodulatory effects of the secretome, and it is claimed that the immunomodulatory effects will be evaluated. There are studies in the literature investigating the immunomodulatory effects of MSC-secretome. The authors did not use these studies for their manuscripts. Additionally, it is unclear how immunomodulatory effects are evaluated. Why has only IL-10 been investigated within the secretome? Why are other cytokines, molecules, and growth factors not mentioned? It should be explained.\n4. In vitro experimental setup is not sufficient to examine immunomodulatory effects. It should be investigated in vivo and the results added. The results of acute toxicity testing are unclear. Why was only IM injection administered? The most common route of administration for conditioned mediums is not IM. Why other routes were not chosen should be stated.\n5. It should be stated under which conditions diluted exosomes were stored.\n6. The morphology of the TEM images is not compatible with the exosome image. The double-membrane structure is not visible. The authors measured exosome diameters, but there is no scale bar in the TEM images. Details regarding the storage conditions of exosomes and the negative-staining method should be specified in the method section. References should be added for the methods used.\n7. Authors should indicate the number of animals used in animal experiments. It is inappropriate to perform statistical analysis with parametric tests with the small sample size.\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? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "12421", "date": "07 Oct 2024", "name": "Dwi Aris AgungNugrahaningsih", "role": "Author Response", "response": "Response to reviewer Reviewer:1 The manuscript investigates important questions however it is not clear what novel information the analyses provide. The abstract should better summarize all the main findings of the manuscript, since it now describes only the results of the in vivo analysis and not the characterization of the in vitro profile. Thank you for the suggestion to improve our manuscript. We have revised the abstract of the manuscript by providing highlight of our study findings. Background: The immune system is a complex network designed to protect the body from harmful pathogen. Phagocytosis process eliminate invaders before they enter the bloodstream. Recent research has highlighted the potential of secreted materials from Mesenchymal Stem Cells (MSCs), called as secretom, as immunomodulatory agent. This study aims to evaluate MSC secretome effect on phagocytosis and its safety. Methods: Characterization of the secretome content was achieved through nanoparticle tractking analysis (NTA), Transmission Elctron Microscopy (TEM), Enzyme-linked Immunosorbent Assay (ELISA), and nanostring. The assessment of immunomodulatory activity was conducted using carbon clearance assay. Additionally, we measure spleen mRNA CD68, and CD206. Safety evaluation involved a single-dose administration of the secretome, followed by acute toxicity testing using fixed dose method. Results: The characterization revealed the presence of interleukin 10 (IL-10), exosome-sized particles, and miRNA within the secretome. Mice treated with the secretome displayed a significantly higher phagocytic index compared to untreated controls and higher CD68 mRNA expression in the spleen. Furthermore, acute toxicity testing showed no significant effects on the mice’s body weight, physical examination results, organ weight, or gross anatomy, indicating a favorable safety profile. Conclusions: This study highlights the novel insights into MSC-derived secretomes, demonstrating their potential as safe and effective immunomodulatory agents. Major criticism The rational of the study and the gap of knowledge is not clear and the analyses performed in vitro and the in vivo are not described as part of the same goal. Why has IL-10 been quantified? Is there any relation between the IL-10 amount in the secretome and the immunomodulatory function? What is the link between the top 10 miR found in the secretome with the in vivo findings? Authors should also better contextualize their findings with what already published in terms of miR characterization. Thank you for the suggestion to improve our manuscript. Our study integrates in vitro and in vivo analyses to provide a comprehensive understanding of the secretome's immunomodulatory effects. The in vitro characterization identifies the content of the secretome, including IL-10, which is known for its role in phagocytic activity and may influence immunomodulation. The in vivo study evaluates the effect of secretome on phagocytic activity. By measuring IL-10, we aim to correlate its levels with observed immunomodulatory effects. Additionally, analyzing the particles in the secretome, and miRNA content helps identify potential molecular mechanisms underlying these effects. This approach bridges the gap between secretome composition and its functional impact, offering insights into the immunomodulatory mechanisms at play. We have corrected the introduction of the manuscript: The immune system is a sophisticated network designed to protect the body from harmful pathogens. It is generally divided into two main categories: the innate immune system and the adaptive immune system [Marshall et al, 2019]. The innate immune system serves as the first line of defence mechanism against pathogens, using processes like phagocytosis to eliminate harmful invaders before they enter the bloodstream and cause further complications [Lim et al, 2017]. Macrophages in the tissue remove pathogens or foreign particles that enter the tissue, while the spleen helps remove pathogens or foreign particles that have entered the bloodstream by filtering the blood and facilitating their destruction [Lewis et al, 2019]. Maintaining homeostasis in the immune system is crucial to ensure that it is prepared to protect the body whenever pathogens or other harmful substances enter. Factors such as daily stress, lifestyle choices, and environmental hazards can weaken the immune system and increase susceptibility to illness. Therefore, it is essential to maintain and enhance immune function to prevent infections and other diseases [Thorbur et al, 2014; Marques et al, 2016] Researchers are finding that the secreted materials from mesenchymal stem cells (MSCs), known as the \"secretome,\" and the liquid containing these materials, referred to as \"conditioned medium,\" are promising as immunomodulatory agents [Muzes & Sipos, 2022; ]. The secretome includes soluble factors like immunomodulatory molecules, cytokines, and growth factors, as well as vesicular factors such as extracellular vesicles (EVs) including exosome [Rostami et al, 2018Munos-Perez et al, 2021]. Notably, MSC-derived exosomes, which are small vesicles containing proteins, nucleic acids (like mRNA and miRNA), and lipids, have shown significant potential [Asgarpour et al, 2020]. Overexpression of IL-10 in the secretome of human umbilical cord MSCs can enhance macrophage function [Jerkic et al, 2019], while MSC-derived exosomes can improve the anti-inflammatory properties of macrophages and aid in reducing inflammation [song et al, 2017]. Additionally, apoptotic bodies from MSCs can influence macrophage behavior in wound healing models, and MSC exosomes have the potential to inhibit the proliferation, activation, and cytotoxicity of natural killer cells [Tang et al, 2022]. Furthermore, miRNAs present in MSC-derived EVs play a crucial role in regulating macrophage functions during inflammation [Wu et al, 2015; Wu et al, 2017]. Although the immunomodulatory effects of the secretome are well-documented, there is limited information on how secretomes derived from human umbilical cord MSCs (UC-MSCs) support immune function in healthy or normal conditions. This study aims to address this gap by evaluating several key aspects of the UC-MSC secretome in a healthy context. We measured interleukin-10 (IL-10) to understand its role in phagocytosis, profiled the miRNA content to uncover the mechanisms behind the secretome’s effects, characterized the extracellular vesicles (EVs) to explore their therapeutic potential, and assessed the impact of the secretome on phagocytosis in vivo. Additionally, we conducted an acute toxicity assay to ensure the safety of UC-MSC-derived secretomes. Methods In the in vivo analysis, healthy mice have been subjected to intramuscular injection of the secretome or control medium. Then they were subjected to carbon clearance assay after 3 days via intravenous injection of carbon ink suspension. What is the rational of the intramuscular injection? Why not perform the IV secretome infusion (as delivery route mostly used)? What is the rational of studying the phagocytic activity in healthy mice? Having the effect in the context of a pathological condition would increase the translational validity of the findings. Thank you for the suggestion to improve our manuscript. Immunomodulatory studies are conducted in healthy animals to establish a baseline understanding of how potential treatments affect the immune system under normal conditions. Healthy animals provide a controlled environment to observe the natural immune responses and assess the impact of interventions without the complications that might arise from pre-existing health conditions. This approach ensures that any observed effects can be attributed to the treatment being studied rather than to underlying health issues. One common method used in these studies is the carbon clearance assay. This assay measures the efficiency of phagocytosis, the process by which immune cells engulf and eliminate particles such as carbon particles. By introducing carbon particles into the bloodstream and monitoring their clearance rate, researchers can evaluate how well the immune system is functioning, particularly the activity of macrophages, which play a crucial role in the immune response. The carbon clearance assay provides valuable insights into how the treatment modulates immune function and can help in understanding its potential therapeutic benefits. We appreciate your question regarding the rationale for choosing intramuscular injection over intravenous infusion of the secretome. While intravenous (IV) delivery is indeed a common method, we opted for intramuscular (IM) administration for several reasons. Firstly, IM delivery allows the secretome to be deposited directly in the muscle tissue, where it can be gradually released into the bloodstream, potentially providing a more sustained effect. Additionally, muscles have a rich blood supply, which facilitates the secretome's absorption into the circulatory system. The large surface area of the muscle also makes intramuscular administration relatively straightforward and practical. Research supports the effectiveness of intramuscular administration for achieving systemic effects. For example, studies have demonstrated that intramuscular delivery of MSCs can result in systemic benefits (Jahromi & Davis, 2019). Furthermore, research has shown that exosomes, a key component of the secretome, can reach systemic circulation even when administered intramuscularly (Rehorova et al., 2019; Fennel et al., 2024). Therefore, while IV infusion is a commonly used route, intramuscular injection offers unique advantages that align with our study's objectives. Reference: Hamidian Jahromi S, Davies JE. Concise Review: Skeletal Muscle as a Delivery Route for Mesenchymal Stromal Cells. Stem Cells Transl Med. 2019 May;8(5):456-465. doi: 10.1002/sctm.18-0208. Epub 2019 Feb 5. PMID: 30720934; PMCID: PMC6477141. Fennel, Z. J., Bourrant, P.-E., Kurian, A. S., Petrocelli, J. J., de Hart, N. M. M. P., Yee, E. M., Boudina, S., Keirstead, H. S., Nistor, G., Greilach, S. A., Berchtold, N. C., Lane, T. E., & Drummond, M. J. (2024). Stem cell secretome treatment improves whole-body metabolism, reduces adiposity, and promotes skeletal muscle function in aged mice. Aging Cell, 23, e14144. https://doi.org/10.1111/acel.14144 Řehořová M, Vargová I, Forostyak S, Vacková I, Turnovcová K, Kupcová Skalníková H, Vodička P, Kubinová Š, Syková E, Jendelová P. A Combination of Intrathecal and Intramuscular Application of Human Mesenchymal Stem Cells Partly Reduces the Activation of Necroptosis in the Spinal Cord of SOD1G93A Rats. Stem Cells Transl Med. 2019 Jun;8(6):535-547. doi: 10.1002/sctm.18-0223. Epub 2019 Feb 25. PMID: 30802001; PMCID: PMC6525562. We have revised the discussion section to include this important points. A characterization of the immune profile of the circulating phagocytic cells after secretome treatment is needed. We agree that profiling circulating phagocytic cells after secretome treatment would offer valuable insights into the mechanism of the secretome as an immunomodulator. Unfortunately, we do not have data on the phagocytic profile in the circulation. However, we do have mRNA expression data for CD68 and CD206 from the spleen. The spleen is a key organ in the immune system, responsible for filtering the blood and removing foreign materials. To assess macrophage activity, we measured the mRNA levels of CD68, a common marker for macrophages, and CD206, a marker for anti-inflammatory macrophages, in the spleen. We have revised the methods, results, and discussion sections to reflect this update. Method: Spleen CD68 mRNA Analysis Total mRNA was extracted from the spleen using the FavorPrep™ Tissue Total RNA Mini Kit (Favorgen) according to the instructions provided in the kit. The extracted mRNA was then converted into complementary DNA (cDNA) using the ReverTraAce™ qPCR RT Master Mix (Toyobo). The mRNA expression was evaluated using the RT-qPCR SensiFAST™ SYBR® Low-ROX Kit (Bioline), with Beta Actin as the housekeeping gene. The primers used were: F 5'-TCT CCA CCT TCC AGC AGA TGT-3' R 5'-GCT CAG TAA CAG TCC GCC TAGA-3'. The CD68 primers were: F 5'- CGC AGA CAA TCA ACC TA-3' R 5'-GGC ATG GTG AAG TGA GG-3'. Result: Spleen CD8 and CD206 mRNA expression The CD68 mRNA expression of the spleen is higher in dose 3 compare to those on negative control group. Figure 6 present the spleen CD68 mRNA expression. Figure 6. Spleen CD68 mRNA expression in each group of treatment. The spleen CD68 mRNA expression was significantly higher in dose 3 compare to those on negative control. A negative control is without secretome treatment. * p < 0.05 vs negative control Acute toxicity test: no details of the kind of observations and measurements have been provided. In the results, it has been reported only the variance of the body weight of living mice or of post mortem organs. Please provide more details. Thank you for the suggestion. We conducted the acute toxicity test using the fixed dose method (OECD Acute Toxicity Test No. 420 and BPOM 2014) to determine whether a single injection of the secretome at the highest dose causes toxicity in animals. This test is an internationally accepted protocol for evaluating the toxicity of single exposures to substances. Briefly, after administering the injection, we observed the animals' behavior at specific time points. We also measured their body weight and, finally, sacrificed the animals to examine the macroscopic appearance of their organs and record organ weights. We agree that our method and results sections may not have clearly described the test conducted. Here is the revised version of the method and results sections related to the acute toxicity test. Methods (acute toxicity) Female Swiss albino mice were used in this test. Healthy female 8-10 weeks mice were used because, generally, female animals are more sensitive to toxic substances than male animals [8]. The method for conducting the acute toxicity test was modified fixed dose according to Regulation of the Head of National Agency of Drug and Food Control (BPOM) No. 7 of 2014 [8]. There are two parts to the fixed-dose methods: preliminary and main parts. In this preliminary part, we used two mice divided into two groups, the treatment group, and the control group. The mice received secretome or MEM-α basal medium intramuscularly with the highest possible volume that can be given intramuscularly to mice, which was 0.05 mL in each thigh or 0.1 mL per mouse. The mice were randomly assigned to receive treatment or control. Observations of their behavior and clinical signs were conducted in the first 30 minutes and every 4 hours for 24 hours. After 24 hours, the mice were observed daily until day 15. Since there was no mortality in the preliminary parts of the acute toxicity test, the main test was carried out with the same dose as the dose used in the preliminary part. In the main test, we used four mice in the secretome group and one mouse in the control group. The mice were observed in the first 30 minutes after injection, every 4 hours during 24 hours, and every 24 hours until day 15. On day 15, all mice were killed, and all vital organs were examined. The behavioral examination includes the following assessments: skin condition, fur piloerection, corneal reflex and corneal opacity, mucous membrane color, type and rate of respiration, palpebral reflexes, digit reflexes, paralysis, seizures, torticollis, somatomotor activity, reverse walking, tremors, salivation, sleep patterns, defecation, and urination. Result (acute toxicity) In the preliminary part of the acute toxicity test, the mice received secretome or MEM-α basal medium intramuscularly of the highest possible volume that can be given intramuscularly to mice which is 0.05 mL in each thigh or 0.1 mL per mice. There was no abnormality in the following behavioral assessment: skin condition, fur piloerection, corneal reflex and corneal opacity, mucous membrane color, type and rate of respiration, palpebral reflexes, digit reflexes, paralysis, seizures, torticollis, somatomotor activity, reverse walking, tremors, salivation, sleep patterns, defecation, and urination of the mice in the control and treatment groups. Reference: OECD (2002), Test No. 420: Acute Oral Toxicity - Fixed Dose Procedure, OECD Guidelines for the Testing of Chemicals, Section 4, OECD Publishing, Paris, https://doi.org/10.1787/9789264070943-en. Minor criticism In the introduction, authors underline the MSC ability to differentiate into specialized cells as main pharmacological activity. However, the study is focused on the use of MSC-derived secretome, the a-cellular counterpart. Please modify. Thank you, we have modified the introduction. Reviewer 2 The number of studies examining the immunomodulatory effects of mesenchymal stem cells through the secretome is increasing, and the safety of the conditioned media used needs to be investigated. In this respect, the authors have drawn attention to a current issue, but essential problems need to be clarified before the article is indexed. 1. First, characterization data of the isolated cells are lacking. Authors must include characterization experiments with immunophenotypic and differentiation data for UCMSCs. Thank you for your recommendation. We have included the secretome provided by the commercial supplier, PT Tristem Indonesia. We have updated the characterization and modified the methods and results sections based on your suggestions. Method: “The characterization of MSCs was performed using flow cytometry at the commercial lab testing facility, PharmaMetricLabs®. Several parameters were measured, including CD105, CD90, CD73, CD45, CD34, CD14, HLA-DR, and CD19. “ Result: Characterization of MSCs The characterization of MSCs was performed using flow cytometry (FACS). High percentages of CD105, CD90, and CD73 were observed, while CD45, CD34, CD14, HLA-DR, and CD19 were present in low percentages. The complete results are presented in Table 1. Table 1. MSC characterization result. Parameter Result CD105 99,98% CD90 99,97% CD73 100% CD45 0,75% CD34 0,22% CD14 0,15% HLA-DR 0% CD19 0,75% 2. It is not appropriate to store the secretome at -20 °C (especially when miRNA research is involved). Thank you for your observation. In our study, we stored the secretome at -80°C for long-term preservation. However, for short-term storage, such as when preparing for studies, we stored the secretome at -20°C. Research has shown that storage at -20°C does not significantly affect miRNA levels for up to 4-5 years (Grasedieck et al., 2012). We also update the method section to include this information. Method: … The secretome was stored at -80°C for long-term preservation. However, for short-term storage, such as when preparing for studies, we stored the secretome at -20°C….. Reference Grasedieck, S., Schöler, N., Bommer, M. et al. Impact of serum storage conditions on microRNA stability. Leukemia 26, 2414–2416 (2012). https://doi.org/10.1038/leu.2012.106 3. In the introduction section, it is stated that there is limited information in the literature about the immunomodulatory effects of the secretome, and it is claimed that the immunomodulatory effects will be evaluated. There are studies in the literature investigating the immunomodulatory effects of MSC-secretome. The authors did not use these studies for their manuscripts. Additionally, it is unclear how immunomodulatory effects are evaluated. Why has only IL-10 been investigated within the secretome? Why are other cytokines, molecules, and growth factors not mentioned? It should be explained. protein concentration was very low 0.04 ug/ul and 0.45 ug/ul. Thank you for your feedback. We have addressed your concerns as follows: Introduction: We have now included references to studies on MSC-secretome and its immunomodulatory effects in the introduction. This addition highlights the existing research and aligns our work with the current literature. Evaluation of Immunomodulatory Effects: We have clarified the criteria and methods used to evaluate the immunomodulatory effects. Specifically, we have detailed why IL-10 was selected for measurement. Protein Concentration: We acknowledge that the concentration of IL-10 was indeed very low (0.04 µg/µl and 0.45 µg/µl). We have addressed this issue in the discussion section, providing an explanation and considering its implications for our findings. Revised sections, including these points, are now incorporated into the introduction and discussion. 4. In vitro experimental setup is not sufficient to examine immunomodulatory effects. It should be investigated in vivo and the results added. The results of acute toxicity testing are unclear. Why was only IM injection administered? The most common route of administration for conditioned mediums is not IM. Why other routes were not chosen should be stated. We conducted the immunomodulatory effect in vivo using carbon clearance assay. We describe the assay in the method section. In the assay the live animal was injected with carbon solution and we calculated the carbon absorbance after 15 minutes. We appreciate your question regarding the rationale for choosing intramuscular injection over intravenous infusion of the secretome. While intravenous (IV) delivery is indeed a common method, we opted for intramuscular (IM) administration for several reasons. Firstly, IM delivery allows the secretome to be deposited directly in the muscle tissue, where it can be gradually released into the bloodstream, potentially providing a more sustained effect. Additionally, muscles have a rich blood supply, which facilitates the secretome's absorption into the circulatory system. The large surface area of the muscle also makes intramuscular administration relatively straightforward and practical. Research supports the effectiveness of intramuscular administration for achieving systemic effects. For example, studies have demonstrated that intramuscular delivery of MSCs can result in systemic benefits (Jahromi & Davis, 2019). Furthermore, research has shown that exosomes, a key component of the secretome, can reach systemic circulation even when administered intramuscularly (Rehorova et al., 2019; Fennel et al., 2024). Therefore, while IV infusion is a commonly used route, intramuscular injection offers unique advantages that align with our study's objectives. We have added this in our discussion section. 5. It should be stated under which conditions diluted exosomes were stored. Thank you for the sugestion, we have added the information in method section: “Diluted exosomes were stored in -80°C for further characterization. ” 6. The morphology of the TEM images is not compatible with the exosome image. The double-membrane structure is not visible. The authors measured exosome diameters, but there is no scale bar in the TEM images. Details regarding the storage conditions of exosomes and the negative-staining method should be specified in the method section. References should be added for the methods used. Thank you for the suggestion we have added the reference for the staining protocol that we used in this study. We also have revised the exosome picture based on the reviewer suggestion. Methods: For TEM analysis, as much as 200 µL of isolated exosomes were diluted using PBS to reach a volume of 1 mL exosome in PBS. Exosomes were dripped onto the 400 mesh Cu coated grid, allowed to absorb, and dried using filter paper. Negative staining was applied based on protocol by Jung and Mun, 2018, using 1% uranyl acetate. The negative staining was dripped on the grid and allowed to be absorbed, then dried with filter paper. After that, the grid stored in an EM grid box for TEM observation. TEM visualizations were performed using JEOL 1400 Transmission Electron Microscope at 120 kV, and images were captured using a fully integrated high resolution camera system (8 million pixel CCD camera). Exosome particle size measurements were carried out using ImageJ software version 1.53K. Figure 3. Size and morphology of isolated exosomes visualization using TEM. The size and morphology of the isolated exosome were varied. The size of the exosome was within the expected size range (30-100 nm). The double membrane appearance is pointed by the black arrow. 7. Authors should indicate the number of animals used in animal experiments. It is inappropriate to perform statistical analysis with parametric tests with the small sample size. Thank you for the suggestion. We have added the information regarding the number of animals in the Methods section. We have 4 groups, with 5 animals in each group, in total 20 animals used in our study. The animal number was calculated using the resource equation method, which states that the E value should be between 10 and 20. The formula for E is: total number of animals minus the total number of groups. In our study, we have 4 groups. Therefore, to keep the E value between 10 and 20, the number of animals in each group should be between 4 and 6 (Charan & Kantharia, 2013). We also conducted statistical analyses using the Kruskal-Wallis and Mann-Whitney tests, and still found a significant difference between the negative control and the dose 3 group. Method: “Twenty male Swiss albino mice 6-8 weeks old, weighing 15 to 25 g, were used in the study. The animal's room temperature is set to 22° ± 3° C, with a relative humidity of 30–70%, 12 hours of light, and 12 hours of darkness. Animals are fed according to laboratory standards and given indefinitely (ad libitum). The animals were maintained under standard conditions according to Regulation of the Head of National Agency of Drug and Food Control (BPOM) No. 7 of 2014 concerning guidelines for in vivo tests [8]. The person conducting the animal handling was not blinded to the treatment group. However, the person conducting the measurement of the carbon clearance assay was blinded to the treatment group”. All data were presented as Mean and SEM. The phagocytic index and spleen CD68 mRNA data were analysed using the Kruskal-Wallis and Mann-Whitney tests. The statistical analysis was done using GraphPad Prism version 9.0.0 (86)." } ] } ]	1	https://f1000research.com/articles/12-421
https://f1000research.com/articles/13-1141/v1	07 Oct 24	{ "type": "Policy Brief", "title": "Upskilling India: The national policy on skill development and entrepreneurship", "authors": [ "Shena Shaikh", "M. P Ganesh", "M. P Ganesh" ], "abstract": "Background India’s National Policy for Skill Development and Entrepreneurship (NPSDE) was designed to capture the demographic dividend and upskill India’s youth, creating an ‘Athmanirbhar Bharat’ (self-reliant India) and in the process, also drive economic growth.\n\nPolicy and Implications The NPSDE’s dual focus on skill development and entrepreneurship was intended to create a framework for empowering India’s workforce and fostering a culture of innovation. However, the policy has encountered several issues, including the ineffective functioning of Sector Skill Councils (SSCs), inadequate infrastructure, and insufficiently skilled trainers. Additionally, the policy’s efforts to include marginalized groups, particularly women, have fallen short due to entrenched social barriers and gender biases, impacting the effectiveness of training programs.\n\nRecommendations To improve the effectiveness of the NPSDE, we propose the following recommendations -adopt an entrepreneurial ecosystem approach to enhance coordination and support within the skill development framework; explicitly define ‘skill’ and ‘skilling’ to better align with socio-political realities and address barriers faced by marginalized individuals; and design training initiatives with an empowerment perspective, focusing on access to resources, agency, and social change. We feel these steps can help direct the NPSDE to create a more inclusive and impactful skilling environment.\n\nConclusions While the NPSDE represents a significant effort towards upskilling India and fostering self-reliance and entrepreneurship, its implementation has revealed critical limitations. The policy’s progress has been insufficient, with persistent issues in meeting industry needs and addressing socio-economic barriers. Future revisions of the policy should focus on systemic improvements, adopting a more inclusive approach to skilling, and addressing the socio-political dimensions of skill valuation to better support India’s developmental aspirations.", "keywords": [ "India", "Upskilling", "Development Policy", "Entrepreneurship" ], "content": "Introduction\n\nIn its 2024 annual budget presentation, India’s right wing BJP led government emphasized a concentrated effort in shaping public policy to achieve a ‘Vikshit Bharat’ (Developed India) by 2047. It aims to primarily achieve this by bolstering its flagship skilling and capability enhancement initiatives. Betting on India’s youth being a significant driver of the economy, the government is attempting to emphasize skill development to address the needs of and prepare a growing population to become ‘Atmanirbhar’ or ‘self-reliant.’ In 2015, as a part of the Skill India Mission, the government of India launched The National Policy for Skill Development and Entrepreneurship (NPSDE), intending to meet the challenge of skilling India at scale with “speed, standard, and sustainability” (Ministry of Skill Development and Entrepreneurship, 2015, p.3). In its attempt to supersede the policy established by the previous congress-led government, which aimed to train 150 million people by 2022, the government sought to re-launch the initiative by setting a lofty target of training 500 million people by 2022—a target which they quickly sought to de-link themselves from (Nanda, 2017).\n\nRecognizing India’s sizeable demographic dividend, the policy was established to empower and skill India’s growing labour force – an estimated 62% of its population. Despite this significant proportion of the population belonging to the labour force, the government was concerned with the fact that only a fraction of that population – 4.69%, had ‘formal’ vocational skills and had undergone training, as opposed to 52% in the USA, 68% in the UK, 75% in Germany, 80% in Japan, and 96% in South Korea (Ministry of Skill Development and Entrepreneurship, 2015). According to several projections, India’s labour force is expected to increase by 32% by 2035 (Ministry of Skill Development and Entrepreneurship, 2015). Such a large population of ‘unskilled’ labour force was, thus, seen as a significant and formidable challenge India had to overcome.\n\nCentral to the NPSDE is an acknowledgment that promoting entrepreneurship is integral to a successful skills strategy. Thus, it set out with the vision to “create an ecosystem of empowerment by skilling on a large scale at speed with high standards and to promote a culture of innovation based entrepreneurship which can generate wealth and employment to ensure sustainable livelihoods for all citizens in the country” (Ministry of Skill Development and Entrepreneurship, 2015, p.11). The policy has two main objectives: (a) empower the individual, enabling them to realize their full potential through lifelong learning, where competencies are accumulated via ‘credible’ instruments, and (b) coordinate and strengthen factors essential for growth and entrepreneurship across the country.\n\nThe policy has two main components – a skill component and an entrepreneurship component. The skill component of the policy aims to target critical challenges within the skill domain, such as low aspiration levels, poor integration with formal education, insufficient emphasis on outcomes, and the quality of training infrastructure and instructors. Its goals include aligning skill supply with demand, addressing current skill gaps, fostering industry involvement, implementing a quality assurance framework, harnessing technology, and advancing apprenticeship programs to address these challenges effectively. The policy also seeks to enhance equitable access to skill development opportunities for women and other socially and geographically marginalized groups. On the other hand, the entrepreneurship component of the policy aims to cultivate an entrepreneurial culture by advocating for and integrating entrepreneurship education into formal and skill-based education systems. It seeks to bolster support for entrepreneurs by facilitating access to credit, establishing market linkages, and nurturing innovation-driven and social enterprises. In particular, the policy proposes measures to encourage entrepreneurship among women and address specific entrepreneurial requirements of socially and geographically marginalized and disadvantaged groups (Ministry of Skill Development and Entrepreneurship, 2016).\n\nThe policy, a pivotal tool in implementing the Skill India Mission, laid the framework for establishing actionable steps to build the necessary infrastructure. The government decided to utilize a ‘mission mode’ approach to meet the policy’s objectives and subsequently launched the National Skill Development Mission to achieve the goals delineated in the policy and contains sub-missions of institutional training, building infrastructure, facilitating convergence of skill development efforts, improving quality of trainers, facilitating oversees employment, emphasizing sustainable livelihoods, and leveraging existing public infrastructure. The institutional mechanisms for achieving the objectives of the Mission were divided into a three-tier structure at the Centre to steer, drive, and execute the Mission’s objectives.\n\nAt the apex level, there was a Governing Council, a Steering Committee, and a Mission Directorate, supported by an Executive Committee as the executive arm of the Mission. At the State level, States were encouraged to establish State Skill Development Missions (SSDM) similar to the National Skill Development Mission, each with its own Steering Committee and Mission Directorate. District Committees operated at the functional tier to support these State-level efforts. The Mission Directorate was supported by three other institutions: the National Skill Development Agency (NSDA), the National Skill Development Corporation (NSDC), and the Directorate General of Training (DGT). These institutions had horizontal and vertical linkages with the Mission Directorate to facilitate the smooth functioning of the national institutional mechanism. Further, to ensure that all stakeholders work in accordance with the needs of the industry, the government set up Sector Skill Councils (SSCs), which are industry-led and industry-governed bodies responsible for identifying industry requirements, accrediting, and certifying qualified trainees.\n\n\nPolicy outcomes and implications\n\nThe NPSDE had been designed to be an outcome-oriented policy, requiring regular monitoring and evaluation of initiatives through a Policy Implementation Unit (PIU). In 2015, India needed to skill a million people a week to meet targets, costing roughly Rs 30,000 per person (Punj, 2015). While the policy set out with an ambitious target of skilling 500 million people by 2022, a target widely regarded as unrealistic, by 2017, official data showed that only 11.7 million people were trained between 2015-17, a clear indication that policy targets were not being met (Srivas, 2018) causing the government to adjust its projections.\n\nThe Ministry of Skill Development and Entrepreneurship launched its flagship scheme, the Pradhan Mantri Kaushal Vikas Yojana (PMKY), aiming to capitalize on the demographic dividend and equip India’s youth with industry-relevant skills that would help facilitate upward economic mobility. By 2024, the government reported that the Skill India mission had successfully trained 14 million youth and upskilling and re-skilling 540,000 youth (Government of India, 2024), a mere 3.5% of its initial target. In the 2024 budget, the scheme was granted a budget of 2686 crores (313 million Dollars).\n\nIn 2017, two years after the policy was launched, a Committee for Rationalisation and Optimisation of the Functioning of the Sector Skill Councils was set up to evaluate SSCs, a crucial component of the Skill India Mission. The report by India Committee for Rationalization and Optimization of the Functioning of the Sector Skills Councils (2016) made several significant observations. Firstly, the 2015 policy removed the labour market information system (LMIS), an essential tool that helped assist in the planning and delivery of training activities—this impaired SSCs from reporting real-time data and demand for skills. Secondly, while the policy listed specific ministries as high importance due to their capacity to generate employment, such as commerce and industry, textiles, and tourism, they have not been assigned skill development tasks. The ministries that do uptake skilling tasks often cannot meet skilling requirements at a competitive standard because they lack the required infrastructure and qualified trainers. While the SSCs have engaged numerous assessing bodies, the proficiency of assessors remains notably inadequate. Many assessors possess only diplomas or degrees lacking practical industry experience. SSCs, driven primarily by revenue considerations, have sought to conduct a high volume of assessments and certifications, often overlooking the critical criteria of competence acquisition and assessment quality. Consequently, sectoral industries are reluctant to employ certified trainees under such conditions.\n\nThe NPSDE emphasizes these training programs to foster entrepreneurship among rural India’s youth and marginalized groups and address their unemployment challenges, paying particular emphasis to rural women. While the policy was designed to promote gender mainstreaming in skill development and articulated the importance of gender inclusivity, its implementation unfortunately fell short of achieving it. The policy delineated the inclusion of marginalized groups and the promotion of women’s skilling as pivotal tenants. Yet, it is not grounded in reality because it is isolated from the vagaries of prevailing social norms. Skilling women in India presents a significant challenge due to several factors.\n\nA high percentage of India’s female workforce participates in the informal economy, which is rife with gender discrimination, wage imparity, and job insecurity (Boeri, 2018; Paula, 2002). While skill training endeavours aim to help women become entrepreneurs and move into the formal economy, they often reinforce traditional gender roles by boosting stereotypical skill programs for women, such as cosmetology. Further, while the programs under the Skill India mission have little success in securing employability for the trainees overall (Nanda, 2021), they find it challenging to find placement for women trainees and retain them in their jobs (Pande, 2017). Women face remarkable societal barriers that hinder entrepreneurial pursuits and financial independence (Khandelwal & Sehgal, 2018; Sen, 1993; Subramaniam, 2011) not limited to social norms and biases, access to tools for development such as education, safe connectivity, and social and legal protection. The policy does not accommodate for gender disparity, discrimination, or societal barriers that women and other marginalized individuals may face which may hinder their participation and post-intervention success.\n\nGiven the current limitations of the National Policy on Skill Development and Entrepreneurship, we propose the following recommendations that may be relevant to the upcoming policy review.\n\n\nActionable recommendations\n\nThe policy emphasizes the need to “create an ecosystem of empowerment by skilling on a large scale at speed with high standards and to promote a culture of innovation-based entrepreneurship which can generate wealth and employment to ensure sustainable livelihoods for all citizens in the country” (Ministry of Skill Development and Entrepreneurship, 2015, p.11). Yet, it has failed to consider the ground realities of India, which have resulted in limited impact. Despite these attempts at skilling, the International Labor Organization (2024) reports that youth unemployment rates in India are higher than the global average, with the unemployment rate of youths with graduate degrees (29.1%) being nine times higher than youths who are illiterate (3.4%). These statistics are worse for young graduate women.\n\nPrimarily, we suggest that as the ministry aims to create an ‘ecosystem of empowerment,’ taking on an entrepreneurial ecosystem approach (Acs et al., 2014, 2018) may help provide relevant insights into how best to design policy to ensure sustainable, ground-up impact. Creating an environment conducive to productive entrepreneurial pursuits requires carefully considering the complex interactions at various ecosystem levels (Acs et al., 2023). Dedicated efforts to enhance multipolar coordination between stakeholders are essential for ecosystem operations’ smooth governance (Motoyama & Knowlton, 2016). Therefore, policy interventions that aim to develop supportive ecosystems must focus on how the entire ecosystem functions to support new trainees and entrepreneurs.\n\nFurther, in agreement with Gooptu (2018), we think it imperative that the policy drafters explicitly define what they mean by ‘skill’ and ‘skilling’ as the concept of skill is socially constructed and carries a heavy connotation of value – assigned for both the job and the worker through socio-politically driven mechanisms and institutions (Gooptu, 2018). The neo-liberalization of skilling reduces individuals to the skills they can provide, which places an additional burden of self-improvement onto the individual (Urciuoli, 2008). While in tune with the government’s agenda of building a self-reliant India, this fails to account for generational societal and cultural barriers faced by marginalized individuals. Periods of skill-intensive training and subsequent development in India has led to ‘exclusive growth’, ensuring that skilling leads to labour that benefits the rich (Ghose, 2023).\n\nFurther, we think there is a need to design training initiatives with an empowerment lens. Drawing on Kabeer (1999), women’s skilling activities should be designed by considering (a) the level of access to resources women have, (b) the agency that allows them to utilize and benefit from their resources, and (c) track achievements that enable a sound understanding of where the initiatives lack and can improve. We call for a shift in perspective from considering entrepreneurial skilling activities as merely a way to gain income to a way to bring about significant social change and emancipation (Branzei, 2012; Calas et al., 2009; Rindova et al., 2009).\n\n\nConclusion\n\nThe National Policy for Skill Development aims to address the country’s substantial skilling needs and foster a culture of self-reliant development and entrepreneurship. The policy underscores the importance of utilizing India’s demographic dividend through robust skill development and entrepreneurial endeavours. However, its implementation has revealed significant challenges which have led to inadequate progress towards meeting policy targets.\n\nIn 2024, data indicate that only a fraction of the projected number of individuals have received training, further illustrating the policy’s struggle to meet its lofty goals. Key issues include the ineffective functioning of SSCs, inadequate infrastructure, insufficiently skilled trainers, and an overall lack of alignment between training outcomes and industry needs. The jobs that are the focus of training are scarce, and trainees do not receive adequate training for the jobs in demand. Additionally, the policy’s focus on skilling does not fully address the socio-economic barriers faced by marginalized groups, particularly women, whose participation and post-training success have been constrained by entrenched gender biases and socio-cultural norms.\n\nThe policy’s shortcomings highlight the necessity for re-evaluating its approach to skilling and entrepreneurship. We recommend that future revisions of the policy consider adopting an entrepreneurial ecosystem approach to focus on developing India’s entrepreneurial ecosystem as a whole, and enhance the coordination and effectiveness of skill development initiatives. This approach emphasizes the need for a supportive environment that nurtures entrepreneurial activities and addresses the systemic barriers individuals face. Furthermore, a more nuanced understanding of what constitutes ‘skill’ and ‘skilling’ is essential, recognizing the socio-political dimensions of skill valuation and ensuring that skilling initiatives contribute to equitable growth and social change.\n\nIn summary, while the NPSDE represents a commendable effort towards achieving a developed India, its current trajectory reveals critical gaps that must be addressed. By focusing on systemic improvements and adopting a more inclusive and realistic approach, future policies can better support India’s aspiration to leverage its demographic potential for sustainable economic growth and social advancement.\n\n\nEthics and consent\n\nEthical approval and Consent were not required.", "appendix": "Data availability\n\nNo data associated with this article.\n\n\nReferences\n\nAcs ZJ, Autio E, Szerb L: National systems of entrepreneurship: Measurement issues and policy implications. Res. Policy. 2014; 43(3): 476–494. Publisher Full Text\n\nAcs ZJ, Estrin S, Mickiewicz T, et al.: Entrepreneurship, institutional economics, and economic growth: An ecosystem perspective. Small Bus. Econ. 2018; 51(2): 501–514. Publisher Full Text\n\nAcs ZJ, Lafuente E, Szerb L: Introduction: Entrepreneurial ecosystems.Acs ZJ, Lafuente E, Szerb L, editors. The Entrepreneurial ecosystem: Palgrave studies in entrepreneurship and society. Palgrave Macmillan; 2023; pp. 1–28. Publisher Full Text\n\nBoeri N: Challenging the gendered entrepreneurial subject: Gender, development, and the informal economy in India. Gend. Soc. 2018; 32(2): 157–179. Publisher Full Text\n\nBranzei O: Social change agency under adversity: How relational processes (re) produce hope in hopeless settings.Golden-Biddle K, Dutton J, editors. Using a positive lens to explore social change in organizations: Building a theoretical and research foundation. Routledge; 2012; pp. 21–47.\n\nCalas M, Smircich L, Bourne K: Extending the boundaries: Reframing ‘entrepreneurship as social change’ through feminist perspectives. Acad. Manag. Rev. 2009; 34(3): 552–569. Publisher Full Text\n\nGhose AK: India’s exclusive growth. Econ. Polit. Wkly. 2023; 58(6).\n\nGooptu N: JSAD special issue on skill development in India. J. South Asian Dev. 2018; 13(3): 241–248. Publisher Full Text\n\nGovernment of India: Budget 2024-2025: Speech of Nirmala Sitharaman, minister of finance. Ministry of Finance; 2024, July 23. Reference Source\n\nInternational Labour Organization: India employment report 2024: Youth employment, education and skills. International Labour Office; 2024.\n\nKabeer N: Resources, agency, achievements: Reflections on the measurement of women’s empowerment. Dev. Chang. 1999; 30(3): 435–464. Publisher Full Text\n\nKhandelwal P, Sehgal A: Exploring work-family interface for Indian women entrepreneurs. Gender in Management. 2018; 33(3): 203–216. Publisher Full Text\n\nMinistry of Skill Development and Entrepreneurship: National Policy for Skill Development and Entrepreneurship 2015. Government of India; 2015. Reference Source\n\nMinistry of Skill Development and Entrepreneurship: Annual Report 2015-2016. Government of India; 2016. Reference Source\n\nMotoyama Y, Knowlton K: From resource munificence to ecosystem integration: the case of government sponsorship in St. Louis. Entrep. Reg. Dev. 2016; 28(5–6): 448–470. Publisher Full Text\n\nNanda PK: Govt abandons goal of training 500 million people in new skills by 2022. The Mint; 2017, June 8. Reference Source\n\nNanda PK: Skills mission underperforms on training, placement goals. The Mint; 2021, August 4. Reference Source\n\nPande R: Get the policies right first: How to get India’s women into the workforce. Business Standard; 2017, March 17. Reference Source\n\nPaula K: A sectoral approach to the study of gender constraints on economic opportunities in the informal sector in India. Gend. Soc. 2002; 16(3): 285–302.\n\nIndia Committee for Rationalization and Optimization of the Functioning of the Sector Skills Councils: Report of the Committee for Rationalization & Optimization of the Functioning of The Sector Skill Councils: Volume I. Ministry of Skill Development and Entrepreneurship; 2016. Reference Source\n\nPunj S: The skill that wasn’t. India Today; 2015, October, 25. Reference Source\n\nRindova V, Barry D, Ketchen DJ: Entrepreneuring as emancipation. Acad. Manag. Rev. 2009; 34(30): 477–491. Publisher Full Text\n\nSen A: The economics of life and death. Sci. Am. 1993; 268: 40–47. Publisher Full Text\n\nSrivas A: Top-Level Exits at NSDC as Modi’s Skill India Agenda Still Struggles to Make Headway. The Wire; 2018, October, 16. Reference Source\n\nSubramaniam M: Grass roots and poor women’s empowerment in rural India. Int. Sociol. 2011; 27(1): 72–95. Publisher Full Text\n\nUrciuoli B: Skills and selves in the new workplace. Am. Ethnol. 2008; 35(2): 211–228. Publisher Full Text" }	[ { "id": "334370", "date": "09 Nov 2024", "name": "Amishi Arora", "expertise": [ "Reviewer Expertise My areas of research has been on Entrepreneurship. cyber security", "education reengineering", "Human resource development", "etc." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article provides a comprehensive analysis of India's National Policy for Skill Development and Entrepreneurship (NPSDE) in the context of the country’s aspiration to achieve a “Developed India” by 2047. The piece effectively outlines the historical background, objectives, and challenges of the policy, alongside the structural and societal barriers limiting its success. The introduction provides an insightful overview, highlighting the government’s goal to leverage India's demographic dividend through skill development. This contextual foundation helps readers understand the urgency behind the skilling initiatives and the immense scale of the government’s targets. The detailed breakdown of the NPSDE’s components, such as the skill and entrepreneurship dimensions, illustrates the multi-faceted approach intended by the government. Each section dives into specific areas—such as the institutional structure, Sector Skill Councils (SSCs), and budgetary allocations—offering readers a clear picture of how the policy operates at both the central and state levels. The challenges described around SSCs, limited alignment with industry needs, and suboptimal trainer quality provide a realistic look at why NPSDE has struggled to meet its targets. The article’s exploration of gender disparities and marginalized groups’ challenges is especially impactful, bringing to light the socio-cultural barriers impeding women’s and rural communities’ participation in the formal economy. Here, the authors do well to critique the policy's limitations in addressing these unique obstacles and the social norms that hinder entrepreneurial activities for marginalized individuals. The recommendations add value by proposing actionable changes that address both structural and societal limitations. The suggestion to adopt an entrepreneurial ecosystem approach is particularly compelling, as it emphasizes the need for cohesive support across various levels of the economy. By urging a shift in the government’s perspective—seeing skill development not just as an economic endeavor but as a vehicle for social change—the recommendations align well with the article’s critique of the policy’s current approach. Some areas for improvement:\nClarification of terms: It could further benefit from defining key terms like \"skill\" and \"skilling\" at the outset to align readers with the socio-economic connotations discussed later in the article. Expanded recommendations: Recommendations could expand on how the government might tackle specific socio-cultural norms that restrict women’s and marginalized groups’ participation in the economy.\nIn conclusion, this article offers a well-researched and critical evaluation of the NPSDE, shedding light on the importance of structural and societal reforms in realizing India’s development goals. The nuanced recommendations align well with the identified issues and suggest practical solutions that would improve the policy's inclusiveness and effectiveness. With these suggestions implemented, the NPSDE could move closer to fostering a truly self-reliant India.\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": [] } ]	1	https://f1000research.com/articles/13-1141
https://f1000research.com/articles/13-524/v1	22 May 24	{ "type": "Research Article", "title": "Experience of observation skill workshop intervention for ophthalmologists in fellowship training", "authors": [ "Snigdha Snigdha", "Avinash Pathengay", "Anamika Patel", "Shefali Pandey", "Shobha Mocherla", "Ruby Kala Prakasam", "Avinash Pathengay", "Anamika Patel", "Shefali Pandey", "Shobha Mocherla", "Ruby Kala Prakasam" ], "abstract": "Background To gauge the impact of an interventional workshop conducted to measure the observation skills of 34 postgraduates during induction into an ophthalmology fellowship.\n\nMethods A seven-hour workshop was conducted with the ophthalmology trainees. Trainees from the 2022 batch of ophthalmology fellowships (21 females and 13 males) were included in the study. The pre-workshop assessment comprised two non-clinical images to spot the difference and five clinical images from various subspecialties of ophthalmology. This was followed by workshop and Post workshop assessment. The pre- and post-observation grades of participants were then compared by masked ophthalmologists. The Wilcoxon signed-rank test was used to compare scores at two time points, with a p-value < 0.05 for statistical significance.\n\nResults Statistical analysis revealed that the observation skill score was significantly higher after the workshop intervention (Md = 4.00, n = 34) compared to the pre-workshop score (Md = 1.85, n = 34), p-value = 0.000.\n\nConclusions Workshops on specific/selected foundational skills, such as observation skills and communication skills, must be integrated into the curricula of basic medical degree and specialty medicine to equip medical professionals with attentive observation and deep learning.", "keywords": [ "Observation skill", "Communication skill", "Ophthalmology education", "Workshop intervention", "Self-rating questionnaire" ], "content": "Practice points\n\n\n\n• Observation is a core skill in the repertoire of foundational skills that enhance medical professionalism, making clinicians good collaborators and communicators with peers and patients.\n\n• Structured training in observational skills could help to improve clinical observation and related clinical diagnoses, sensitizing clinicians to the functional vulnerability of patients, and hastening collaborative decision making, treatment plans, and patient outcomes.\n\n\nIntroduction\n\nObservation refers to gathering sensorial information, and learning refers to making sense of these observations based on previous knowledge, discerning (the commonalities and differences), deducing (combing and appropriately reacting to the input received), and differentiating (the rope from a snake). Such observational learning helps form perceptions and improve functioning. ‘Observation skill’ is a quintessential foundational ‘skill,’ requiring its cultivation and refinement from the moment one enters the medical profession. In medicine, observational skills are fundamental to developing competencies, such as clinical reasoning and interpretation. As observation is a core art skill, exposure to the art in medical schools demonstrably paves the way for the development of enhanced visual perception, observation skills, and empathy.1 Being introduced to spirituality in medical education leads to students’ intrapersonal development, health, and genial responsiveness.2 The depth of perception quickly rises above mere superfluous assessment to a oneness with the observed that takes the observer’s breath away. Training in observational skills is required to develop ability, depth, and consistency. Studies have shown that crucial details can be missed even when observing closely, prompting the need for a flexible and adaptable approach to training oneself and others in observation skills.3\n\nThroughout history, honing one’s observational skills has been emphasized in the medical sciences, recognizing its fundamental role in clinical medicine and applicable across all specialties. Regrettably, observation is frequently assumed and, despite its significance, marginalized in today’s world.4 Being linked to critical thinking, the capacity to observe is venerated to provide a spot-on solution to a problem. We know that observation effectively, efficiently, and responsibly resolves an issue that begins by identifying the problem early. Observation skill helps us to develop a keen eye for detail, familiarity with the nomenclature, procedure and technique, going-by-the-book recognition and cross verification, with curious intention and implementation ‘using peripheral vision and subsidiary awareness’.5 Taking a leaf from some medical schools that have successfully integrated art into their teaching approach for skill development in observation, our team of educators designed workshops to train ophthalmology trainees at the fellowship level in much-needed observation skills. We share our experiences with the outcomes of an observation skill enhancement workshop.\n\n\nMethods\n\nThe Education Academy recognized some essential foundation skills for good clinical practice, with observation skill as one of these. The seven-hour physical workshop was conducted on the first of July 2022 for post-graduate fellows at the institute. Learnings acquired from virtual workshops held one year earlier helped us improve the structure and quality of the present physical workshop. The data captured through this workshop were reviewed retrospectively. This study complied with the tenets of the Declaration of Helsinki. The Study involved study participants’ perceptions, and study approval was obtained from the Institutional Review Board (IRB) of the Institute Ethics Committee (IEC) Hyderabad Eye Research Foundation. Ethics Reference Number: LEC-BHR -01-23-151 was approved on 22nd March 2023.\n\nThe details are given below.\n\nPost-graduate fellows (Batch 2022, N=34) were invited via e-mail to participate in the foundation skill workshops. The e-mail communication included clear guidelines for the fellows to bring their own laptop/tablet device to fill the pre- and post-workshop assessment. The actual workshop started with an introductory speech by the facilitator/moderator explaining the structure and content of the workshop and the program schedule. The introduction included information regarding the research component of the workshop and invited participants to participate in the workshop and the pre-post assessment.\n\nThe pre-workshop assessment comprised two non-clinical images to spot the difference and five clinical images from various subspecialties of ophthalmology, such as medical retina, uveitis, cornea, oculoplasty, and strabismus. The pre-workshop assessment of trainees was conducted using Quizizz, an online gamified student engagement platform. Each image was projected for five minutes, and participants’ responses were obtained. The total duration was 35 minutes, and the responses were stored in the Quizizz application and later retrieved. Clinical images were graded by two expert ophthalmologists who were blinded to the intended use.\n\nAfter the pre-workshop assessment, the facilitator/moderator made a presentation on observation as a preeminent foundational skill, dwelling on its importance in daily practice in the clinical setting and in academic research. Such interventions have been made in the past in ophthalmology and various fields of medicine. The entire workshop was interactive, piquing audience interest by showcasing images and then inviting all trainees to comment on and add points to the description of the image if they considered that information was inaccurate or insufficient. After attending the workshop, participants were asked to form four groups and take a tour of the campus where various photographs and paintings were displayed that riveted their attention. The trainees were encouraged to describe their observation points by looking at random sketches/paintings, or photographs. The facilitator/moderator further guided the groups while making collective observations. In the last segment of this workshop, the participants were assessed on the Quizizz platform for their observation skills, using a new set of two non-clinical images and five clinical images.\n\nAt the end of the workshop, the participants’ reflections were collected after committing to confidentiality and anonymity. The pre- and post-observation grades of participants were then compared.\n\nAnalyses were performed using SPSS Version 21.0 (IBM SPSS Statistics Inc., Armonk, NY, USA) software.6 Normality was checked using the Shapiro–Wilk test. Continuous data are presented as median or interquartile range. Categorical data are presented as proportions. Comparative analyses were performed using the Wilcoxon signed-rank test, and a probability value < 0.05 was considered statistically significant.\n\n\nResults\n\nAnalyses of the average rubric scores of 34 first-year ophthalmology fellows {21 (62%) females and 13 (38%) males} training at two different time points are illustrated in the box-whisker plot in Figure 1.15 The mean age of the participants was 31.2 ± 3.7 (Mean, SD) years.\n\nThe Wilcoxon signed-rank test revealed that the score for observation skill was significantly higher after the workshop intervention (Md = 4.00, n = 34) compared to the pre-workshop score (Md = 1.85, n = 34), p-value = 0.000. Box-Whisker Plot illustrating participants’ average scores about attribute ‘observation’ skill acquisition on a scale of 1-10 at two timepoints – before and after the workshop shows improvement in observation skills scores after attending the workshop (Figure 1).\n\nOverall, our study indicates that our observation skill workshop positively affected ophthalmology trainees.\n\n\nDiscussion\n\nObservation is the predominant way of learning for a significant proportion of undergraduate and post-graduate training in medical education. However, it is difficult to ascertain a template for observation skill training that can be applied in all learning situations. While it is seen that the exposure to observation skill training can be largely standardized, the outcomes vary. This intractability may be because much of what is learned is as imaginary mental maps, building on the foundations created by our past exposure, learning, and recall, all of which vary among individuals.\n\nConstructivism, a key principle of learning in which both trainees and educators create new knowledge by building on their existing information, has a significant impact on clinical practice. This new knowledge, born out of teacher-trainee synergy and team spirit, empowers medical educators and their trainees to uncover the unknown.7\n\nTraining courses have been developed in the past to transfer much-needed observation skills to medical students. Unfortunately, lacunae are evident in the transfer of observation skills. There are several reasons why observation skills are not formally taught in medical schools. One reason is that the capacity to observe is often seen as a ‘soft skill,’ which is not as important as technical skills. Another reason is the commonly held belief that observation skills are directly associated with individual cognition and response and cannot be systematized or formulated. Another reason is that, due to the complexity of observation and its elusiveness, the assessment of observation skill cannot be entirely standardized.\n\nIn 2020, we began to actively teach observation skills to our trainees. The COVID19 lockdowns gave us an opportunity to explore deep learning and look at our current challenges, and that is when we planned to focus on teaching comprehensive clinical observation skills, integrating it into the formal course curriculum by conducting workshops during the ophthalmology fellowship induction program. This was further propagated in various learning forums when learners were encouraged to collaborate to make valid observations in greater quantity and interpret their observations in chronological order. Providing trainees with opportunities to practice their observation skills can be a good start to help them enhance their own understanding of various aspects of observation and practice. Feedback from peers and educators can help trainees significantly improve their observation skills within a set time frame.\n\nIntegrating art and medicine, as demonstrated in the collaboration between a medical school and an art museum, promises to enhance the observation, description, and interpretation skills of medical students.8 Ongoing unlearning and relearning leads to clarity in our perceptions, conquering setbacks, leading to newer ways of doing something, and eventually, distinctive new knowledge. Authors adhering to traditional scholasticism have endeavored to preserve this art, challenging its decline by reinvigorating observation skills through unique methods, much like an art form.9\n\nResearch highlights that clinical methods excel in pattern recognition, whereas art-based approaches uniquely foster emotional recognition, empathy, narrative understanding, and a multifaceted perspective, which extends to healthcare.10 Concepts like the spider web narrative and the Golden Minute underscore the importance of trainees honing their observation skills and attending to subtle patient details.11 Moreover, integrating visual art training into medical education, primarily focusing on preclinical students, addresses various skills, such as observation, empathy, and teamwork, using established methods, such as visual thinking strategies or artistic thinking.12 Further, a study in ophthalmology demonstrates that formal art observation training significantly improves observation skills in medical students, with potential applications in specialized medical fields.13\n\nJust as an owl can easily see what is at the back of its head by flexing its neck three-quarters on both sides, the observant nature of a Master of Cognition (known in India as an Ashtavadhani) permits a speedy and appropriate response to difficult questions from multiple directions with great nonchalance. However, how can one observe which is invisible, inaudible, imperceptible, unknowable, or beyond the horizon, reach, or ken? Historically, humankind has willed the individual and collective consciousness to access power beyond what is known (hailing discovery, invention, innovation, wait and watch, intuition, extra-sensory perception, serendipity, and so on). Again, the purposeful leap of faith that helped outer space practitioners of our cosmos land a rover nearest to the unknown south side of the moon may well be the prescription for us to bring into the known great and small mysteries closer home waiting to be noticed, studied, and unraveled by the observant eye.\n\nObservation skills are important for medical professionals to initiate self-efficacy in the care setting, benefiting their patients and themselves in achieving self-dependence and self-care. At the meso level, these help to resolve health issues for the community using multimodal preventive and promotive care. At the macro level, clinicians provide curative, rehabilitative, or palliative care, collated and systematized based on long, hard, sensitive, and personal observation. At the micro level, the good doctor’s sensitivity in the doctor-patient interaction helps them to be aware of their own biases which prevent the doctor from providing care that would make the patient self-dependent.14\n\nBeing observant is essential for success in many areas of life including education, work, and relationships. The importance of observation skills is speedily sizing up, facilitating process improvement, identifying a concern early (before it becomes a problem), and resolving knotty problems. At the tertiary level, a guided approach to enhance one’s observation skill and arrive at a logical interpretation can help doctors make more accurate clinical diagnoses. However, as clinical knowledge cannot in isolation serve patients, medical professionals must also readily impart new learning about the theory and practice of observation skills, actively letting go of inherent biases. By sharing their clinical prowess with their peers, superiors, and trainees in other specialties of medicine, they can become better collaborators and enhance their professionalism. Similarly, through observant empathy of functional vulnerability, such as vision loss in patients (their significant others), medical professionals can practice providing better care to the human being in every patient, collaborating without exception.\n\n\nEthics and consent\n\nStudy approval was obtained from the Institutional Review Board (IRB) of the Institute Ethics Committee (IEC) Hyderabad Eye Research Foundation. Ethics Reference Number: LEC-BHR -01-23-151 was approved on 22nd March 2023. The seven-hour physical workshop was conducted on the 1st of July 2022 for post-graduate fellows at the institute. Ethical approval was taken at a later date as we were unaware that we would publish the results from the workshop. The success of the workshop encouraged us to evaluate the retrospective data collected from the workshop and write a manuscript, therefore we needed to seek ethical approval to move forward and with formal manuscript writing. This study complied with the tenets of the Declaration of Helsinki.\n\nInformed consent was taken verbally in the beginning of the workshop. Taking verbal consent was approved by the ethics committee. The workshop instructor then explained the entire workshop in a stepwise manner. On the research aspect, the instructor circulated an online questionnaire link for data capture with the following remarks as a part of the link “You are invited to participate in a research study on “observation skills”. The purpose of the study is to capture the perceptions of ophthalmology fellows on the importance of “observation skills” for clinical management. Please take a few moments and complete this survey by clicking on Next page. By completing this survey, you are consenting to participate in this study.”", "appendix": "Data availability\n\nFigshare: Observational Skills data. https://doi.org/10.6084/m9.figshare.25138505.v1. 15\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\nEducators from the Standard Chartered LVPEI Academy for Eye Care Education for developing the initial foundational skill workshops.\n\n\nReferences\n\nHe B, Prasad S, Higashi RT, et al.:The art of observation: a qualitative analysis of medical students’ experiences.BMC Med. Educ.2019 Jun 26; 19(1): 234. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNahardani SZ, Ahmadi F, Bigdeli S, et al.:Spirituality in medical education: a concept analysis.Med. Health Care Philos.2019 Jun; 22(2): 179–189. PubMed Abstract \| Publisher Full Text\n\nElkins J:The Object Stares Back: On the Nature of Seeing.New York:Harcourt Inc.;1996; vol. 11. : 41–56.\n\nFaustinella F, Jacobs RJ:The decline of clinical skills: a challenge for medical schools.Int. J. Med. Educ.2018 Jul 13; 9: 195–197. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEpstein RM:Mindful practice.JAMA.1999 Sep 1; 282(9): 833–839. PubMed Abstract \| Publisher Full Text\n\nIBM Corp:IBM SPSS Statistics for Windows, Version 21.0.Armonk, NY:IBM Corp;2012.\n\nDennick R:Constructivism: reflections on twenty-five years teaching the constructivist approach in medical education.Int. J. Med. Educ.2016 Jun 25; 7: 200–205. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBardes CL, Gillers D, Herman AE:Learning to look: developing clinical observational skills at an art museum.Med. Educ.2001 Dec; 35(12): 1157–1161. PubMed Abstract \| Publisher Full Text\n\nRussell SW:Improving Observational Skills to Enhance the Clinical Examination.Med. Clin. North Am.2018 May; 102(3): 495–507. PubMed Abstract \| Publisher Full Text\n\nScienceDaily:Art courses could help medical students become better clinical observers.University of Pennsylvania School of Medicine;2017, September 6.\n\nSidebotham CE:Observation: what do you see?Br. J. Gen. Pract.2019 Oct 31; 69(688): 559. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMukunda N, Moghbeli N, Rizzo A, et al.:Visual art instruction in medical education: a narrative review.Med. Educ. Online.2019 Dec; 24(1): 1558657. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGurwin J, Revere KE, Niepold S, et al.:A Randomized Controlled Study of Art Observation Training to Improve Medical Student Ophthalmology Skills.Ophthalmology.2018 Jan; 125(1): 8–14. PubMed Abstract \| Publisher Full Text\n\nMajumdar B, Browne G, Roberts J, et al.:Effects of cultural sensitivity training on health care provider attitudes and patient outcomes.J. Nurs. Scholarsh.2004; 36(2): 161–166. PubMed Abstract \| Publisher Full Text\n\nSnigdha S, Prakasam R, Patel A:Observational Skills data. [Dataset]. figshare.2024. Publisher Full Text" }	[ { "id": "303776", "date": "08 Aug 2024", "name": "Purvi Bhagat", "expertise": [ "Reviewer Expertise Ophthalmology", "Glaucoma", "Medical Education" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article highlights the importance of including subtle skills like observation, communication and critical thinking in the clinical training of postgraduate students. The article is written well but certain important aspects of the methodology need mention and elaboration. 1. Validation of the pre and post assessment including the images needs to be mentioned. Also, who were the validators and what was the type of validation done - face, content etc.? 2. The images form the core of the study. These need to be shared. 3. The effect of a one day 7-hour workshop may not be transferable to similar observation skills in clinical / patient care. An added assessment through OSCE or Mini CEX would have been more relevant. 4.The qualitative analysis of the reflections is not mentioned. Needs to be added. 5.The study addresses only the first level of the Kirkpatrick. Utility is when the higher levels are achieved.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "12327", "date": "30 Aug 2024", "name": "Snigdha Snigdha", "role": "Author Response", "response": "Dear Dr Bhagat Thank you for spending your precious time and effort it reviewing our manuscript. We have tried our best to answer/make amends as suggested. 1. Validation of the pre and post assessment including the images needs to be mentioned. Also, who were the validators and what was the type of validation done - face, content etc.? Thank you for the question. A panel of five ophthalmologists, each specializing in a distinct subspecialty, were convened to assess images. These experts conducted a comprehensive analysis of each image, identifying key observation points that were used to develop a scoring rubric. The same was then applied to both pre- and post-assessment data, enabling a direct comparison of participant performance. This validation approach ensured that the assessment instruments were aligned with current ophthalmic standards and provided a robust foundation for evaluating the effectiveness of the workshop. We have added the images as an addition supplement to this paper. 2. The images form the core of the study. These need to be shared. We have added this data: https://doi.org/10.6084/m9.figshare.26861617.v1 3. The effect of a one day 7-hour workshop may not be transferable to similar observation skills in clinical / patient care. An added assessment through OSCE or Mini CEX would have been more relevant. We accept you suggestion. We will certainly add this additional assessment in our future workshops and studies. 4. The qualitative analysis of the reflections is not mentioned. Needs to be added. We have added this data: https://doi.org/10.6084/m9.figshare.26869246.v1 5. The study addresses only the first level of the Kirkpatrick. Utility is when the higher levels are achieved. Thank you for the valuable feedback. Your observation regarding the study's focus on the first level of the Kirkpatrick model is well-noted. We acknowledge the importance of achieving higher-level outcomes, such as utility, in our educational endeavors. It is very crucial for us to implement a certain pedagogy which further reinforces the learnings from this workshop which is provided during our immersive induction program. We have integrated this exercise of manifesting observations and correlating them in clinical scenarios as a regular lesson plan in most of our academic sessions." } ] }, { "id": "303770", "date": "08 Aug 2024", "name": "Helena Prior Filipe", "expertise": [ "Reviewer Expertise Ophthalmology", "healyth professions 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\nPlease accept my appreciation for the opportunity to review the manuscript that discusses the impact of an interactive educational program aimed at enhancing observational skills at the fellowship level in ophthalmology. The abstract provides a clear summary of the manuscript. The use of the term \"foundational skills\" instead of the more common \"soft skills,\" deserves emphasis as it acknowledges the significance of skills beyond medical expertise in defining the identity of a healthcare professional. The keyword selection is strategic, and the practice points effectively convey the main research messages. The manuscript is well-structured and consistently presents information. The research methods and results are appropriately described and supported by statistical analysis, and the discussion is comprehensive in its reflection on the impact of improved observation skills on communication, collaboration, and professionalism. The study is based on an online closed-answer survey. In future work, the authors might consider incorporating semi-structured interviews to gather more comprehensive data using a mixed methods approach. Additionally, further evaluation of the intervention's impact would be valuable, considering the organization and its potential effects on faculty, retention fellows preference, the hidden curriculum, organizational culture, and 360º feedback. The authors might consider detailed information about the educational delivery methods utilized in the workshop, including the implementation of educational science strategies, eg. visual thinking strategies [ ref 1 ] and specific methods of social and active learning. The manuscript raises important questions about the changing landscape of medical practice and the evolving role of foundational skills. The authors could potentially explore cultural competence in teaching and practicing ophthalmology, particularly in the context of Western and Eastern cultural differences [ ref 2 ]. Moreover, they may continue investigating how foundational skills can be effectively learned, practiced, and assessed to impact wellbeing and patient care positively. In conclusion, kudos to the authors for their research in this vital area to deliver high-quality eye care, focusing on a visually engaging specialty such as ophthalmology.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-524
https://f1000research.com/articles/13-1140/v1	07 Oct 24	{ "type": "Research Article", "title": "Impact of Green Supply Chain Management on Sustainable Performance: A Dual Mediated-moderated Analysis of Green Technology Innovation And Big Data Analytics Capability Powered by Artificial Intelligence", "authors": [ "Quswah Makhdoom", "Ikramuddin Junejo", "Jan Muhammad Sohu", "Syed Mir Muhammad Shah", "Belal Mahmoud Alwadi", "Faisal Ejaz", "Md Billal Hossain", "Quswah Makhdoom", "Jan Muhammad Sohu", "Syed Mir Muhammad Shah", "Belal Mahmoud Alwadi", "Faisal Ejaz" ], "abstract": "Background This study aims to empirically test a comprehensive interrelationship between green supply chain management (GSCM), green technology innovation (GTI), waste management (WM), big data analytics capability powered by artificial intelligence (BDAC-AI), and their collective impact on sustainable performance (SP) in organizational contexts.\n\nMethods This study was conducted in Pakistan’s food processing sector. The respondents included 495 managers working in the food processing industry. A structural equation modelling (SEM) approach is used to examine direct and indirect relationships between the variables. The originality of this study lies in integration of the technology acceptance model (TAM) and dynamic capability theory (DCT) to understand sustainable practices in the context of the provided model.\n\nResults This study highlights that GSCM, GTI, WM, and BDAC-AI have positive, strong, and direct impacts on SP. Furthermore, GTI and WM only partially mediate the link between GSCM and SP, whereas the two moderate the link. In addition, BDAC-AI had a moderating effect on the relationship between GTI and SP. This study has managerial implications, including strategies that involve the use of theoretical frameworks for technological acceptance and dynamic capabilities to support sustainable initiatives. However, it is worth noting that the findings provide a practical contingency for managers and businesses interested in implementing green studies effectively, improving technologies, and strengthening sustainable performance capabilities.\n\nConclusions The study extends the literature by establishing a model for operationalizing GSCM in the food processing sector. Furthermore, it adds value in that it first integrates TAM and DCT to explain sustainable operations and their impact on organizations. Furthermore, it extends the existing literature by establishing a relationship between GSCM and SC. It offers a model through which GSCM can be operationalized in the context of the FS sector.", "keywords": [ "Sustainable Performance", "Green supply chain Management", "Waste management", "Green Technology innovation", "SMEs", "Developing country" ], "content": "Introduction\n\nThe food sector has become increasingly important in the present era, with short environmental concerns and a growing awareness of problems related to sustainable consumption and production. Global demand places immense pressure on supply chains (Attinasi et al., 2022), whereas waste management systems incur significant costs (Kumar et al., 2021). This situation is constantly tight (Attinasi et al., 2022). However, some critical large-scale limitations limit the full implementation of green supply chain management (GSCM) as a viable concept for sustainable challenges within supply chains (Debnath et al., 2023). Different organizations are inclined to focus on short-term financial revenue, which may be an environmental perspective, which in turn leads to the issue of limited continuation of GSCM measures in different fields and areas (Söderholm, 2020). The above knowledge and resources gap is highly original in less developed countries, where GSCM program implementation is often poor (Rambaldi, 2022).\n\nNeglecting proper waste disposal severely harms the environment and inhabitants’ quality of life internationally (Kumar et al., 2021). Despite some improvements, there are many difficulties and inequalities in the global community (Bayu et al., 2022; Yousefloo & Babazadeh, 2020). Some of the issues that can be highlighted are as follows: recycling processes are said to be very slow in this regard (Bruhn et al., 2023). Most plastic waste does not effectively undergo recycling; however, it ends up in landfills or pollutes ecosystems (Praveenkumar et al., 2024). The World Bank Report 2022 “Solid Waste Management” indicates that, in contrast to developed countries, recycling rates in low-income countries remain significantly lower; in other words, people generate more trash, and the environment inevitably suffers. However, the state of dealing with and discharging similar wastes differs widely between Asian countries (Darko et al., 2023). Insufficient waste collection and disposal practices present challenges, such as open dumping and incineration, in several urban areas (Mor & Ravindra, 2023). According to the World Bank (2020), prioritizing waste management is crucial for Pakistan to ensure the sustainability of its supply chain (Haque et al., 2023; Ragasri and Sabumon, 2023). The issue of unreliable supply chains is a significant challenge for Pakistan’s food-producing sector in Pakistan (Tsai et al., 2021). Distribution networks are characterized by the presence of waste, inefficiency, and lack of environmental concern (Zuberi & Ali, 2015). This chronic issue not only escalates production expenses but also significantly diminishes operational effectiveness, amplifies resource use, and exacerbates environmental consequences (Papamichael et al., 2024). The future economic prosperity of Pakistan will be greatly impacted by the degree to which the food industry welcomes and incorporates green technology innovation (GTI) in a timely fashion, as stated in the World Bank report in a press release on April 3, 2023. While the environmental and economic benefits of GTI have been extensively discussed, its use in Pakistan’s food industry has not been thoroughly explored (Yu et al., 2023). The food industry in Pakistan plays a vital role in the country’s economic development and overall well-being of its population (Ashraf et al., 2023a). The implementation of the GTI presents an opportunity for the food industry in Pakistan to effectively mitigate waste generation, optimize resource utilization, and embrace ecologically sustainable practices (Rahman et al., 2023). The insufficiency of resources and energy in Pakistan contributes to shortages, inefficiencies, and wastage within the agricultural sector (Ashley, 2016; Rahman et al., 2023).\n\nApplying big data analytics capability powered by artificial intelligence (BDAC-AI) is the only possible way to significantly increase the food production sectors in Pakistan to a significantly higher level (Ali et al., 2023). It is possible to gain enhanced decision-making with data fabric technologies to improve industrial processes (Niu et al., 2023), supply chains (AL-Khatib, 2022), and product quality (Saini et al., 2023a) among other areas and provide substantial input to advancing sustainable resource management (Asha et al., 2023), waste confinement. Pakistan has two main issues: continuing population growth and minimizing environmental impacts (Waseem & Rana, 2023). Therefore, the available literature indicates that sustainable practices implemented in the food industry improve resource efficiency and emission reduction (Ashley, 2016), as well as the sustainability of the food value chain (Asha et al., 2023).\n\nSeveral studies have theoretically analyzed BDAC, AI, GTI, and GSCM; however, more research is needed to address the food industry (Feng et al., 2022). This study examined the relationship between GSCM, waste management (WM), GTI, and BDAC-AI in Pakistan’s food industry. These elements comprise the framework of the food industry’s sustainable performance initiatives. The integration of these components offers a favorable background for studying the existence of these factors in sustainable food industry (Roy et al., 2023). As such, the choice of this model for review stems from its ability to improve the theorization of sustainability and offer prescriptions on how corporations, governments, and individuals can support the movement for a sustainable food system in a developing country.\n\nOn several occasions, it has been realized that the food business contributes significantly to employment generation and stimulation of the economy within emerging nations (Nikseresht et al., 2023). The release of greenhouse gases and the notion of resource depletion are some of the main ways through which this specific behavior contributes to a host of environmental losses (Bhattacharya & Kalakbandi, 2022; Torres, 2018). Thus, for the continuous stability and profitable future of the food business in the globalized world, which is going to experience enhanced ecological volatilities, the sector must transform to adhere to ecological sustainability (Trivedi et al., 2023). GTI and BDAC have drastically impacted the food business, and further development has been made through artificial intelligence (AL-Khatib, 2022; Acciarini et al., 2023; Sohu et al., 2024). All of these advancements have the potential to improve sustainable practices through enhanced efficiency across multiple domains, such as energy generation and demand prediction (Cavazza et al., 2023). In addition, they have a high level of use in reducing waste and increasing effectiveness in matters related to the supply chain (Frempong et al., 2020). Realizing the growing recognition of sustainability imperatives in food production, it is time to obtain a clear idea of how the manner is to be understood.\n\nThe objective of this research is to explore these variables and their relationship with sustainable performance in Pakistan’s food industry. The present study enhances the theoretical concept concerning sustainable practices in the food industry. Identifying the mediated and regulated relationships between these factors supports the improvement of theory-based models in sustainability research. The characteristics of this model make it applicable to many emerging nations and sectors. It also encourages the use of paradigms associated with sustainability and widens the knowledge of sustainable supply chains worldwide. The theoretical developments in this study entail the utilization of the proposed model. This model aims to improve the sustainability of food business in developing countries. These outcomes can be perceived as evidence of the model’s effectiveness. The importance of this study model is that it enables the consideration of other unaddressed sustainability issues in Pakistan’s food production sector. Given the interrelation between the variables, the proposed model provides a more complex view and overview of sustainability measures and their development. To the best of our knowledge, few studies have focused on Pakistan’s global food industry from Pakistani perspectives (Ali et al., 2020; Ishaq et al., 2023). Thus, there is a need for more quantitative and qualitative studies on interrelated variables and their cumulative impact on Pakistan’s food sector, a developing country marked by challenges and growth opportunities. The significance of the topic of appropriate food business in Pakistan arises because of its relevance to the existing customer needs in planning their diet programs and creating a positive impact towards global sustainability missions on earth (Oyedijo et al., 2023; Shamsuddoha, 2015).\n\nThe following sections of the present research will provide the necessary insights into the global body of scientific literature, methods of carrying out the studies, findings, and their implications for understanding the study frameworks and their outcomes.\n\n\nLiterature review\n\nThe importance of sustainability within Pakistan’s food business has been raised due to rising concerns related to the environment, along with an incline towards fair trade practices from the customer’s point of view. This literature review aims to evaluate the contribution of scholars and knowledge regarding the challenges and opportunities faced by Pakistan’s food industry, considering variables such as GSCM, WM, GTI, BDAC-AI, and SP.\n\n\nTheoretical foundations\n\nThe TAM is a theoretical framework that seeks to explain the factors influencing individuals’ adoption and acceptance of new technologies (Scherer et al., 2019). The TAM mainly considers the individual reasons influenced by peer pressure and the perceived usefulness of the product (Magsamen-Conrad et al., 2022). Keeping in mind that the core of TAM can be further elaborated to cover organizational fields (Dhagarra et al., 2019). TAM is a vital model that helps us understand how technological innovations, namely BDAC-AI (Kraus et al., 2021), combine with the model as a whole. The moderator’s role facing BDAC-AI and SP is placed between managers’ views on how easy AI adoption will be along with the perceived gain of using AI (Chen, 2023). The link between GSCM-SP and user perspectives in processing food sector of Pakistan embraces moderating role of BDAC-AI, where TAM (Technology Acceptance Model) draws the inner mechanism. Organizations turn to digital methods, exploring the viability and efficiency of doing so in step with GTI and Transformation being considered (Poláková-Kersten et al., 2023). The topic can be expanded in the sense that the TAM should determine whether businesses see digital technology as a convenient option, which is capable of reducing their expenditures, and whether they are willing to reorganize the structures of their work to meet the required circumstances to be competitive. As a straightforward device, the TAM interface can guide the assessment of whether new technologies can be successfully implemented in any project. TAM has been investigated as part of the potential mechanisms or pathways towards the successful management of the challenges of GTI, BDAC, and the use of AI in organizational contexts (Wang and Su, 2021).\n\nIn accordance with (Jiang et al., 2019), the DTC is a process of adjusting, integrating, and rearranging the resources of flexible manufacturing, capability of the organization, and procedures of operation, so the competitive position of the organization will be more prominent and higher productivity will be achieved. Individuals and teams need to be open to learning about organizational change and the use of technology. DTT provides information that is appropriate for organizations planning the growth of technologies that can provide innovation or performance. The model we propose lays great emphasis on the DCT principles that help keep the organizational evolutionary theory running and sustainable, as it encompasses both the continuous adaptation and incorporation of new methods. One of the major points addressed by both GSCM and SP in the field of DCT is the adequate and necessary capabilities of a company to quickly adapt and change its supply chain steps, mostly in the case of external shocks and events (Ellström et al., 2021). Flexible organizations that inhibit GSCM practices, such as GTI, are fully capable of supporting, controlling, and implementing these practices (Zhou et al., 2019) and the target of DCT is to develop a wide range of knowledge, and on the basis of that knowledge, how enterprises of the food processing industry of Pakistan can adapt their business (Kraus et al., 2022). Therefore, these factors are vital for the long-run sustainability of the sector and its competitive edge, in which speed and adaptability are key components (Ellström et al., 2021).\n\nHowever, despite the findings of the research stated before, there is a gap when it comes to studying these factors completely within the actual Pakistani food business context among the researchers. The precise functions of trade between the Pakistani food industry were not considered. These involve channels driven by the GTI, WM, and BDAIC AI as mediators and moderators. This gap in recognition still holds even in the presence of literature and information on the subjects of GSCM and SP. The findings of existing studies that are lacking in terms of explaining the underlying mechanisms are insufficient for a comprehensive understanding of how GSCM practices create SP and how this works in the particular context of Pakistan. The wide range of benefits resulting from the development of GSCM has been acknowledged in previous studies (Debnath et al., 2023; Rupa & Saif, 2022).\n\nIn fact, they show up in cost curtailing, efficiency upgrades, and environmental protection measures as long as they are effectively implemented. In the human realm of the food business, the impact and balance of artificial intelligence on the resilience of GSCM, GTI, and WM links is not being communicated properly (Schintler & McNeely, 2022). It will have worthwhile additions to not just literature but also to the actual applications as an outcome of the analysis of the relationship between GSCM, GTI, WM, BDAC-AI, and SP in the Pakistani food industry. Through this knowledge gap, we aim to understand how sustainable and integral supply chain processes may be implemented in the context of Pakistan. This is set to allow us to provide support to companies or props their initiatives on sustainability improvement, where breakthroughs in technology and innovation can be applied.\n\nThe purpose of this study is to add to the constantly developing phenomenon of sustainability practices in the context of a newly industrialized country. The primary goal of the conversation is to provide enterprises, the government, and consumers with useful feedback.\n\nSP is the level of the organization that has been observed to have reached economic, environmental, and social environmental sustainability at the same time as success (Abu-Rayash & Dincer, 2021). The social responsibility, environmental sustainability, and social effects of modern business are shifting to financial facts (Kofi Opoku et al., 2023). Such a country would consider this for both ethical and financial reasons (Ma et al., 2023). One of the goals of the company that made it achieve the SP is to fulfill its financial and social goals, in addition to the prescription of the environment (Zhang et al., 2023; Kherazi et al., 2024). As a result of this achievement, the organization can be certain that it will remain in business for a long time to come (Kofi Opoku et al., 2023), and it will stand out in the market (Peng et al., 2020). SP drops its signature of an unsolicited vocabulary that is relevant to the situations of the poorest nations in the world, as a discovery realized in a research study in this regard (Castillo-Díaz et al., 2023).\n\nThe purpose of this study is to examine the operations of the food processing sector in Pakistan. Furthermore, the study examines whether business operations can make this trade-off effectively between profitability and the pressure that the business pressurizes on the community and the environment. The food-processing industry scores well in contributing to the health and welfare of the nation (Ashraf et al., 2023b). Thus, business sustainability is required. Several measures, such as eco-friendly practices (Zhen et al., 2023), minimizing the amount of waste for production (Hemphill, 2022) and efficiently using the available resources (Ahmad et al., 2023) must be taken. These initiatives are of even greater relevance to countries such as Pakistan, where this component of development is yet to fully evolve (Hashmi et al., 2023). Moreover, it is noteworthy that Pakistan personalizes and standardizes its SP food processing industry, which shows that the products being produced are not only risk free but also of premium quality (Maaz et al., 2021). In such cases, we must remain committed to protecting public and customer health and the innumerable needs of customers.\n\nSeveral studies have established the presence of SP factors in GSCM strategy planning and operation (Castillo-Díaz et al., 2023; El Ayoubi & Radmehr, 2023; van der Meulen et al., 2022). It has been documented that SSCM approaches help firms acquire SP for many activities (Castillo-Díaz et al., 2023; El Ayoubi & Radmehr, 2023). Green supply chain management has received much attention worldwide as a target for sustainable production and consumption planning, especially in Pakistan’s food industry (Saini et al., 2023b; Das et al., 2023). Sustainable procurement hinges on green supply chain management, which is one of the most crucial components. This bond between the GSCP and SP is very significant for Pakistan’s food industry; it is paramount because of its economic influence and the unique obstacles it overcomes. The links between progress and cleaner environments are critical for attaining sustainable objectives in all sectors. Numerous studies have shown that GSCM practices are financially (Samad et al., 2021), environmentally, and socially beneficial, as these parameters relate to SP within the food industry (Yang et al., 2023a). Tostivint et al. (2017) highlight that GSCM can play three main roles: waste lowering, optimal resource use, and system-wide efficiency improvement. For an organization to benefit from cost savings and gain a competitive advantage, the choice to practice GSCM strategies that focus on the procurement of ethically sourced raw materials, waste minimization, and the use of environmentally friendly materials should always be an option (Li et al., 2022). A Recent study conducted by (Jalil et al., 2023), cited that implementation of GSCM yields an increase in the social dimension of SP through the creation of favorable working conditions and good treatment of local communities. The provision of GSCM for Pakistan’s food industry has been introduced as the latest solution, which implies achieving a good pace of economic growth while remaining responsible for the environment and society (Tariq et al., 2023). Companies that work to reduce their carbon footprint are important not only for human society and the environment, but also for increasing their brand equity (Rehman et al., 2023).\n\nTechnologies such as AI and BDAC should be implemented (Al-Nuaimi et al., 2021), in order to operate SPs in an up-to-date environment (Belhadi et al., 2020). The management of data using these technologies is a trend. The implementation of technologies, such as AI and bDND, could positively impact the food processing industry in Pakistan (Khan & Tao, 2022). These tasks represent technologies that have evolved over time and are capable of working with large volumes of data. Thus, they help to identify areas that deserve improvement (Bresciani et al., 2021). Such technologies are also a blessing for businesses that they should remain in the world according to socially acceptable standards but still earn their income (Qin et al., 2022), adjusting to the rapidly changing environment of the market (Morimura & Sakagawa, 2023). The regulation of BDAC-AI provides them with agility and flexibility in restructuring their operations while pursuing the goal of a sustainable future (Junaid et al., 2022).\n\nGSCM’s main task of GSCM is to integrate the green approach across the entire supply chain (Chatzoudes & Chatzoglou, 2022). The goal of an energy production scheme is to achieve the best economic performance as well as to reduce waste (Ali et al., 2019), while also offsetting the adverse environmental effects that arise from supply chain operations such as transportation (Ghosh et al., 2021a). The field of GSCM comprises fundamental ideas (Nirmal et al., 2023). The trend of GSCM and other responsible sourcing measures is increasingly being observed in Pakistan’s developing food sector in Pakistan (Qazi et al., 2022). The application of GSCM strategies might improve supply chain operations, manage both environmental and customer demand factors (Chatzoudes & Chatzoglou, 2022; Nikseresht et al., 2023), and meet the increasing customer demand for environmentally friendly products (Ye et al., 2023).\n\nThe adaptation of GSCM in the Pakistani food sector has become more widely perceived because of the growing tendency towards environmental protection (Mubarik et al., 2021) and strictly imposed governmental requirements (Chatzoudes & Chatzoglou, 2022). Findings from multiple studies show the influence of sourcing from sustainable avenues (Fallahpour et al., 2021), efficient (Ghosh et al., 2021b), and inventory management (Tasnim et al., 2022). Thus, it is imperative that the measures be included when implementing strategies, as they will help in the regulation of the negative environmental impact (Shi et al., 2022) and efficient utilization of natural resources (Jha et al., 2021). In Pakistan, the food business is a very important segment of the economy (Iftikhar et al., 2023); At the same time, it is being challenged by stricter regulations and environmental issues (Waseem & Rana, 2023). In the context of the logistics industry, organizations are poised to shift to the paradigm of GSCM strategies because of the necessity of maintaining their competitiveness, as outlined by (Das et al., 2023). Iqbal et al. (2020) introduced some elements of this chain strategy, including but not limited to environmentally sound procurement (Wang et al., 2020), efficient and lucrative turnaround as far as logistics activities are concerned (Nikseresht et al., 2023), and the efficient use of resources accompanied by waste minimization (Yildiz Çankaya & Sezen, 2018; Zuberi & Ali, 2015). These orientations are part of the global aspiration for a cleaner planet and should indeed be a top concern for Pakistan’s food industry in Pakistan (Ashley, 2016).\n\nThe idea of GSCM is an innovative approach that is still in its adolescent stage, which intends to deliberately involve environmental sustainability practices in a variety of aspects of supply chain operations (Hazen et al., 2020). Recent studies, such as Jabbour et al. (2020), put forward the notion that it is an effective instrument for diminishing the level of carbon emissions, conserving resources (Ishaq et al., 2023) and amplifying the levels of productivity (Ali et al., 2020). Within GSCM, components such as responsible inventory management, effective transportation, material reduction in waste (Rahman et al., 2023), and responsible sourcing (Trujillo-Gallego & Sarache, 2021) are only a few. Zhu et al. (2019) are convincing that GSCM principles should be added to SC operations. The adoption of these planned measures is fundamental, as it reduces the negative effects that the manufacturing process brings to the environment while increasing the percentage of items that are both sourced and made using ethical means (Das et al., 2023).\n\nGreen procurement methods are considered important in Pakistan’s logistics in Pakistan (Irfan et al., 2020). Rasheed et al. (2019) stress that orderly procurement requires ethical farming, fair labor, and ecological sourcing. The use of ethical sourcing strategies in the food industry has two significant advantages: improvement in quality and safety (Asha et al., 2023). Additionally, it increases competition by establishing a higher benchmark for competitors (DeBoer et al., 2017). The optimization of the transport sector’s operation will be a critical point in the context of GSCM in Pakistan’s food supply chains of Pakistan according to (Qin et al., 2022). This study, led by (Ahmed & Sarkar, 2019) revealed that optimizing transportation can play a crucial role in successfully combating carbon emission issues and reducing costs. Hence, this improves the supply chain system and helps meet the targets that state the importance of sustainability factors (Lopes de Sousa Jabbour et al., 2020).\n\nGSCM positively related to SP.\n\nGSCM positively related to GTI.\n\nGSCM positively related to WM.\n\n\nGreen technology innovation\n\nEnvironmental factors are issues that can slowly and surely gain importance in SCM and new product development strategies (Davidescu et al., 2023). This study investigates the connection between GSCM and GTI, seeking to give them the credit they deserve to promote sustainability (Sarkis, 2003). GTI actively participates in helping the environment conserve its bits and pieces (Boye & Arcand, 2013). Implementing and using environment-saving technologies is the most effective way to prevent and mitigate adverse environmental effects. GTI’s success of GTIs depends on the displacement of conventional energy sources with renewable energy sources (Zuberi & Ali, 2015), the utilization of energy-efficient machinery (Praveenkumar et al., 2024) and the application of environmentally acceptable building materials (Hossain & Thomas Ng, 2019). Such technological advancements allow businesses, regardless of size, to benefit, as their environmentally conscious move concurrently enhances their competitive edge (Rehman et al., 2021).\n\nThe sustainability of technology has received particular attention, and many times, sustainable technological advances involving production chains can be observed. A new study by Srivastava and Dey (2018) points to the possibility of implementing technology to foster sustainability of logistics (Srivastava & Singh, 2020) along the lines of real-time energy consumption monitoring (Birgonul, 2021) and predictive maintenance of logistical equipment (Wakiru et al., 2021). The application of GTI stimulates supply chain networks to utilize data-driven policies ((Hassoun et al., 2022) as a result, leading to the reduction of excess means for processes and waste streams (Hassoun et al., 2022). An important result highlighted in the literature is the existence of an interconnection between GSCM and GTI. For supply chains to be sustainable, GTI offers tools that facilitate this process (Bukchin & Kerret, 2018), whereas GSCM provides a program that is the basis of this process (Micheli et al., 2020). When incorporated into organizational operations, these methodologies are heading towards the progress of sustainability (Saberi et al., 2019; Das et al., 2023). The literature exposes the possibility that GSCM integration with GTI by the organization is a competitive advantage for the business (Zhang et al., 2022). Söderholm (2020) mentioned that the application of greener supply operations might effectively facilitate company compliance with environmental regulations, decrease running expenses, and attain consumer loyalty that is environmentally (Hossain & Thomas Ng, 2019). Regarding GSCM and GTI, existing research shows a pronounced correlation between them towards better sustainability in many sectors (Lerman et al., 2022). The GTI is driven by the use of smart tools and technology in the fields of sustainable procurement (Rejeb et al., 2023), innovative transport, and waste reduction (Zuberi & Ali, 2015), focusing on providing a strategic framework for these activities as the next step.\n\nThe GSCM strategy for circulating environmental sustainability in supply chain management involves several critical features, including ethical purchasing (Lim et al., 2023), waste reduction (Haque et al., 2023), eco-friendly transportation (Ge et al., 2023), and controlled inventory (Jauhar et al., 2023). Additionally, the GTI provides technical tools and breakthroughs that allow a cleaner and better way of doing things (Xie & Teo, 2022). Customers who try to act in accordance with the environmental sustainability value and acknowledge the initiatives that they are by all means proud of. In the event that clients would be willing to undertake more sustainable shopping as well as ensure the ethically correct nature of the products they have bought and the shipping processes they have used (Ghosh et al., 2021a), the chances of them continuing to do the same is highly probable. The concept of GTI is of significant importance in this context. The implementation of green technical breakthroughs has enabled supply chains to enhance operational efficiency, mitigate emissions, and eliminate waste (Roy et al., 2023). A recurring outcome of these advancements is the production of ecologically sustainable (Tasnim et al., 2022). The use of the GTI has the potential to enhance supply chain visibility and traceability as well (Lai et al., 2023). Therefore, the following hypothesis was developed:\n\nGTI is positively related to SP.\n\nThe long-term viability of Pakistan’s food sector relies on the effective implementation of environmentally friendly WM methods (Rahman et al., 2023), in accordance with existing worldwide trends, which suggests an increasing focus on waste reduction, recycling, and appropriate waste management practices (Kayikci et al., 2019). The implementation of effective waste management systems has the potential to yield financial savings and mitigate the environmental impact of organizations (Hemphill, 2022). As Pakistan, through the process of urbanization (Ali et al., 2023), experiences population increase and expands its industrial sector (Ashraf et al., 2023a), the need for viable ways to address the escalating challenges associated with waste buildup becomes more pronounced (Ashraf et al., 2023b). The importance of effective WM increases as metropolitan areas continue to develop (Hashmi et al., 2023). WM presents many complex difficulties for a country (Salam et al., 2023). According to (Yousafzai et al., 2020), the exacerbation of this problem may be attributed to a lack of public awareness, financial resources, and adequate infrastructure. In densely populated urban regions, the presence of trash streets and public places is visually unappealing and inconvenient for the general population (Filimonau et al., 2023). Informal waste pickers also provide a significant function in the realm of waste management through their efforts to extract recyclable materials from landfills (O’Connor, 2021).\n\nIn response to these challenges, the government of Pakistan passed a series of legislative measures and undertaken several activities aimed at enhancing the nation’s WM infrastructure (Yousafzai et al., 2020). One notable government-wide project aimed at promoting cleanliness and educating the public about trash management is the “Clean Green Pakistan” campaign (Khatibi et al., 2021). Based on the findings of Rasheed et al. (2019) on the 18th Amendment, municipal and state governments are conferred with more powers in waste management, which promotes the use of integrated and economically viable approaches to waste management (Filimonau et al., 2023) (18th Amendment gives more powers to municipal and state governments; thus, they can implement integrated and economic\n\nTechnology is being increasingly applied and innovation is emerging as one of the main tools in Pakistan in battling the ever-growing waste crisis (Salam et al., 2021). Salam et al. (2023), various smartphone apps that create the best functionalities for the methane management system wipe out the inefficiencies of the entire waste system. Along with the functional consequences of GM on PMM, there are social repercussions. Nowadays, the distribution of natural resources and waste management is a complex issue in which policymakers set up legislative tools to restrict the production process and disposal of harmful materials. Therefore, the application of environmentally sustainable practices has become a prime strategy for businesses (Mor & Ravindra, 2023). As a result, businesses in the area have moved towards those that incorporate WM in their GSCM plans, according to the study by Kannan et al. (2022). Subsequently, the attainment of standards in sustainable environmental scenarios and world sustainability will be accomplished through the synergistic activity of GSCM and WM practices in developing countries (Sabumon, 2023). The use of WM denotes an inextricable portion of GSCM policy that is geared towards curbing the negative influence of industrialization on this area through this tool (Haider Naqvi et al., 2023).\n\nA specific growing trend in Pakistan’s waste management sector is evident in the increasing grassroots community involvement and higher social activity levels. Concerns about solid waste collection and disposal as a critical environmental issue in Pakistan have now emerged as a result of many factors (Ahmad et al., 2023) initially, the increasing levels of economic challenges and decaying infrastructure caused people to face severing opinions on the necessity of taking in innovative strategies as well as passing legislative changes that also include encouraging public participation to effectively address these grave issues (Yousafzai et al., 2020). Emerging technologies, such as automatic sorting and data analytics systems (Salam et al., 2023), as well as the process of integrating them, can offer opportunities to enhance waste management in the country (van der Meulen et al., 2022). In light of the circumstances, it becomes inevitable that the forthcoming studies and policies should have the will to carry on with plan which seeks the contextual as well as sustainable solution. Ultimately, it will prepare the foundation for a sustainable (Zhen et al., 2023).\n\nWM is positively related to SP.\n\nIn this context, GTI is a general strategy model that promotes new clean technologies and hitches them with appropriate attitudes in different sectors (Punj et al., 2023). It focuses on the food and beverage industry (O’Connor, 2021). The generation and development of the GTI can be due to an appreciation of ecological and environmental sustainability, together with the fact that climate challenges need immediate intervention (Hassoun et al., 2022). Innovations in these fields cover an extensive range of topics, such as energy-saving machines (Xie & Teo, 2022), green production methods (Lai et al., 2023), environmentally friendly packaging (Hong et al., 2018), and product design, which has no influence on the environment (Peng et al., 2020). Nevertheless, the GTI is not just a technological development (Lepore et al., 2023). It incorporates new business strategies that focus on environmental gain, optimization of resource efficiency, and ensuring the long-term commercial sustainability of organizations (Alyahya et al., 2023; Yousafzai et al., 2020).\n\nThe accomplishment of the food processing industry against SP without aid from the GTI may be extensive (Alyahya et al., 2023). Energy conservation using sustainable technologies; green production and packaging; all of these developments hold very bright prospects for food processing industries as they are concerned with the carbon footprint and resource efficiency of the food processing firms (Yang et al., 2023b). The employment of GTI is a way to meet the growing needs of conscientious customers who are environmentally friendly are met (Xie & Teo, 2022). As a result, it not only increases market share but also investor value, which is measured by return on equity, return on invested capital, and cash flow (de Burgos-Jiménez et al., 2013). Moreover, the highly inclusive green practice promotes a company that has been able to sustain itself because it is able to fit various market conditions and sustainability issues (Haider Naqvi et al., 2023). The successful implementation of GTI into operational processes indeed facilitates the promotion of sustainability (Galanakis et al., 2021), reduction of ecological impact (Filimonau et al., 2023), and Sustainable Performance (Ma et al., 2023). Overall, such results are key to the competitiveness of the industrial sector and to achieving environmental targets that are valid around the world (Ren et al., 2023).\n\nIn view of their efforts to create sustainability, enterprises that operate in these industries are more likely to implement GTI (Ma et al., 2023). The exploitation of the GTI could be the most potential feature that plays a role in the evaluation of operations management (Zhang et al., 2023). A previous study by Maaz et al. (2021) showed us the same aim. These technologies are particularly suitable for managing this area because they are designed to deal with many nuances (Ashaari et al., 2021) . BDAC-AI provides solutions that help to concentrate on control and supervision (Alyahya et al., 2023), of the information on how well environmentally friendly measures are being used or implemented by organizations. The benefit of decision-making on a data basis is important for the realization of GTI goals because it helps align tech investments with sustainability purposes (Hassoun et al., 2022). The joint venture between the GTI and the food processing sectors of low-income countries is the BDAC-AI initiative targeting the gulf (Al-Nuaimi et al., 2021). It holds a hegemonic position in the global innovation market, so its prime task is to ensure that modified solutions provided by the GTI are targeted to the peculiarities of these countries, such as opportunities and difficulties (Cheng et al., 2023).\n\nGTI significantly mediates the relations between GSCM and SP.\n\nWM significantly mediates the relations between GSCM and SP.\n\nIn addition, BDAC-AI has the ability to carry out instant adjustments to any change in the market and to any customer preference changes (Bag et al., 2023; Hongyun et al., 2023; Sohu et al., 2023). The integration of BDAC-AI technology is the only method through which food processing companies can properly deal with environmental sustainability of the environment (Zhen et al., 2023) and health concerns (Ashraf et al., 2023b). This is achieved through the development of RT logistics and product propositions, along with the establishment of supply chain activities (Bag et al., 2023). The fact that the capacity for change and adaptability among its members needs to be employed as a crucial determinant of the long-term success of the firm (Agyabeng-Mensah & Tang, 2021) is a definitive factor instrumental in the long-term success of the firm. The arrival of green technology has played a part in initiatives aimed at keeping the planet environmentally friendly, in this way promoting the conservation and careful use of limited resources such as water, energy, land, and wildlife (Calza et al., 2020), Ren et al., 2023). The BDAC-AI system plays the role of this correlation, which is known as data-driven decision-making and enables market players to adapt to dynamic market environments (Ashaari et al., 2021).\n\nSustainability of agriculture in Pakistan has become a vital area of concern for the agricultural sector, which is actively interested in recent ideas of sustainability (Gupta et al., 2020). The presence of the private sector is essential to achieving the fundamental objectives of the SDP in Pakistan’s food (Ashraf et al., 2023b; Yousafzai et al., 2020). GTI aims to be a pathfinder organization that doctrines eco-friendly technologies and methods to help target Pakistani businesses achieve their sustainability objectives (Raeesi et al., 2023). As Pakistan is experiencing prevailing circumstances, we need to ensure that BDAC-AI will be essential Ashaari et al. (2021). Bag et al. (2020) wrote on the importance of BDAC-AI in that business companies are supplied with the necessary anchors for monitoring and evaluating the use and effectiveness of environmentally sustainable technology equipment. Based on the results of (Belhadi et al., 2020; Dakhan et al., 2020), many places have invested in technology while achieving sustainability targets efficiently and effectively.\n\nBDAC-AI is positively related to SP.\n\nBDAC-AI significantly moderates the relations between GTI and SP\n\n\nMethod\n\nIn this study, a quantitative approach was adopted because it suggests that this approach is suitable for understanding the relationships between variables through complex models. The independent variable, green supply chain management; two mediating variables, including waste management and green technology innovation; and one moderating variable, big data analytics capacity-artificial intelligence, were tested in this study. The conceptual model illustrating the intricate relationships among the variables is presented in Figure 1.\n\nSource: Authors’ calculations.\n\nThis study “Impact of Green Supply Chain Management on Sustainable performance: A dual mediated-moderated analysis of Green Technology Innovation and Big Data Analytics Capability powered by Artificial Intelligence” was approved by the Ethics Committee of The University of Okara, which constitutes the departmental Ethics Approval Committee (REBSSH/2023/2-7) on July 04, 2023. All informants provided written and oral informed consent to participate in this study.\n\nIn this study, food manufacturing firms and those with managerial positions in Pakistan were targeted. Four hundred ninety-five cases were used for data analysis, and the sampling strategy was a random sampling strategy to give all employees of the stated firms a chance. The individuals’ personal information was kept confidential, and all individuals were provided with a consent form before data collection. Furthermore, in this study, a structured, closed-ended questionnaire was distributed among manufacturing SMEs in food processing in Pakistan. They were requested to fill the form through Google Forms, which took one and two weeks.\n\nThe quantitative approach helped analyze the data gathered through various statistical tools. The present research employed structural equation Modelling (SEM) because it supports the study of the hypotheses regarding the relationship among the variables (Hair et al., 2021). SEM facilitated the simultaneous analysis of the complicated relationships within the study. However, at this start, SPSS was used to clean the data and deal with missing values. Subsequently, a study using SEM was performed, followed by applying Smart PLS (Partial Least Squares) to determine the correlations among the variables.\n\nThe methodology chosen aligns with the primary aim of this study. The use of a carefully constructed questionnaire facilitated the acquisition of comprehensive and detailed responses (George, 2019) from the executives of the respective companies. The hypothesized associations were thoroughly investigated using quantitative methodology and SEM. Nevertheless, the quantitative approaches and other procedures used may have been insufficient in terms of statistical seriousness, limiting the ability to establish reliable correlations and to present a more comprehensive analysis. Owing to the inherent quantitative character of the research issue, statistical analysis was used to quantify the connections, whereas a survey-based technique was considered the most suitable approach.\n\nTo measure the above-stated variables, instruments were adopted from past studies published in reputable journals, ensuring reliability and validity. The six research items of green supply chain management were adopted from study of (Le, 2023), who developed these items based on a comprehensive review of the literature and validated them through expert feedback and pilot testing. The second variable, green technological innovation, consists of five research items taken from (Sahoo et al., 2023). The third variable, waste management, was obtained from the study (Obuobi et al., 2022). Fourth variable big data analytics capacity-artificial intelligence four items are adopted from study (Benzidia et al., 2021). Finally, sustainable development was taken from the research of Le et al. (2022) and Tjahjadi et al. (2022) with six items. These items were formulated based on an extensive literature review and validated through confirmatory factor analysis (CFA) to ensure their accuracy and relevance. Most studies used rigorous methodologies, including pilot studies and validation through structural equation modeling, to establish the scales’ validity and reliability.\n\n\nResults and discussions\n\nFactor loadings indicate the strength of the relationship between each question and its respective constructs (such as BDAC-AI, GSCM, GTI, SP, and WM). Higher item loadings signified stronger relationships. Cronbach’s alpha (α) is a measure of internal consistency. Higher values (α > 0.7) indicated good reliability, suggesting that the items within each construct reliably measured the same underlying concept. Similar to α, Composite Reliability (CR) measures the internal consistency reliability, and a CR value > 0.7 Shmueli et al. (2019) is considered acceptable, indicating that the items reliably measure their respective constructs (Hair et al., 2021). An AVE above 0.5 suggests that more than 50% of the variance is captured by the construct, indicating good convergent validity. The outer variance inflation factor (VIF) checks for multicollinearity among the items within a construct, and the inner VIF represents multicollinearity between variables. VIF Values of < 5 are generally acceptable, indicating that multicollinearity is not problematic.\n\nTable 1 highlights factor loadings, α, and CR values > 0.7, indicating robust relationships between the items and their respective constructs. The items reliably measure their constructs, and indicate consistency in measuring the constructs (Hair et al., 2019). AVE values >0.5 show that a significant amount of variance is explained by the variables, indicating good convergent validity. VIF values <5 indicated no significant multicollinearity issues among the items within each construct.\n\nThe Heterotrait-Monotrait Ratio of Correlations (HTMT) and the Fornell and Larcker (FnL) criteria were used to assess discriminant validity in this study. In the present study, two critical values, the HTMT and the Fornell and Larcker criteria, helped determine discriminant validity (Henseler et al., 2015). The values are shown in Table 2 below; all values are less than the suggested 0.90 (Hair et al., 2019). The HTMT values ranged from 0.617 to 0.897, and the FnL diagonal values are the square root of AVE, indicating no issue in discriminant validity.\n\nF-Square is used to measure the proportion of variance explained in the dependent variable or effect size by adding a specific independent variable to the model. This helps to understand how much of the variance in the endogenous variable is accounted for by the inclusion of the exogenous variable. Higher F-Square values indicate that a larger proportion of the variance in the higher-order construct can be explained by its constituent variables. Table 3 shows that the F Square values for GTI and GSCM are 0.570. The remaining f-squared values are listed in Table 3. The inner VIF and F Square values suggest that multicollinearity is not an issue in the model, and all constructs are well explained by their constituent variables, which adds to the credibility of this research model. The measurement model is depicted in Figure 2. The structural model is illustrated in Figure 3.\n\nSource: Authors’ calculations.\n\nSource: Authors’ calculations.\n\nThe model’s goodness of fit was evaluated by the values of R-squared (R2) and Adjusted R-Squared (R2 adjusted). They provide information on how well the independent variables explain the variance in the dependent variable. Along with R2, Q2, SRMR, and NFI values were used to predict the goodness of fit of the model. Table 4 shows that the SRMR and NFI values are 0.061 and 0.802, respectively, which suggests that the model offers a good fit for the data analysis. The explanatory power of the model was quantified by calculating its R2 value. For the GTI, R2 is 0.363, which suggests that approximately 36.3% of the variance in DP is explained by the GTI in the model. All other values are listed in Table 4.\n\nIn summary, both R2 and R2 adjusted values for all constructs are relatively high, suggesting that a considerably large amount of variance in the endogenous constructs (SP, WM, and GTI) is explained by the exogenous variables in the current model, which indicates that the model provides a reasonably good fit to the data and supports the relationships between the variables. To evaluate the predictive power of the model, researchers used the Q2 value technique (Shmueli et al., 2019). Q2 determines the extent to which an independent variable influences the dependent variable in the model. For the current study, the Q2 values of GTI and WM are 0.360 and 0.301, respectively, which implies a substantial predictive importance of the depedent6 variables.\n\nA direct path analysis examines the direct relationships between exogenous and endogenous constructs. All hypotheses (H1–H6) were supported, showing significant relationships. In Table 5, H1 suggests that GSCM has a positive effect on the GTI, and the T-value (22.781) and P-value (significant at 0.000) confirm that this relationship is significant. Similarly, H5 shows that WM has a positive effect on SP, supported by a T-value of 7.831 and a significant p-value (0.000).\n\nSpecific indirect path analysis examines the mediating effect of constructs on the relationships between exogenous and endogenous constructs. The GTI and WM play mediating roles in the relationship between GSCM and SP. All the mediating paths (H7a–H7b) were positive and significant. H7a and H7b show that the mediating effect of GSCM on SP through GTI and WM is positive and significant (T-value: 9.019, p-value: 0.000, T-value: 6.977, P-value: 0.000). Here, the total indirect path analysis suggests partial and full mediation. All indirect paths are significant, so all mediating relations are partially mediated.\n\n\nModeration\n\nFinally, the researchers examined the moderating role of environmental dynamism. The moderating effect of H8 is significant and positive. Table 5 shows that the interaction between BDAC-AI and GTI significantly affected ECP (T-value: 4.454, P-value = 0.000). These findings support Hypothesis H8. Therefore, environmental dynamism enhances the positive impact of BDAC-AI and GTI on ECP, highlighting its crucial role in achieving sustainable performance.\n\n\nDiscussion and concluding remarks\n\nThe findings from the empirical analysis provide important insights into the relationships among GSCM, GTI, WM, BDAC-AI, and SP within the food processing multinational organizational context within Pakistan. There was a positive and significant relationship between GSCM and GTI, WM, and SP. This implies that an emphasis on GSCM practices is positively associated with fostering GTI, Waste Management strategies, and overall environmental performance within organizations. The mediated paths indicate partial mediation of GTI and WM in the relationship between GSCM and SP. These findings underscore the importance of intermediary processes in translating GSCM practices into enhanced sustainability outcomes. Additionally, the moderation effect of BDAC-AI on the relationship between GTI and SP demonstrates the influence of advanced analytics capabilities augmented by Artificial Intelligence in moderating the impact of GTI on SP.\n\nThe present study’s findings confirm the direct effects of GSCM, GTI, and WM on the sustainable performance of SME manufacturing in the food processing sector in Pakistan. Furthermore, TAM and DCT theories suggested these variables, and their relationship was confirmed in the present study. However, the unique finding of the present study is that green technological innovation was found to have a more significant and positive impact on sustainable performance due to higher beta values than other variables in this study. Furthermore, the indirect effect of GTI between GSCM and SP was found to have a more significant impact on SP compared to the indirect effect of WM, due to higher path coefficients. Finally, the moderating role of BDAC-AI must be addressed in the present study. This moderates the relationship between GTI and SP.\n\nIn the present study, two TAM and DCT supported the variables of the study, including GSCM as an independent variable, two mediating variables (GTI and WM), and one moderating variable (BDAC-AI) on SP in SMEs manufacturing food supply chain processing firms in Pakistan, a developing country. TAM supports technology acceptance in today’s business environment, where environmental protection is a key concern. Similarly, the DCT confirmed responsiveness towards environmental protection and adaptability within the organization. Policymakers and top management of SME manufacturing in the context of the food processing sector in Pakistan can adopt these variables in their future strategies. They can benefit from using scarce resources and better productivity within firms.\n\n\nLimitations and future research directions\n\nAlong with a few contributions, the present study has certain limitations. Data limited to a cross-sectional approach in future longitudinal data types can be collected to validate the existing findings. This study was limited to two theories: TAM and DCT. However, other theories that support the current conceptual model can be tested in the future. This is limited to food-processing manufacturing SMEs in Pakistan. Other sectors, such as textiles and pharmaceuticals, will be considered in the future.\n\nThis study “Impact of Green Supply Chain Management on Sustainable performance: A dual mediated-moderated analysis of Green Technology Innovation and Big Data Analytics Capability powered by Artificial Intelligence” was approved by the Ethics Committee of The University of Okara constitutes the departmental Ethics Approval Committee (REBSSH/2023/2-7) on July 04, 2023. All informants provided written and oral informed consent to participate in this study.", "appendix": "Data availability\n\nFigshare: Dataset & Questionnaire: DOI: https://doi.org/10.6084/m9.figshare.26247548 (Junejo, 2024)\n\nThis project contains the following underlying data:\n\n• Dataset. csv. Dataset\n\n• Final Questionnaire.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe would like to thank all participants in this research for their voluntary participation.\n\n\nReferences\n\nAbu-Rayash A, Dincer I: Development of integrated sustainability performance indicators for better management of smart cities. Sustain. Cities Soc. 2021; 67: 102704. Publisher Full Text\n\nAcciarini C, Cappa F, Boccardelli P, et al.: How can organizations leverage big data to innovate their business models? A systematic literature review. Technovation. 2023; 123: 102713. Publisher Full Text\n\nAgyabeng-Mensah Y, Tang L: The relationship among green human capital, green logistics practices, green competitiveness, social performance and financial performance. J. Manuf. Technol. Manag. 2021; 32(7): 1377–1398. Publisher Full Text\n\nAhmad S, Jia H, Ashraf A, et al.: Water resources and their management in Pakistan: A critical analysis on challenges and implications. Water-Energy Nexus. 2023; 6: 137–150. Publisher Full Text\n\nAhmed W, Sarkar B: Management of next-generation energy using a triple bottom line approach under a supply chain framework. Resour. Conserv. Recycl. 2019; 150: 104431. Publisher Full Text\n\nAL-Khatib AW: The impact of big data analytics capabilities on green supply chain performance: Is green supply chain innovation the missing link? Bus. Process. Manag. J. 2022; 29(1): 22–42. Publisher Full Text\n\nAli Y, Saad TB, Sabir M, et al.: Integration of green supply chain management practices in construction supply chain of CPEC. Management of Environmental Quality: An International Journal. 2019; 31(1): 185–200. Publisher Full Text\n\nAli Y, Younus A, Khan AU, et al.: Impact of Lean, Six Sigma and environmental sustainability on the performance of SMEs. Int. J. Product. Perform. Manag. 2020; 70(8): 2294–2318. Publisher Full Text\n\nAli ZA, Zain M, Pathan MS, et al.: Contributions of artificial intelligence for circular economy transition leading toward sustainability: An explorative study in agriculture and food industries of Pakistan. Environ. Dev. Sustain. 2023; 26: 19131–19175. Publisher Full Text\n\nAlNuaimi BK, Khan M, Ajmal MM: The role of big data analytics capabilities in greening e-procurement: A higher order PLS-SEM analysis. Technol. Forecast. Soc. Chang. 2021; 169: 120808. Publisher Full Text\n\nAlyahya M, Aliedan M, Agag G, et al.: Understanding the Relationship between Big Data Analytics Capabilities and Sustainable Performance: The Role of Strategic Agility and Firm Creativity. Sustainability. 2023; 15(9): 7623. Publisher Full Text\n\nAnser MK, Yousaf SU, Usman B, et al.: Beyond climate change: Examining the role of environmental justice, agricultural mechanization, and social expenditures in alleviating rural poverty. Sustainable Futures. 2023; 6: 100130. Publisher Full Text\n\nAsha AA, Dulal M, Dr. Habib A : The influence of sustainable supply chain management, technology orientation, and organizational culture on the delivery product quality-customer satisfaction nexus. Clean. Logist. Supply Chain. 2023; 7: 100107. Publisher Full Text\n\nAshaari MA, Singh KSD, Abbasi GA, et al.: Big data analytics capability for improved performance of higher education institutions in the Era of IR 4.0: A multi-analytical SEM & ANN perspective. Technol. Forecast. Soc. Chang. 2021; 173: 121119. Publisher Full Text\n\nAshley JM: Chapter Five—Prevention of Future Food Insecurity.Ashley JM, editor. Food Security in the Developing World. Academic Press; 2016; pp. 81–140. Publisher Full Text\n\nAshraf I, Ahmad SR, Ashraf U, et al.: Community perspectives to improve flood management and socio-economic impacts of floods at Central Indus River, Pakistan. Int. J. Disaster Risk Reduct. 2023a; 92: 103718. Publisher Full Text\n\nAshraf W, Rehman A, Rabbani M, et al.: Aflatoxins posing threat to food safety and security in Pakistan: Call for a one health approach. Food Chem. Toxicol. 2023b; 180: 114006. PubMed Abstract \| Publisher Full Text\n\nAttinasi MG, Balatti M, Mancini M, et al.: Supply chain disruptions and the effects on the global economy.2022. Reference Source\n\nBag S, Rahman MS, Srivastava G, et al.: Examining the role of virtue ethics and big data in enhancing viable, sustainable, and digital supply chain performance. Technol. Forecast. Soc. Chang. 2023; 186: 122154. Publisher Full Text\n\nBag S, Wood LC, Xu L, et al.: Big data analytics as an operational excellence approach to enhance sustainable supply chain performance. Resour. Conserv. Recycl. 2020; 153: 104559. Publisher Full Text\n\nBayu F, Berhan E, Ebinger F: A System Dynamics Model for Dynamic Capability Driven Sustainability Management. J. Open Innov.: Technol. Mark. Complex. 2022; 8(1): 56. Publisher Full Text\n\nBelhadi A, Kamble SS, Zkik K, et al.: The integrated effect of Big Data Analytics, Lean Six Sigma and Green Manufacturing on the environmental performance of manufacturing companies: The case of North Africa. J. Clean. Prod. 2020; 252: 119903. Publisher Full Text\n\nBenzidia S, Makaoui N, Bentahar O: The impact of big data analytics and artificial intelligence on green supply chain process integration and hospital environmental performance. Technol. Forecast. Soc. Chang. 2021; 165: 120557. Publisher Full Text\n\nBhattacharya S, Kalakbandi VK: Barriers to circular supply chain: The case of unorganized tire retreading in India. Int. J. Logist. Manag. 2022; 34(3): 523–552. Publisher Full Text\n\nBirgonul Z: A receptive-responsive tool for customizing occupant’s thermal comfort and maximizing energy efficiency by blending BIM data with real-time information. Smart Sustain. Built. Environ. 2021; 10(3): 504–535. Publisher Full Text\n\nBoye JI, Arcand Y: Current Trends in Green Technologies in Food Production and Processing. Food Eng. Rev. 2013; 5(1): 1–17. Publisher Full Text\n\nBresciani S, Huarng K-H, Malhotra A, et al.: Digital transformation as a springboard for product, process and business model innovation. J. Bus. Res. 2021; 128: 204–210. Publisher Full Text\n\nBruhn NCP, Viglioni MTD, Nunes RF, et al.: Recyclable waste in Brazilian municipalities: A spatial-temporal analysis before and after the national policy on solid waste. J. Clean. Prod. 2023; 421: 138503. Publisher Full Text\n\nBukchin S, Kerret D: Food for Hope: The Role of Personal Resources in Farmers’ Adoption of Green Technology. Sustainability. 2018; 10(5): Article 5. Publisher Full Text\n\nde Burgos-Jiménez J , Vázquez-Brust D, Plaza-Úbeda JA, et al.: Environmental protection and financial performance: An empirical analysis in Wales. Int. J. Oper. Prod. Manag. 2013; 33(8): 981–1018. Publisher Full Text\n\nCalza F, Parmentola A, Tutore I: Big data and natural environment. How does different data support different green strategies? Sustainable Futures. 2020; 2: 100029. Publisher Full Text\n\nCastillo-Díaz FJ, Belmonte-Ureña LJ, López-Serrano MJ, et al.: Assessment of the sustainability of the European agri-food sector in the context of the circular economy. Sustain. Prod. Consum. 2023; 40: 398–411. Publisher Full Text\n\nCavazza A, Dal Mas F, Paoloni P, et al.: Artificial intelligence and new business models in agriculture: A structured literature review and future research agenda. Br. Food J. 2023; 125(13): 436–461. Publisher Full Text\n\nChatzoudes D, Chatzoglou P: Antecedents and effects of green supply chain management (GSCM) practices. BIJ. 2022; 30: 4014–4057. Publisher Full Text\n\nChen C: Influence of Employees’ Intention to Adopt AI Applications and Big Data Analytical Capability on Operational Performance in the High-Tech Firms. J. Knowl. Econ. 2023; 15: 3946–3974. Publisher Full Text\n\nCheng J, Mahinder Singh HS, Zhang Y-C, et al.: The impact of business intelligence, big data analytics capability, and green knowledge management on sustainability performance. J. Clean. Prod. 2023; 429: 139410. Publisher Full Text\n\nDakhan SA, Sohu JM, Jabeen A, et al.: Impact of Green HRM on Employees Pro-Environmental Behavior: Mediating Role of Women Environmental Knowledge at Higher Education Institutions. Int. J. Comput. Sci. Netw. Secur. 2020; 20(12): 202–208. Publisher Full Text\n\nDarko C, Yung PWS, Chen A, et al.: Review and recommendations for sustainable pathways of recycling commodity plastic waste across different economic regions. Resour. Environ. Sustain. 2023; 14: 100134. Publisher Full Text\n\nDas G, Li S, Tunio RA, et al.: The implementation of green supply chain management (GSCM) and environmental management system (EMS) practices and its impact on market competitiveness during COVID-19. Environ. Sci. Pollut. Res. 2023; 30(26): 68387–68402. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDavidescu AA, Manta EM, Pisică A, et al.: Exploring the Relationship Between Digitalisation, Sustainable Development and Industry: A Bibliometric Analysis.Akkaya B, Andreea Apostu S, Hysa E, et al., editors. Digitalization, Sustainable Development, and Industry 5.0. Emerald Publishing Limited; 2023; pp. 209–248. Publisher Full Text\n\nDebnath B, Siraj MT, Rashid KHO, et al.: Analyzing the critical success factors to implement green supply chain management in the apparel manufacturing industry: Implications for sustainable development goals in the emerging economies. Sustainable Manufacturing and Service Economics. 2023; 2: 100013. Publisher Full Text\n\nDeBoer J, Panwar R, Rivera J: Toward A Place-Based Understanding of Business Sustainability: The Role of Green Competitors and Green Locales in Firms’ Voluntary Environmental Engagement. Bus. Strateg. Environ. 2017; 26(7): 940–955. Publisher Full Text\n\nDhagarra D, Goswami M, Sarma PRS, et al.: Big Data and blockchain supported conceptual model for enhanced healthcare coverage. Business Process Management Journal. 2019; 25(7): 1612–1632. Publisher Full Text\n\nEl Ayoubi MS, Radmehr M: Green food supply chain management as a solution for the mitigation of food supply chain management risk for improving the environmental health level. Heliyon. 2023; 9(2): e13264. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEllström D, Holtström J, Berg E, et al.: Dynamic capabilities for digital transformation. J. Strateg. Manag. 2021; 15(2): 272–286. Publisher Full Text\n\nFallahpour A, Yazdani M, Mohammed A, et al.: Green sourcing in the era of industry 4.0: Towards green and digitalized competitive advantages. Ind. Manag. Data Syst. 2021; 121(9): 1997–2025. Publisher Full Text\n\nFeng Y, Lai K, Zhu Q: Green supply chain innovation: Emergence, adoption, and challenges. Int. J. Prod. Econ. 2022; 248: 108497. Publisher Full Text\n\nFilimonau V, Algboory H, Mohammed NK, et al.: Food waste and its management in the foodservice sector of a developing economy: An exploratory and preliminary study of a sample of restaurants in Iraq. Tour. Manag. Perspect. 2023; 45: 101048. Publisher Full Text\n\nFrempong J, Chai J, Ampaw EM, et al.: The relationship among customer operant resources, online value co-creation and electronic-word-of-mouth in solid waste management marketing. J. Clean. Prod. 2020; 248: 119228. Publisher Full Text\n\nGalanakis CM, Rizou M, Aldawoud TMS, et al.: Innovations and technology disruptions in the food sector within the COVID-19 pandemic and post-lockdown era. Trends Food Sci. Technol. 2021; 110: 193–200. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGe Y, Qi H, Qu W: The factors impacting the use of navigation systems: A study based on the technology acceptance model. Transport. Res. F: Traffic Psychol. Behav. 2023; 93: 106–117. Publisher Full Text\n\nGeorge AL: Case Studies and Theory Development: The Method of Structured, Focused Comparison.Springer International Publishing; 2019. https://www.springerprofessional.de/en/case-studies-and-theory-development-themethod-of-structured-foc/159679702\n\nGhosh S, Mandal MC, Ray A: Selection of environmental-conscious sourcing: An empirical investigation. BIJ. 2021a; 28(6): 2130–2155. Publisher Full Text\n\nGhosh S, Mandal MC, Ray A: Strategic sourcing model for green supply chain management: An insight into automobile manufacturing units in India. BIJ. 2021b; 29(10): 3097–3132. Publisher Full Text\n\nGupta S, Drave VA, Dwivedi YK, et al.: Achieving superior organizational performance via big data predictive analytics: A dynamic capability view. Ind. Mark. Manag. 2020; 90: 581–592. Publisher Full Text\n\nHaider Naqvi SL, Ayub F, Yasar A, et al.: Pollution status monitoring and indices development for evaluating sustainable environmental management practices (SEMP) in Quaid-e-Azam Industrial Estate, Pakistan. J. Clean. Prod. 2023; 405: 136944. Publisher Full Text\n\nHair JF, Hult GTM, Ringle CM, et al.: An Introduction to Structural Equation Modeling.Hair JF Jr., Hult GTM, Ringle CM, et al., editors. Partial Least Squares Structural Equation Modeling (PLS-SEM) Using R: A Workbook. Springer International Publishing; 2021; pp. 1–29. Publisher Full Text\n\nHair JF, Risher JJ, Sarstedt M, et al.: When to use and how to report the results of PLS-SEM. Eur. Bus. Rev. 2019; 31(1): 2–24. Publisher Full Text\n\nHaque F, Fan C, Lee Y-Y: From waste to value: Addressing the relevance of waste recovery to agricultural sector in line with circular economy. J. Clean. Prod. 2023; 415: 137873. Publisher Full Text\n\nHashmi SI, Hewage HTSA, Visvanathan C: Cleaner production auditing for plastic recycling industry in Pakistan: A baseline study. Chemosphere. 2023; 337: 139338. PubMed Abstract \| Publisher Full Text\n\nHassoun A, Prieto MA, Carpena M, et al.: Exploring the role of green and Industry 4.0 technologies in achieving sustainable development goals in food sectors. Food Res. Int. 2022; 162: 112068. PubMed Abstract \| Publisher Full Text\n\nHazen BT, Russo I, Confente I, et al.: Supply chain management for circular economy: Conceptual framework and research agenda. Int. J. Logist. Manag. 2020; 32(2): 510–537. Publisher Full Text\n\nHemphill TA: Managing food waste in the United States: A proposed public-private governance and sustainability model. Technological Sustainability. 2022; 2(1): 67–88. Publisher Full Text\n\nHenseler J, Ringle CM, Sarstedt M: A new criterion for assessing discriminant validity in variance-based structural equation modeling. J. Acad. Mark. Sci. 2015; 43(1): 115–135. Publisher Full Text\n\nHong J, Zhang Y, Ding M: Sustainable supply chain management practices, supply chain dynamic capabilities, and enterprise performance. J. Clean. Prod. 2018; 172: 3508–3519. Publisher Full Text\n\nHongyun T, Sohu JM, Khan AU, et al.: Navigating the digital landscape: Examining the interdependencies of digital transformation and big data in driving SMEs’ innovation performance. Kybernetes. 2023; 53(1): 1–29. Publisher Full Text\n\nHossain MU, Thomas Ng S: Influence of waste materials on buildings’ life cycle environmental impacts: Adopting resource recovery principle. Resour. Conserv. Recycl. 2019; 142: 10–23. Publisher Full Text\n\nIftikhar A, Ahmed N, Shah S, et al.: ANALYZING DIGITAL DIVIDE AMONG UNIVERSITY STUDENTS OF PAKISTAN. Turk. Online J. Dist. Educ. 2023; 24(2): 261–271. Publisher Full Text\n\nIqbal R, Raza M, Valipour M, et al.: Potential agricultural and environmental benefits of mulches—A review. Bull. Natl. Res. Cent. 2020; 44. Publisher Full Text\n\nIrfan M, Wang M, Zafar AU, et al.: Modeling the enablers of supply chain strategies and information technology: Improving performance through TISM approach. VINE J. Inf. Knowl. Manag. Syst. 2020; 51(3): 461–491. Publisher Full Text\n\nIshaq MI, Sarwar H, Franzoni S, et al.: The nexus of human resource management, corporate social responsibility and sustainable performance in upscale hotels: A mixed-method study. Int. J. Emerg. Mark. 2023. ahead-of-print. Publisher Full Text\n\nJalil F, Yang J, Rehman SU, et al.: Post-COVID-19’s impact on green supply chain management and sustainable E-commerce performance: The moderating role of big data analytics. Environ. Sci. Pollut. Res. 2023; 30: 115683–115698. PubMed Abstract \| Publisher Full Text\n\nJauhar SK, Jani SM, Kamble SS, et al.: How to use no-code artificial intelligence to predict and minimize the inventory distortions for resilient supply chains. Int. J. Prod. Res. 2023; 62: 5510–5534. Publisher Full Text\n\nJha A, Sharma RRK, Kumar V, et al.: Designing supply chain performance system: A strategic study on Indian manufacturing sector. Supply Chain Manag. 2021; 27(1): 66–88. Publisher Full Text\n\nJiang Y, Ritchie BW, Verreynne M-L: Building tourism organizational resilience to crises and disasters: A dynamic capabilities view. Int. J. Tour. Res. 2019; 21(6): 882–900. Publisher Full Text\n\nJunaid M, Zhang Q, Syed MW: Effects of sustainable supply chain integration on green innovation and firm performance. Sustainable Production and Consumption. 2022; 30: 145–157. Publisher Full Text\n\nJunejo I: Impact of Green Supply Chain Management on Sustainable performance: A dual mediated-moderated analysis of Green Technology Innovation and Big Data Analytics Capability powered by Artificial Intelligence. Dataset. figshare. 2024. Publisher Full Text\n\nKannan D, Solanki R, Kaul A, et al.: Barrier analysis for carbon regulatory environmental policies implementation in manufacturing supply chains to achieve zero carbon. J. Clean. Prod. 2022; 358: 131910. Publisher Full Text\n\nKayikci Y, Ozbiltekin M, Kazancoglu Y: Minimizing losses at red meat supply chain with circular and central slaughterhouse model. J. Enterp. Inf. Manag. 2019; 33(4): 791–816. Publisher Full Text\n\nKhan A, Tao M: Knowledge absorption capacity’s efficacy to enhance innovation performance through big data analytics and digital platform capability. J. Innov. Knowl. 2022; 7(3): 100201. Publisher Full Text\n\nKhatibi FS, Dedekorkut-Howes A, Howes M, et al.: Can public awareness, knowledge and engagement improve climate change adaptation policies? Discov. Sustain. 2021; 2(1): 18. Publisher Full Text\n\nKherazi FZ, Sun D, Sohu JM, et al.: The role of environmental knowledge, policies and regulations toward water resource management: A mediated-moderation of attitudes, perception, and sustainable consumption patterns. Sustain. Dev. 2024; 32(4): 1370–1593. Publisher Full Text\n\nKofi Opoku R, Yeboah Nyamah E, Yeboah Nyamah E, et al.: Sustainable manufacturing practices and sustainable performance: Evidence from Ghana’s food manufacturing sector. Clean. Logist. Supply Chain. 2023; 9: 100120. Publisher Full Text\n\nKraus S, Durst S, Ferreira JJ, et al.: Digital transformation in business and management research: An overview of the current status quo. Int. J. Inf. Manag. 2022; 63: 102466. Publisher Full Text\n\nKraus S, Jones P, Kailer N, et al.: Digital Transformation: An Overview of the Current State of the Art of Research. SAGE Open. 2021; 11(3): 21582440211047576. Publisher Full Text\n\nKumar S, Kumar R, Pandey A: Chapter 1 - Solid waste and wastewater management: A social and global perspective.Kumar S, Kumar R, Pandey A, editors. Current Developments in Biotechnology and Bioengineering. Elsevier; 2021; pp. 1–22. Publisher Full Text\n\nLai K, Feng Y, Zhu Q: Digital transformation for green supply chain innovation in manufacturing operations. Transp. Res. E Logist. Transp. Rev. 2023; 175: 103145. Publisher Full Text\n\nLe TT: The association of corporate social responsibility and sustainable consumption and production patterns: The mediating role of green supply chain management. J. Clean. Prod. 2023; 414: 137435. Publisher Full Text\n\nLe TT, Vo XV, Venkatesh VG: Role of green innovation and supply chain management in driving sustainable corporate performance. J. Clean. Prod. 2022; 374: 133875. Publisher Full Text\n\nLepore D, Vecciolini C, Micozzi A, et al.: Developing technological capabilities for Industry 4.0 adoption: An analysis of the role of inbound open innovation in small and medium-sized enterprises. Creat. Innov. Manag. 2023; 32(2): 249–265. Publisher Full Text\n\nLerman LV, Benitez GB, Müller JM, et al.: Smart green supply chain management: A configurational approach to enhance green performance through digital transformation. Supply Chain Manag. 2022; 27(7): 147–176. Publisher Full Text\n\nLi L, Shan S, Dai J, et al.: The impact of green supply chain management on green innovation: A meta-analysis from the inter-organizational learning perspective. Int. J. Prod. Econ. 2022; 250: 108622. Publisher Full Text\n\nLim WM, O’Connor P, Nair S, et al.: A foundational theory of ethical decision-making: The case of marketing professionals. J. Bus. Res. 2023; 158: 113579. Publisher Full Text\n\nLopes de Sousa Jabbour AB, Chiappetta Jabbour CJ, Hingley M, et al.: Sustainability of supply chains in the wake of the coronavirus (COVID-19/SARS-CoV-2) pandemic: Lessons and trends. Modern Supply Chain Research and Applications. 2020; 2(3): 117–122. Publisher Full Text\n\nMa L, Iqbal N, Bouri E, et al.: How good is green finance for green innovation? Evidence from the Chinese high-carbon sector. Res. Policy. 2023; 85: 104047. Publisher Full Text\n\nMaaz MAM, Ahmad R, Abad A: Antecedents and consequences of green supply chain management practices: A study of Indian food processing industry. BIJ. 2021; 29(7): 2045–2073. Publisher Full Text\n\nMagsamen-Conrad K, Billotte-Verhoff C, Dillon J: Technology Acceptance Models.2022. Publisher Full Text\n\nvan der Meulen B , Card MM, Din A, et al.: Chapter 3—Food regulation around the world.Martinović A, Oh S, Lelieveld H, editors. Ensuring Global Food Safety. Academic Press; Second Edition2022; pp. 11–137. Publisher Full Text\n\nMicheli GJL, Cagno E, Mustillo G, et al.: Green supply chain management drivers, practices and performance: A comprehensive study on the moderators. J. Clean. Prod. 2020; 259: 121024. Publisher Full Text\n\nMor S, Ravindra K: Municipal solid waste landfills in lower- and middle-income countries: Environmental impacts, challenges and sustainable management practices. Process Saf. Environ. Prot. 2023; 174: 510–530. Publisher Full Text\n\nMorimura F, Sakagawa Y: The intermediating role of big data analytics capability between responsive and proactive market orientations and firm performance in the retail industry. J. Retail. Consum. Serv. 2023; 71: 103193. Publisher Full Text\n\nMubarik M, Raja Mohd Rasi RZ, Mubarak MF, et al.: Impact of blockchain technology on green supply chain practices: Evidence from emerging economy. Management of Environmental Quality: An International Journal. 2021; 32(5): 1023–1039. Publisher Full Text\n\nNikseresht A, Golmohammadi D, Zandieh M: Sustainable green logistics and remanufacturing: A bibliometric analysis and future research directions. Int. J. Logist. Manag. 2023; 35: 755–803. Publisher Full Text\n\nNirmal DD, Nageswara Reddy K, Singh SK: Application of fuzzy methods in green and sustainable supply chains: Critical insights from a systematic review and bibliometric analysis. BIJ. 2023; 31: 1700–1748. Publisher Full Text\n\nNiu Y, Wen W, Wang S, et al.: Breaking barriers to innovation: The power of digital transformation. Financ. Res. Lett. 2023; 51: 103457. Publisher Full Text\n\nO’Connor G: Shifting the value of food and organic waste management in the food services sector in Brisbane, Australia. Resources, Conservation & Recycling Advances. 2021; 12: 200052. Publisher Full Text\n\nObuobi B, Zhang Y, Adu-Gyamfi G, et al.: Fruits and vegetable waste management behavior among retailers in Kumasi, Ghana. J. Retail. Consum. Serv. 2022; 67: 102971. Publisher Full Text\n\nOyedijo A, Kusi-Sarpong S, Mubarik MS, et al.: Multi-tier sustainable supply chain management: A case study of a global food retailer. Supply Chain Manag. 2023; 29; 68–97. Publisher Full Text\n\nPapamichael I, Voukkali I, Stylianou M, et al.: Chapter 12—Concept of waste-to-energy strategies.Jeguirim M, Zorpas AA, editors. Advances in Biofuels Production, Optimization and Applications. Elsevier; 2024; pp. 241–267. Publisher Full Text\n\nPeng B, Wang Y, Zahid S, et al.: Platform ecological circle for cold chain logistics enterprises: The value co-creation analysis. Ind. Manag. Data Syst. 2020; 120(4): 675–691. Publisher Full Text\n\nPoláková-Kersten M, Khanagha S, van den Hooff B , et al.: Digital transformation in high-reliability organizations: A longitudinal study of the micro-foundations of failure. J. Strateg. Inf. Syst. 2023; 32(1): 101756. Publisher Full Text\n\nPraveenkumar TR, Sekar M, Pasupuleti RR, et al.: Current technologies for plastic waste treatment for energy recovery, it’s effects on poly aromatic hydrocarbons emission and recycling strategies. Fuel. 2024; 357: 129379. Publisher Full Text\n\nPunj N, Ahmi A, Tanwar A, et al.: Mapping the field of green manufacturing: A bibliometric review of the literature and research frontiers. J. Clean. Prod. 2023; 423: 138729. Publisher Full Text\n\nQazi SA, Moazzam M, Ahmed W, et al.: Green in-store operations and sustainability performance: The moderating role of organization size. Int. J. Product. Perform. Manag. 2022; 72; 2765–2781. Publisher Full Text\n\nQin X, Godil DI, Sarwat S, et al.: Green practices in food supply chains: Evidence from emerging economies. Oper. Manag. Res. 2022; 15(1): 62–75. Publisher Full Text\n\nRaeesi R, Sahebjamnia N, Mansouri SA: The synergistic effect of operational research and big data analytics in greening container terminal operations: A review and future directions. Eur. J. Oper. Res. 2023; 310(3): 943–973. Publisher Full Text\n\nRagasri S, Sabumon PC: A critical review on slaughterhouse waste management and framing sustainable practices in managing slaughterhouse waste in India. J. Environ. Manag. 2023; 327: 116823. PubMed Abstract \| Publisher Full Text\n\nRagasri S, Sabumon PC: A critical review on slaughterhouse waste management and framing sustainable practices in managing slaughterhouse waste in India. J. Environ. Manage. 2023; 327: 116823. Publisher Full Text\n\nRahman HU, Zahid M, Ullah M, et al.: Green supply chain management and firm sustainable performance: The awareness of China Pakistan Economic Corridor. J. Clean. Prod. 2023; 414: 137502. Publisher Full Text\n\nRambaldi C: A review of the development divide between Global North and South through a Foucauldian perspective. Development Studies Research. 2022; 9(1): 67–69. Publisher Full Text\n\nRasheed T, Bilal M, Nabeel F, et al.: Environmentally-related contaminants of high concern: Potential sources and analytical modalities for detection, quantification, and treatment. Environ. Int. 2019; 122: 52–66. PubMed Abstract \| Publisher Full Text\n\nRehman SU, Bresciani S, Ashfaq K, et al.: Intellectual capital, knowledge management and competitive advantage: A resource orchestration perspective. J. Knowl. Manag. 2021; 26(7): 1705–1731. Publisher Full Text\n\nRehman SU, Elrehail H, Poulin M, et al.: Green managerial practices and green performance: A serial mediation model. Int. J. Innov. Stud. 2023; 7(3): 196–207. Publisher Full Text\n\nRejeb A, Rejeb K, Appolloni A, et al.: The landscape of public procurement research: A bibliometric analysis and topic modelling based on Scopus. Journal of Public Procurement. 2023; 23(2): 145–178. Publisher Full Text\n\nRen X, He J, Huang Z: Innovation, natural resources abundance, climate change and green growth in agriculture. Res. Policy. 2023; 85: 103970. Publisher Full Text\n\nRoy S, Rautela R, Kumar S: Towards a sustainable future: Nexus between the sustainable development goals and waste management in the built environment. J. Clean. Prod. 2023; 415: 137865. Publisher Full Text\n\nRupa RA, Saif ANM: Impact of Green Supply Chain Management (GSCM) on Business Performance and Environmental Sustainability: Case of a Developing Country. Bus. Perspect. Res. 2022; 10(1): 140–163. Publisher Full Text\n\nSöderholm P: The green economy transition: The challenges of technological change for sustainability. Sustainable Earth. 2020; 3(1): 6. Publisher Full Text\n\nSaberi S, Kouhizadeh M, Sarkis J, et al.: Blockchain technology and its relationships to sustainable supply chain management. Int. J. Prod. Res. 2019; 57(7): 2117–2135. Publisher Full Text\n\nSahoo S, Kumar A, Upadhyay A: How do green knowledge management and green technology innovation impact corporate environmental performance? Understanding the role of green knowledge acquisition. Bus. Strateg. Environ. 2023; 32(1): 551–569. Publisher Full Text\n\nSaini N, Malik K, Sharma S: Transformation of Supply Chain Management to Green Supply Chain Management: Certain investigations for research and applications. Cleaner Materials. 2023a; 7: 100172. Publisher Full Text\n\nSaini R, Kaur S, Aggarwal P, et al.: Conventional and emerging innovative processing technologies for quality processing of potato and potato-based products: A review. Food Control. 2023b; 153: 109933. Publisher Full Text\n\nSalam M, Alam F, Dezhi S, et al.: Exploring the role of Black Soldier Fly Larva technology for sustainable management of municipal solid waste in developing countries. Environ. Technol. Innov. 2021; 24: 101934. Publisher Full Text\n\nSalam M, Zheng L, Shi D, et al.: Exploring Insect-based technology for waste management and livestock feeding in selected South and East Asian countries. Environ. Technol. Innov. 2023; 32: 103260. Publisher Full Text\n\nSamad S, Nilashi M, Almulihi A, et al.: Green Supply Chain Management practices and impact on firm performance: The moderating effect of collaborative capability. Technol. Soc. 2021; 67: 101766. Publisher Full Text\n\nSarkis J: A strategic decision framework for green supply chain management. J. Clean. Prod. 2003; 11(4): 397–409. Publisher Full Text\n\nScherer R, Siddiq F, Tondeur J: The technology acceptance model (TAM): A meta-analytic structural equation modeling approach to explaining teachers’ adoption of digital technology in education. Comput. Educ. 2019; 128: 13–35. Publisher Full Text\n\nSchintler LA, McNeely CL: Artificial intelligence, institutions, and resilience: Prospects and provocations for cities. J. Urban Manag. 2022; 11(2): 256–268. Publisher Full Text\n\nShamsuddoha M: Integrated Supply Chain Model for Sustainable Manufacturing: A System Dynamics Approach. Sustaining Competitive Advantage Via Business Intelligence, Knowledge Management, and System Dynamics. Emerald Group Publishing Limited; 2015; Vol. 22B. : pp. 155–399. Publisher Full Text\n\nShi P, Han K, Hou R: Modeling and analysis of a sustainable supply chain with fairness concerns and green-sensitive consumer demand. Manag. Decis. 2022; 61(5): 1298–1319. Publisher Full Text\n\nShmueli G, Sarstedt M, Hair JF, et al.: Predictive model assessment in PLS-SEM: Guidelines for using PLSpredict. Eur. J. Mark. 2019; 53(11): 2322–2347. Publisher Full Text\n\nSohu JM, Hongyun T, Akbar US, et al.: Digital Innovation, Digital Transformation, and Digital Platform Capability: Detrimental Impact of Big Data Analytics Capability on Innovation Performance. International Research Journal of Management and Social Sciences. 2023; 4(3). Publisher Full Text\n\nSohu JM, Hongyun T, Junejo I, et al.: Driving sustainable competitiveness: Unveiling the nexus of green intellectual capital and environmental regulations on greening SME performance. Front. Environ. Sci. 2024; 12(3). Publisher Full Text\n\nSrivastava K, Dey S: Role of digital technology in teaching-learning process. IOSR Journal of Humanities and Social Science (IOSR-JHSS). 2018; 23(1): 74–79.\n\nSrivastava S, Singh RK: Exploring integrated supply chain performance in healthcare: A service provider perspective. BIJ. 2020; 28(1): 106–130. Publisher Full Text\n\nTariq MI, Abbass K, Chebbi K, et al.: Assessing the role of green supply chain management in enhancing Pakistan manufacturers’ performances. Environ. Sci. Pollut. Res. 2023; 30(32): 78495–78506. PubMed Abstract \| Publisher Full Text\n\nTasnim Z, Hamid ABA, Dwivedi YK, et al.: Sustainable disaster supply chain management for relief operations in Bangladesh. Journal of Humanitarian Logistics and Supply Chain Management. 2022; 12(2): 285–304. Publisher Full Text\n\nTechnology Acceptance Model—An overview\|ScienceDirect Topics: n.d. Retrieved November 19, 2023. Reference Source\n\nTjahjadi B, Soewarno N, Karima TE, et al.: Business strategy, spiritual capital and environmental sustainability performance: Mediating role of environmental management process. Bus. Process. Manag. J. 2022; 29(1): 77–99. Publisher Full Text\n\nTorres P: Facing disaster: The great challenges framework. Foresight. 2018; 21(1): 4–34. Publisher Full Text\n\nTostivint C, de Veron S , Jan O, et al.: Measuring food waste in a dairy supply chain in Pakistan. J. Clean. Prod. 2017; 145: 221–231. Publisher Full Text\n\nTrivedi M, Bulsara HP, Shukla Y: Why millennials of smart city are willing to pay premium for toxic-free food products: Social media perspective. Br. Food J. 2023; 125(9): 3368–3388. Publisher Full Text\n\nTrujillo-Gallego M, Sarache W: A Conceptual Framework of Green Supply Chain Management: Influential Factors, Green Practices, and Performance.García-Alcaraz JL, Realyvásquez-Vargas A, Z-Flores E, editors. Trends in Industrial Engineering Applications to Manufacturing Process. Springer International Publishing; 2021; pp. 3–33. Publisher Full Text\n\nTsai FM, Bui T-D, Tseng M-L, et al.: Sustainable supply chain management trends in world regions: A data-driven analysis. Resour. Conserv. Recycl. 2021; 167: 105421. Publisher Full Text\n\nWakiru JM, Pintelon L, Muchiri P, et al.: A comparative analysis of maintenance strategies and data application in asset performance management for both developed and developing countries. Int. J. Qual. Reliab. Manag. 2021; 39(4): 961–983. Publisher Full Text\n\nWang C, Qiao Y, Li X: A systems approach for green public procurement implementation. Journal of Public Procurement. 2020; 20(3): 287–311. Publisher Full Text\n\nWang W, Su L: Identifying latent group structures in nonlinear panels. J. Econom. 2021; 220(2): 272–295. Publisher Full Text\n\nWaseem HB, Rana IA: Floods in Pakistan: A state-of-the-art review. Nat. Hazards Res. 2023; 3: 359–373. Publisher Full Text\n\nWorld Bank, R: Solid Waste Management.2020. Reference Source\n\nXie R, Teo TSH: Green technology innovation, environmental externality, and the cleaner upgrading of industrial structure in China—Considering the moderating effect of environmental regulation. Technol. Forecast. Soc. Chang. 2022; 184: 122020. Publisher Full Text\n\nYang G, Nie Y, Li H, et al.: Digital transformation and low-carbon technology innovation in manufacturing firms: The mediating role of dynamic capabilities. Int. J. Prod. Econ. 2023a; 263: 108969. Publisher Full Text\n\nYang Y, Chen J, Lee PKC, et al.: How to enhance the effects of the green supply chain management strategy in the organization: A diffusion process perspective. Transportation Research Part E: Logistics and Transportation Review. 2023b; 175: 103148. Publisher Full Text\n\nYe Y, Lau KH, Teo L: Alignment of green supply chain strategies and operations from a product perspective. Int. J. Logist. Manag. 2023; 34: 1566–1600. Publisher Full Text\n\nYildiz Çankaya S, Sezen B: Effects of green supply chain management practices on sustainability performance. J. Manuf. Technol. Manag. 2018; 30(1): 98–121. Publisher Full Text\n\nYousafzai MT, Nawaz M, Xin C, et al.: Sustainability of waste picker sustainopreneurs in Pakistan’s informal solid waste management system for cleaner production. J. Clean. Prod. 2020; 267: 121913. Publisher Full Text\n\nYousefloo A, Babazadeh R: Designing an integrated municipal solid waste management network: A case study. J. Clean. Prod. 2020; 244: 118824. Publisher Full Text\n\nYu H, Wang J, Hou J, et al.: The effect of economic growth pressure on green technology innovation: Do environmental regulation, government support, and financial development matter? J. Environ. Manag. 2023; 330: 117172. PubMed Abstract \| Publisher Full Text\n\nZhang P, Li Z, Ghardallou W, et al.: Nexus of institutional quality and technological innovation on renewable energy development: Moderating role of green finance. Renew. Energy. 2023; 214: 233–241. Publisher Full Text\n\nZhang Q, Gao B, Luqman A: Linking green supply chain management practices with competitiveness during covid 19: The role of big data analytics. Technol. Soc. 2022; 70: 102021. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhen H, Yuan K, Qiao Y, et al.: Eco-compensation quantification of sustainable food waste management alternatives based on economic and environmental life cycle cost-benefit assessment. J. Clean. Prod. 2023; 382: 135289. Publisher Full Text\n\nZhou SS, Zhou AJ, Feng J, et al.: Dynamic capabilities and organizational performance: The mediating role of innovation. J. Manag. Organ. 2019; 25(5): 731–747. Publisher Full Text\n\nZhu Q, Sarkis J, Lai K: Choosing the right approach to green your supply chains. Modern Supply Chain Research and Applications. 2019; 1(1): 54–67. Publisher Full Text\n\nZuberi MJS, Ali SF: Greenhouse effect reduction by recovering energy from waste landfills in Pakistan. Renew. Sust. Energ. Rev. 2015; 44: 117–131. Publisher Full Text" }	[ { "id": "333916", "date": "03 Jan 2025", "name": "Md Rokibul Hasan", "expertise": [ "Reviewer Expertise Supply chain. Business Data Analytics", "Artificial Intelligence", "Machine learning" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn summation, the article logically explores the impact of GSCM on sustainable performance within the food processing sector in Pakistan with the inclusion of GTI and BDAC-AI as mediating and moderating variables, respectively. This study examines the role of green supply chain management in driving green technology innovation and waste management for better sustainable performance by applying the Technology Acceptance Model and Dynamic Capability Theory to interpret such a relationship. With the use of SEM and data from 495 managers, the authors found that GSCM, GTI, WM, and BDAC-AI have a positive impact on firms' sustainable performance.\nConstructive Criticism: Shortcomings in the sample case studies and generalizability concerns: The manuscript has only been focused on the food processing industry of Pakistan, limiting the generalizability of its findings to other industries or regions. To address this shortcoming the author should consider expanding the sample case studies to include other sectors, such as textiles or manufacturing, to improve the applicability of the findings across various industries. Additionally, cross-country comparisons with other developing nations could strengthen insights into regional differences in green supply chain management (GSCM) practices. Susceptible Self-Reported Data: The study mostly used self-reported data from managers which could possibly introduce bias and distortions in the study. Respondents might overstate the potential benefits of their GSCM practices. Future studies should consider using objective performance metrics or third-party assessments in order to enhance the reliability of responses. Equally important, it would be interesting to integrate observational data or industry Benchmarks that would add rigor and reduce reliance on potentially biased self-reports. Overreliance on Cross-section Data: The cross-sectional data used in the study may not represent the long-run influence GSCM, GTI, and BDAC have on sustainability performance. To resolve this issue the author should consider incorporating a longitudinal design to engage in the observation of changes and evaluation of long-term effects from GSCM initiatives. This will serve to reinforce the identification of any lagged effects of GTI and BDAC on SP. Inadequate discussion on the Barriers to Implementation: The study briefly discusses GSCM, GTI, and BDAC but has not gone into details about the particular barriers companies may face in terms of financial constraints, lack of technical expertise, and resistance to change in the implementation of these practices. It is recommended that at least one section be dedicated to the implementation challenges and possible solutions or strategies to overcome such impediments. Qualitative insights will enrich the study with a more real approach toward these challenges, probably obtained from interviews with industry professionals. Limited Attention to Policy Implications: The study omits detailed discussions on policy implications, which could be particularly valuable in fostering sustainable practices within the food sector. To improve, the author should add a section to discuss ways in which government and industry policies can support GSCM and green technology innovation adoption. Specifically, the policy recommendations may include financial incentives for green technology, waste management good practice incentives, or guidance on data analytics adoption to enhance sustainable performance.\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": [] }, { "id": "342802", "date": "03 Jan 2025", "name": "Samir Zic", "expertise": [ "Reviewer Expertise Industrial management", "Inventory optimization", "Supply chain optimization", "Operational 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\nStudy design follows positive practice and established routines in scientific literature. The authors have provided enough recent studies as references.\nThe authors mentioned that “food manufacturing firms and those with managerial positions in Pakistan were targeted.” An explanation of important aspects of participating companies, such as size (number of employees), maturity, years in business, financial results, number of subsidiaries, etc., is not provided and is an important aspect of the research. By reading this paper in its current form, readers can't find more details about companies that participated in this research (except they are classified as SMEs, but that classification changes from country to country. The authors didn’t provide information about Pakistan’s definition of SME). This is an important aspect and needs to be addressed appropriately. With a lack of information about participating companies, research can’t be repeated outside of Pakistan or even within Pakistan but in different regions.\nVariables have different names in Excel file and text. It should be uniform.\nThe authors state, “SPSS was used to clean the data and deal with missing values”. This process affects the results and outcomes of the study, but information on the number of missing values and the cleaning process is not provided.\nWe don’t know how many questionnaires were sent and how many were received.\nIn the text, the authors mention 495 responses from managers in the food processing industry; however, only 492 are listed in Excel.\n“In this study, food manufacturing firms and those with managerial positions in Pakistan were targeted. Four hundred ninety-five cases were used for data analysis, and the sampling strategy was a random sampling strategy to give all employees of the stated firms a chance.” In the end, who did fulfill the questionnaire – managers or “all employees of the stated firms”?\nThe questionnaire has 5 variables with a total of 26 questions. Each question can be answered with values of 1 to 5. This is not clearly defined within the paper. Results from 492 (based on Excel) or 495 (based on paper) questionnaires can have a cumulative value from 26 up to 130. Having identical cumulative values for different answers is not uncommon. In this research, based on 492 results, there are 26 groups with a cumulative value of 71, 18 groups with a cumulative value of 76 etc.). However, out of 492 questionnaires, 65 (13%) have identical answers on all 26 questions, which is challenging to explain statistically. Furthermore, some of these 65 duplicate questionnaires occur in larger groups. This is noticeable for questionnaires with a cumulative value of 65, where the same questionnaire repeats 8 times. Statistically, there is a very small chance of something like that. Authors are invited to explain or correct this. This is a crucial question since further analyses and conclusions arise from this data.\nAn explanation of the conceptual model, as presented in Figure 1, is not provided. The authors didn’t provide info on why they are connected to the framework as they are. Positioning Big Data Analytics Capability – Artificial Intelligence on different positions seems reasonable but would completely change the outcomes of this research. More explanations are required.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1140
https://f1000research.com/articles/13-1139/v1	07 Oct 24	{ "type": "Systematic Review", "title": "Effect of Methocarbamol on acute low back pain: A systematic review", "authors": [ "Bahria Wided", "Makhlouf Yasmine", "Boussaid Intissar", "Walha Yasmine", "Nouira Nour Elhouda", "Laater Ahmed", "Makhlouf Yasmine", "Boussaid Intissar", "Walha Yasmine", "Nouira Nour Elhouda", "Laater Ahmed" ], "abstract": "Introduction Pharamcological treatment for acute low back pain (ALBP) typically involves opioid drugs, and non-steroidal anti-inflammatory drugs (NSAIDs). Methocarbamol is utilized primarily for managing muscle spasms and pain. This systematic review aims to provide an updated synthesis of published literature on the effects of Methocarbamol on pain outcomes in ALBP.\n\nMethods This systematic review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Original articles published until December 2023 were sourced from PubMed, Embase, and the Cochrane Library. Articles focusing on the impact of Methocarbamol on pain outcomes in ALBP patients were included.\n\nResults Three studies met the inclusion criteria, published between 2018 and 2023. The total study population comprised 405 ALBP patients, with 163 receiving Methocarbamol. Compared to patients not receiving Methocarbamol, those in the Methocarbamol group showed pain improvement at one week. However, at 30 and 60 minutes after intravenous administration, Methocarbamol was less effective than Diazepam. The primary reported adverse event was nausea.\n\nConclusion When administered in combination with Indomethacin or Naproxen, Methocarbamol shows potential for improving pain outcomes at one week in ALBP patients. However, its efficacy appears inferior to Diazepam in the short-term management of pain", "keywords": [ "Methocarbamol", "Back pain", "Acute" ], "content": "Introduction\n\nAcute low back pain (ALBP) is defined as acute pain located below the costal margin and above the inferior gluteal folds.1 It can arise from a variety of causes and affects individuals of all ages.1 The intensity of ALBP can range from mild to severe, potentially leading to functional limitations such as difficulty walking and impaired daily activities.2 Consequently, ALBP imposes a significant burden on the healthcare system.2 In 2017, it accounted for 65 million years lived with disability in low- and middle-income countries.3 Additionally, ALBP is a common reason for visits to emergency departments (EDs).4 In the United States, it accounts for 2.4% of ED visits, totaling approximately 2.4 million visits annually.5\n\nRegarding treatment modalities, ALBP is typically managed with non-steroidal anti-inflammatory drugs (NSAIDs), level 1 analgesics, and opioids, alongside physical therapy, which alleviates pain in most cases.6 However, despite adequate treatment with NSAIDs, half of the patients continue to experience pain after discharge from the ED. Additionally, methocarbamol, a central muscle relaxant, has been reported to have a beneficial effect on ALBP.7 Although its mechanism of action is not completely understood, it is believed to act through the central nervous system rather than directly on skeletal muscles.8 In the literature, there are still disagreements regarding the prescription of methocarbamol, primarily due to the lack of clear consensus on its appropriateness.\n\nTo provide a more comprehensive assessment, we conducted this systematic review to present the most up-to-date published literature on the effectiveness of methocarbamol in treating ALBP.\n\n\nMethods\n\nThis systematic review adhered to the preferred reporting items for systematic review and metanalysis (PRISMA) guidelines.9 The data analyzed were sourced from published studiesand no ethical approval or written informed consent was necessary for this research.\n\nLiterature searches were performed in MEDLINE, EMBASE and Cochrane library from inception to December 2023. For PubMed, The searches used a combination of the MeSH (Medical Subject Headings) terms “Acute low back pain”, “methocarbamol” and “randomised controlled trial” or their synonyms. The inclusion criteria of this review was detailed in Table 1. Citation tracking was performed from included full-text articles and previous relevant systematic reviews. We included papers written in English language. In the Embase and Cochrane Library, the specified terms were searched within the article title, abstract, or keywords.\n\nWe included for the present paper 1) Randomized controlled trials including patients with ALBP and treated with Methocarbamol 2) Studies that compared Methocarbamol to another treatment or placebo in the management of ALBP 3) We did not restrict to any specific symptom severity or duration compared to groups with other medical treatments.\n\nPublications that did not align in compliance with the purpose of this systematic review as well as those that were not original research including (metaanalysis, reviews, editorials, qualitative papers, case reports, comments, and letters to editors) were excluded. Additional articles were manually identifieng by reviewing the references of selected articles. In cases of studies had overlapping data, the most comprehensive one was chosen. After a through examination of titles and abstracts, articles not meeting the inclusion criteria were excluded. Data extraction and quality assessment Extracted data from each study was conducted independently by both investigators (YM and BW) then compared, discussed and finally any disagreements were resolved.\n\nThe extracted data encompassed the key methodological characteristics of the 3 studies: (year of publication, country, study design, number of included subjects, mean age of participants, inclusion and exclusion criteria and follow-up duration). Our primary outcome was the evaluation of the effect of Methocarbamol on relieving pain in patients with ALBP.\n\nFurthermore, we identified potential biases of the RCTs using the revised Cochrane collaboration’s tool for assessing risk of bias (RoB2).10 Only studies that met high quality belonged to our final selection.\n\n\nResults\n\nFor this update, we identified 104 papers through the database. After removing duplicates, we screened 4 titles and abstracts. We excluded a German language paper. In total, we finally included 3 papers for analysis. The flow chart of this systematic review is summarized in the extended data 1 (Refer extended data).\n\nThe main characteristics of the three studies included in this systematic review are summarized in extended data 2. These three RCTs were published in 2018, 2021, and 2023.11–13 The studies were conducted in United States (n=1)11 and Iran (n=2).12,13 Inclusion criteria for these studies were adult patients aged 18 years or older with ALBP. Exclusion criteria included non-traumatic ALBP for all studies4–6 and the presence of radicular pain in the study by Benjamin W. et al.\n\nOverall, 405 patients were included in the three studies, with sample sizes ranging from 6412 to 240.11 The mean age, when reported, was 41.4 years, although age extremes were not specified. Baseline characteristics were comparable between the groups. The control groups received either Orphenadrine or placebo,11 Indomethacin,12 or Diazepam.13 Methocarbamol was administered to 163 patients [32-81], in combination with Naproxen,11 Indomethacin,12 or morphine.13 The administration of methocarbamol was oral in two studies, with dosages ranging from 250 mg three times daily to 500 mg three times daily,11,12 and intravenous in one study, with a dosage of 100 mg in 10 ml IV over 3 minutes.13\n\nThe effectiveness of Methocarbamol was evaluated at 30 and 60 minutes post-administration,13 at one week,11,12 and after three months.11 Pain was assessed with the Numeric Rating Scale (NRS),13 the Visual Analogue Scale (VAS),12 the Back Pain Function Scale (BPFS),12 and the ordinal pain scale.11 Only Friedman’s study evaluated functional impairment post-intervention using the RMDQ.11 At one week post-intervention, patients in the Methocarbamol + Indomethacin group experienced significantly greater reductions in VAS scores and improvements in BPFS compared to the Indomethacin alone group (VAS: 3.66 ± 3.17 vs. 1.84 ± 1.53; P < 0.001; BPFS: 19.44 ± 8.66 vs. 4.75 ± 4.35; p < 0.001).12 Similarly, the mean RMDQ score improved by 8.1 (95% CI: 6.1, 10.1) in the Methocarbamol group compared to the Orphenadrine and placebo groups, though this did not surpass the clinical significance threshold.11 No differences were observed in pain or functional outcomes at three months among the groups. In the study by Sharifi and al., NRS scores improved at 60 minutes compared to baseline in both groups, with a slightly greater reduction in pain in the Diazepam group compared to the Methocarbamol (mean difference: −6.1, 95% CI: −6.5 to −5.7 vs. −5.2, 95% CI: −5.7 to −4.7, respectively; p < 0.001).13 The distribution of various pain score measures is represented in Table 2.\n\n* P < 0.05.\n\n** P < 0.001.\n\nFactors associated with acute low back pain (ALBP) were assessed in two studies.12,13 In the study by Sharifi et al., baseline pain scores were comparabke between men and women measauring 8.8 (1.2) vs. 8.6 (1.4) (95% CI for the difference: -0.3 to 0.8, p = 0.326).13 In contrast, Shiva et al. found that male patients in the Methocarbamol + Indomethacin group had a significantly greater mean increase in back pain functional status (BPFS) compared to those in the Indomethacin alone group following the intervention (49.87 ± 10.82 vs. 39.67 ± 8.89; p < 0.05).12\n\nAdverse events were evaluated in two studies.11,13 No serious or unexpected adverse events were reported. In the Methocarbamol group, side effects included central nervous system (CNS) adverse effects such as drowsiness,11,13 somnolence,13 drowsiness,11 stomach irritation11 and dizziness. However, side effects were comparable between the groups11,13 and were reported by 17% (95%CI: 10, 28%) of placebo patients, 9%(95%CI:4, 19%) of orphenadrine patients, and 19%(95%CI: 11, 29%) of methocarbamol patients. More importantly, Diazepam was significantly associated with CNS adverse effects compared to Methocarbamol.\n\n\nDiscussion\n\nWe conducted a systematic review of recent literature focusing on the impact of Methocarbamol on ALBP, encompassing three articles. The key findings derived from this review are as follows: 1) Methocarbamol demonstrated an overall beneficial effect in treating ALBP, and 2) This positive effect did not correlate with an increase in adverse events.\n\nThe management of ALBP in the emergency department varies and is specific to each unit, primarily due to conflicting evidence regarding the efficacy of analgesics.14 While acetaminophen, NSAIDs, and muscle relaxants have shown modest analgesic effects in short-term trials,15 they continue to be widely used in daily practice. However, the limited alternatives available have led some to resort to other medications such as opioids and diazepam.16 The latter was more effective than placebo in improving ALBP. However, opioids are associated with several adverse events mainly sedation and constipation, and are not recommended as a long-term treatment.\n\nSimilarly, muscle relaxants are also considered a treatment option for reducing muscle spasms. Several guidelines recommend the use of Methocarbamol in the management of ALBP in general, with varying effects. Two systematic reviews yielded robust results, indicating the effectiveness of muscle relaxant therapy in treating simple ALBP, with maximum benefit observed within the first 2 weeks.17,18 Similarly, muscle relaxants are also a treatment option through reducing muscle spasms. Several guidelines recommend the use of Methocarbamol in the management of LBP in general with variable effect. Two systematicreviews provided robust results indicating the effectiveness of muscle relaxant therapy in treating simple acute low back pain with a maximum benefit in the first 2 weeks.17,18\n\nIn this review, the effect was observed at one week, although 30% still had LBP at 3 months.2 Ideally, this subgroup of patients should be targeted for close follow-up to prevent the transition from acute to chronic pain.4 Similarly, current evidence suggests that Methocarbamol may be more beneficial when used alongside other therapeutic modalities, particularly analgesics and NSAIDs.18 This was corroborated in our review, which found strong evidence that combining Methocarbamol with NSAIDs enhances recovery. Furthermore, our review highlighted the adverse events associated with Methocarbamol, particularly those affecting the central nervous system, similar to those seen with Benzodiazepine treatments.18 As a result, while Methocarbamol shows promise as an alternative for reducing ALBP, caution is advised in its use.\n\nTo the best of the authors’ knowledge, this is first systematic review evaluating the effect of Methocarbamol on ALB. However, there are some limitations to consider. Firstly, the number of investigated studies was limited. Nonetheless, this review incorporated RCTs with sufficient sample sizes to yield statistically significant results and the quality of the studies was rated as good according to the Cochrane tool risk assessment bias. On the other hand, Methocarbamol was combined with NSAIDs in two studies,4,5 which may hinder the real effect of the studied molecule. Future trials should adress this issues by including larger sample sizes and control groups to better understand the specific implication of each subset ultimately leading to a more comprhensive approach.\n\n\nConclusion\n\nCurrent evidence suggests that Methocarbamol may improve pain in ALBP patients after one week of use. However, more rigorous prospective controlled studies with extended follow-up are necessary to.\n\nFinding suggests that Methocarbamol may improved pain in patients with acute low back pain (ALBP) after one week of use. Moreover, it is suggested that additional and rigourous prospective controlled research should be undertaken to further explore these treatments with longer follow-up periods.\n\n\n\n- Bahria Wided, Makhlouf Yasmine: Data collection, conceptualization, editing, Final approval of the version of the article to be published\n\n- Others: Substantial contributions to analysis and interpretation of data, Final approval of the version of the article to be published", "appendix": "Data availability statement\n\nFigshare: Effect of Methocarbamol on acute low back pain: A systematic review. Dataset for analysis: DOI: https://doi.org/10.6084/m9.figshare.27073633.v7. 19\n\nThis project contains following datasets:\n\n1. Flow chart fig 1\n\n2. Prisma Checklist Guidelines table 2\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Effect of Methocarbamol on acute low back pain: A systematic review. Dataset for analysis: DOI: https://doi.org/10.6084/m9.figshare.27073633.v7. 19\n\nThis project contains following extended datasets:\n\n1. Characteristics of the studies Table 1\n\n2. Biasis risk\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nKreiner DS, Matz P, Bono CM, et al.: Guideline summary review: an evidence-based clinical guideline for the diagnosis and treatment of low back pain. Spine J. 2021 Apr; 21(4): 726–727. PubMed Abstract \| Publisher Full Text\n\nKahere M, Ngcamphalala C, Östensson E, et al.: The economic burden of low back pain in KwaZulu-Natal, South Africa: A prevalence-based cost-of-illness analysis from the healthcare provider’s perspective. PLoS One. 2022; 17(10): e0263204. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu A, March L, Zheng X, et al.: Global low back pain prevalence and years lived with disability from 1990 to 2017: estimates from the Global Burden of Disease Study 2017. Ann Transl Med. 2020; 8(6): 299. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrudwick K, McPhee M, Bell A, et al.: Review article: Best practice management of low back pain in the emergency department (part 1 of the musculoskeletal injuries rapid review series). Emerg Med Australas EMA. 2018; 30(1): 18–35. PubMed Abstract \| Publisher Full Text\n\nWaterman BR, Belmont PJ, Schoenfeld AJ: Low back pain in the United States: incidence and risk factors for presentation in the emergency setting. Spine J Off J North Am Spine Soc. 2012; 12(1): 63–70. PubMed Abstract \| Publisher Full Text\n\nPrice MR, Cupler ZA, Hawk C, et al.: Systematic review of guideline-recommended medications prescribed for treatment of low back pain. Chiropr Man Ther. 13 mai 2022; 30(1): 26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEmrich OMD, Milachowski KA, Strohmeier M: Methocarbamol in acute low back pain. A randomized double-blind controlled study. MMW Fortschr Med. juill 2015; 157 Suppl 5: 9–16. PubMed Abstract \| Publisher Full Text\n\nAljuhani O, Kopp BJ, Patanwala AE: Effect of Methocarbamol on Acute Pain After Traumatic Injury. Am J Ther. 2017; 24(2): e202–e206. PubMed Abstract \| Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021; 372: n71. Publisher Full Text\n\nRisk of Bias 2 (RoB 2) tool\|Cochrane Methods.[cité 24 févr 2024].\n\nFriedman BW, Cisewski D, Irizarry E, et al.: A Randomized, Double-Blind, Placebo-Controlled Trial of Naproxen With or Without Orphenadrine or Methocarbamol for Acute Low Back Pain. Ann Emerg Med. 2018; 71(3): 348–356. e5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSamsamshariat S, Sharifi-Sade M, Zoofaghari S, et al.: Efficacy of the Combination of Indomethacin and Methocarbamol versus Indomethacin Alone in Patients with Acute Low Back Pain: A Double-Blind, Randomized Placebo-Controlled Clinical Trial. J Res Pharm Pract. 2021; 10(2): 96–101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharifi M, Abdorazzaghnejad A, Yazdchi M, et al.: Methocarbamol versus diazepam in acute low back pain in the emergency department: a randomised double-blind clinical trial. Emerg Med J EMJ. juill 2023; 40(7): 493–498. PubMed Abstract \| Publisher Full Text\n\nWewege MA, Bagg MK, Jones MD, et al.: Comparative effectiveness and safety of analgesic medicines for adults with acute non-specific low back pain: systematic review and network meta-analysis. BMJ. 22 mars 2023 [cité 25 févr 2024]; 380: e072962. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnderson DB, Shaheed CA: Medications for Treating Low Back Pain in Adults. Evidence for the Use of Paracetamol, Opioids, Nonsteroidal Anti-inflammatories, Muscle Relaxants, Antibiotics, and Antidepressants: An Overview for Musculoskeletal Clinicians. J Orthop Sports Phys Ther. juill 2022; 52(7): 425–431. PubMed Abstract \| Publisher Full Text\n\nJones CMP, Day RO, Koes BW, et al.: Opioid analgesia for acute low back pain and neck pain (the OPAL trial): a randomised placebo-controlled trial. Lancet Lond Engl. 22 juill 2023; 402(10398): 304–312. Publisher Full Text\n\nBeebe FA, Barkin RL, Barkin S: A clinical and pharmacologic review of skeletal muscle relaxants for musculoskeletal conditions. Am J Ther. 2005; 12(2): 151–171. PubMed Abstract \| Publisher Full Text\n\nvan Tulder MW , Touray T, Furlan AD, et al.: Muscle relaxants for non-specific low-back pain. Cochrane Database Syst. Rev. 2003; 2017: CD004252. Publisher Full Text\n\nBahria W, Bahria W: PRISMA _2020_checklist. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "337418", "date": "20 Nov 2024", "name": "Thiru Annaswamy", "expertise": [ "Reviewer Expertise 25 plus years of clinical and research expertise in evaluation and management of low back pain and related disorders" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral Comments: This is a SR on effect of Methacarbamol on acute low back pain.\nThe justification (need) for this systematic review of the effect of Methacarbamol on acute low back pain has not been well supported. The authors detail that the mechanism of action of methocarbamol is not understood, but doing a SR on its effectiveness does not answer mechanism of action questions. The authors mention \"disagreements regarding prescription\" and \"...lack of clear consensus on its appropriateness\", but don't substantiate this any further with citations and or additional details. In the discussion section, they cite 2 recent systematic review articles both of whom include muscle relaxants including methocarbamol in their scope. Therefore, it is unclear why this review focusing on Methacarbamol alone is clearly needed.\nSpecific comments: Under \"search strategy\", please provide your definition of \"acute low back pain\" and describe if you included review of this definition in your article search. Please rewrite: \"did not align in compliance with the purpose...\", \"were manually identifying\", \"Data extraction and quality assessment Extracted...\" How were \"disagreements resolved\"? Under \"Characteristics of Studies\", why was \"non-traumatic ALBP\" pointed out? Was traumatic ALBP an inclusion criterion in your review?\nEdit typos in \"comparabke\" and \"measauring\" BPFS is defined two different ways. Please provide only one definition for this acronym.\nUnder \"Discussion\" section, you mention \"recent literature\"... however, your search strategy is not \"recent\". Please explain. Rewrite 3rd paragraph of this section. It is redundant and unclear the way it is currently written. Cite the \"several guidelines\" you mention in this paragraph. How does your review compare to the 2 SRs you mention in this paragraph? Add space between \"systematicreviews\"\n\"This was corroborated in our review...\". Re-word this line. I am not sure if the results of this review are sufficient to make a statement that there is \"strong evidence\" for combined treatment with Methacarbamol and NSAIDs\nTable 2: Please define \"N\" and \"CI\" Please add column titles for columns 1 & 2. Please reword rest of column titles, which are unclear as currently defined.\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? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] }, { "id": "342495", "date": "28 Dec 2024", "name": "Zachary Cupler", "expertise": [ "Reviewer Expertise guideline recommend non-pharmacological and pharmacological management of acute low back pain" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the invitation to review “Effect of Methocarbamol on acute low back pain: A systematic review”. This systematic review assessed the effectiveness of methocarbamol in treating acute low back pain. The author’s major findings indicate that methocarbamol may be useful in the short term for acute low back pain.\nThis submission aligns with F1000’s scope. The methods of are appropriate to the research question.\nThere are a number of major concerns we wish to draw the authors’ attention to that we believe are fundamentally necessary to improve this manuscript.\nMajor comments Introduction\nThe framing in the introduction does give robust reasoning for why this systematic review is needed. Please expand on the current state of the use of pharmacotherapy for acute low back pain and the current gaps in the literature, thus providing better support for the investigating primary inquiry regarding methocarbamol. What disagreements remain? See Price et al. regarding a review of guideline recommendations for skeletal muscle relaxants.\n\nContrary to what is stated, this is not the first systematic review to evaluate skeletal muscle relaxant effectiveness for acute low back pain. Please revise and cite other studies in which the use of skeletal muscle relaxants is evaluated in ALBP. Reframing the statement that this is to first to “solely” assesses methocarbamol may better display the novelty of this research question.\n\nThe American College of Physicians’ landmark paper recommends an array of pharmacological and non-pharmacological interventions including exercise, manual therapy, yoga, and tai chi for acute low back pain. Please consider revising paragraph 1-2 of the introduction\n\nRefer 1 and 2.\n\nRegarding the objective, “we conducted this systematic review to present the most up-to-date published literature on the effectiveness of methocarbamol in treating ALBP”. Was this limited to adults, adolescents, or adult and children? Please revise for clarity.\nMethods\nAt least one full database string strategy should be reported. Please add as a table or appendix.\n\nA ‘PICO question’ format would serve to better guide the reporting of this study. Consider revising.\n\nWhat is the defined duration of acute low back pain for the purposes of this study? This should be introduced in the introduction and/or at the very least in the methods (Selection Criteria). Further, for results, as duration definitions of ALBP may vary between studies, describing the acute duration time frame for each study is valuable to the reader.\n\nThe content of “Data extraction and quality assessment” in Methods seems to be transposed and should be included in “Selection criteria” instead. “Publications that did not align…” up to “… the inclusion criteria were excluded.” Please revise for consistency in reporting for Selection Criteria. This should include inclusion and exclusion criteria.\n\nWas screening of title/abstract and full-text paper performed by one author or multiple authors in duplicate? Please revise and clarify. Best practice is to perform in duplicate independently whereby consensus is met.\n\nWere the extraction and risk of bias steps performed by one author or multiple authors in duplicate? Please revise and clarify. Best practice is to perform in duplicate independently whereby consensus is met.\n\nTrauma is indicated as an exclusion reason in the results, but trauma is not mentioned as an inclusion or exclusion criteria in the methods. Please clarify.\n\nRadicular pain is indicated as an exclusion reason in the results, but radicular pain is not mentioned as an inclusion or exclusion criteria in the methods. Please clarify.\nResults\nThere is marked inconsistency between Fig1 Flow Chart and Results. “…we identified 104 papers through the database. After removing duplicates, we screened 4 titles and abstracts.” Vs. Flow Chart indicates 136 papers were identified, 7 papers were reviewed for title and abstract and 3 were excluded. The recorded exclusion reasons make no sense because it appears this would meet the described objective of the paper. Finally, the Fig 1 Flow Chart is incomplete and has missing information.\n\nPrimary and secondary outcomes were not specifically described in the Methods. It appears that evaluating the use of methocarbamol for relieving pain is the primary outcome per the abstract only; however, disability and adverse events are discussed as well, and function is highlighted at length in the Results. Please revise to resolve these discrepancies.\n\n“Exclusion criteria included non-traumatic ALBP for all studies4-6 and the presence of radicular pain in the study by Benjamin W. et al.” does not make sense in the context of the 3 papers reviewed in this SR. Comments are previously noted regarding trauma and radicular pain which should be reconciled with this comment. Please clarify.\n\nThe second paragraph of the results, “The effect of Methocarbamol on pain and functional disability”, contrasts pain scores and functional scores, which does not make sense in the context of the research question or methods. Please clarify and consider with previous comments regarding primary and secondary outcomes.\n\nTable 2: Define “N”, “3M” and “CI.”.\n\nParagraph 3 of the Discussion is copy/paste information stated twice. Please revise for clarity. “Similarly, muscle relaxants are also a treatment option through reducing muscle spasms. Several guidelines recommend the use of Methocarbamol in the management of LBP in general with variable effect. Two systematic reviews provided robust results indicating the effectiveness of muscle relaxant therapy in treating simple acute low back pain with a maximum benefit in the first 2 weeks.17,18”\n\nTwo systematic reviews are cited in paragraph 3 of the Discussion that would be useful sources in the Introduction to help differentiate previous studies on skeletal muscle relaxants, and how this study intends to solely discuss methocarbamol.\n\nThere are several concerns with accuracy of information in Paragraph 4 of Discussion.\n\nUse of citation 2 (discussing economic burden of low back pain) does not make sense in the context of sentence. Please revise and accurately cite. Citation 18 inaccurately supports a statement regarding methocarbamol when the review supports only non-specific skeletal muscle relaxants, not methocarbamol in particular. “Similarly, current evidence suggests that Methocarbamol may be more beneficial when used alongside other therapeutic modalities, particularly analgesics and NSAIDs”. This is somewhat misleading. Please revise.\n\nThe authors state “strong evidence” based on what was found in this review. This is inaccurate and inappropriate use of the terminology considering this study did not include the appraisal of the strength of evidence for various conclusions using a rating system based on the quality and outcomes of the studies included. Please revise. The second sentence of Conclusion is likely truncated. Please expand.\nMinor comments\nIntroduction\nConsider defining a level 1 analgesics (i.e., ).\n\nMethods:\nTypo “studiesand”\n\nSelection criteria:\n“3)” does not make sense in context. May be an issue with the transposed information.\n\nExtended data 1:\n“N=”, needs number\n\nCharacteristics of patients:\n“[32-81]” does not make sense in context.\n\nResults:\n“For this update,” does not make sense in context. “BPFS” is defined twice, and may lead to confusion for readers. Please remove the second defining location. There is also the use of “Shiva et al.” which is not a reference cited. This citation should be listed as “Samsamshariat et al.” if referring to citation 12, as it stands in the text.\n\nThe effect of Methocarbamol on pain and functional disability:\nplease define the acronym “RMDQ” in the text prior; typos “comparable” and “measuring”\n\nDiscussion:\n“Cochrane tool risk assessment bias” – already defined previously as “RoB2” Typo “address”\n\nConclusion:\nTense is incorrect. “…may improved pain in patients”.\n\nExtended Data:\nTypo: “Biasis risk”. Please revise.\n\nTable 1: Column 2 “Study Design”\nThe mean age is represented and then there is an additional number in parentheses. It is unclear what this represents. See Friedman row – what does ‘12’ represent\nMethocarbamol : 81, (38 (12))\n\nFlow Chart Figure 1: “Records after duplicates removed” is missing a numeric value for n= as is “Embase (n= )”. Please revise.\n\nWas citation searching performed forward and backward or unidirectional? Please specify.\n\nA German language paper was excluded. Search strategy indicates only papers written in English were considered. Consider revision to the Selection Criteria section.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-1139
https://f1000research.com/articles/13-1137/v1	07 Oct 24	{ "type": "Research Article", "title": "Social epidemiology of female breast cancer in the region of Varna-Bulgaria in 2013-2021 – A retrospective study", "authors": [ "Galina Yaneva", "Tsonka Dimitrova", "Oskan Tasinov", "Galina Yaneva", "Tsonka Dimitrova" ], "abstract": "Background Female breast cancer remains the most common malignant disease and a leading cause of death worldwide. We aim to follow up on the annual dynamics of its incidence, prevalence and mortality rates in the region of Varna, Bulgaria.\n\nMethods Data for the recent retrospective analyses was accessed through the information system of Marko Markov Specialized Hospital for Oncological Diseases of Varna for 2017-2021 and two most recent publications for 2013-2017, in accordance with the Medical University-Varna Ethical committee guidelines.\n\nResults The total number of newly registered cases of breast cancer in women aged between 24 and 95 years amounted to 1,341. Mean crude incidence rate in 2017-2021 was 108.83 per 100,000, ranging from 119.89 to 105.25 per 100,000 in 2017 and 2020, respectively. The age group of 61-70 years was most affected (26.55% of the cases). Mean crude prevalence rate during this period was 1496.32 per 100,000, varying from 1447.75 to 1549.71 per 100 000 in 2017 and 2020, respectively. The total number of deaths until the end of 2022 reached 310 with 2018 being the greatest in mortality rate (30.22% of the cases). In 2017-2021, bilateral breast cancer was diagnosed as synchronous in 15 women and metachronous in 9 women.\n\nConclusions The regular regional epidemiological investigations could contribute to the enhancement of the effectiveness and quality of prevention, timely diagnosis and adequate complex treatment.", "keywords": [ "female breast cancer", "incidence rate", "prevalence rate", "mortality rate", "Region of Varna" ], "content": "Introduction\n\nDuring the last several years, breast cancer has been the most common malignant disease and a leading cause of death in women worldwide and in Bulgaria as well. In 2020, approximately 2,300,000 new breast cancer cases and 685,000 deaths in women were registered worldwide.1 Breast cancer continues to be the most common cancer globally, affecting 7.8 million males and females at the end of 2020.\n\nThe analysis of data on breast cancer outcomes obtained from the 2019 Global Burden of Disease Survey during the period between 1990 and 2019 in five big countries such as Brazil, Russia, India, China, South Africa as well as in 30 other Asian countries demonstrates that in 2019, there are 900,000 female breast cancer cases and 350,000 million deaths in these parts of the world.2 China and India have the largest proportion of incident cases and deaths followed by Pakistan. High body mass index, high fasting plasma glucose, and a diet high in red meat contribute to the highest breast cancer death rates in most of these countries in 2019.\n\nIn 2019, there were 19,726 breast cancer deaths in the nine Central and Eastern Europe countries: Bulgaria, Croatia, Czech Republic, Hungary, Poland, Romania, Serbia, Slovakia, and Slovenia.3 These breast cancer deaths result in 267,184 years of life lost. The mean present value of future lost productivity in these countries is the following: €85 M in Poland, €46 M in Romania, €39 M in Hungary, €21 M in Slovakia, €18 M in Serbia, €16 M in Czech Republic, €15 M in Bulgaria, €13 M in Croatia, and €7 M in Slovenia. In 2019 alone, lost productivity costs due to premature breast cancer-related mortality exceed €259 million.\n\nThe investigation of breast cancer burden in 28 European Union member states demonstrates age-standardized (world standard) incidence and mortality rates in adolescents and young adults aged 15-39 years in 2020 of 20.1 per 100,000 and 2.70 per 100,000, respectively, in Bulgaria only.4 The age-adjusted mortality rate in Poland is 2.70 per 100,000, too. It is highest in Iceland (of 2.80 per 100,000) and lowest in Luxembourg (of 0,66 per 100,000) against a mean value in Europe of 1.94 per 100,000.\n\nThe aim of this study was to follow up on the annual dynamics of the incidence, prevalence and mortality rates of female breast cancer in the region of Varna, Bulgaria, in the period from 2013 to 2021.\n\n\nMethods\n\nWe conducted a retrospective analysis of the statistical data devoted to the crude incidence, prevalence and mortality rates of breast cancer in women living in the region of Varna from the information system of Marko Markov Specialized Hospital for Oncological Diseases of Varna for 2017-2021. Study cohort includes 1341 diagnosed patients aged between 24 and 95 years, distributed by years and age. The information about the age-standardized incidence and prevalence rates from two most recent official Bulgarian publications5,6 for 2013-2017 was also analysed.\n\nThe graphical presentation and statistical analyses were performed using, GraphPad Prism V.6 (San Diego, CA, USA). GraphPad Prism software is accessible online from https://www.graphpad.com/features.\n\n\nResults\n\nThe total number of newly registered cases of breast cancer in women aged between 24 and 95 years stands at 1,341 (Table 1). The incidence rate gradually decreases during the period from 2017 to 2021.\n\nAs shown in Table 1, the age group between 61 and 70 years is most frequently affected during the whole period (356 patients or 26.55% of the cases). There are eight young women, too (0.5% of the cases).\n\nThe mean breast cancer crude incidence rate per 100,000 population decreases from 2017 to 2021 while mean breast cancer crude prevalence rate per 100,000 population varies considerably during this period (Table 2).\n\nThe annual dynamics of the newly registered cases and of the death cases by year of diagnosis in the region of Varna during the period between 2013 and 2021 are illustrated in Figure 1 and Figure 2, respectively.\n\nThe annual dynamics of the newly registered cases by year of diagnosis of female inhabitants in the city of Varna only during the period between 2017 and 2021 are displayed in Figure 3.\n\nThe annual dynamics of the mean breast cancer age-standardized incidence and prevalence rates per 100,000 population in the region of Varna between 2013 and 2017 are presented in Table 3.\n\nThe total number of deaths until the end of 2022 amounts to 310 being the greatest 2018 (81 or 30.22%) and in 2017 (79 or 27.24% of the cases). We observed that since 2019 lethal cases are gradually reduced (Figure 4).\n\nIn 2017-2021, bilateral breast cancer is diagnosed in twenty-four women. The malignant neoplasm is synchronous in fifteen and metachronous in the rest nine patients. Of them, three women with a synchronous and one woman with a metachronous breast cancer decease.\n\nIn 2013 and 2014, breast cancer age-adjusted incidence and mortality rates are much higher in the region of Varna than those in five other regions in North Eastern Bulgaria such as Ruse, Shumen, Dobrich, Razgrad, and Silistra.7\n\n\nDiscussion\n\nThere is a dramatic reduction of the number of lethal cases following the radical surgical intervention since 2019 proving the effectiveness of the timely application of this method of treatment (Figure 4). Our findings are similar to these recently reported by foreign authors.\n\nDuring the period between 2004 and 2018, 915,417 new breast cancer cases are diagnosed in the USA.8 Among all races, there is an increased incidence rate by 0.3% (between 0.1% and 0.4% at 95% confidence interval; p<0.001) per year during the study. There is a decreased mortality rate by 14.3% (between 18.1% and 10.4% at 95% confidence interval; p<0.001). This reduction is most outlined from 2016 to 2018 by 48.6% (between 52.6% and 44.3% at 95% confidence interval; p<0.001). The analysis of 1999 to 2020 overall mortality rate due to female breast cancer in the USA according to data from the Centres for Disease Control and Prevention and the National Centre for Health Statistics indicates that it decreases and varies by race/ethnicity, age group, and US Census region.9 Its largest decrease is observed among non-Hispanic white women, women aged between 45 and 64 years, and women living in the Northeast, while its smallest decrease is established among non-Hispanic Asian or Pacific Islander women, women aged 65 years or older, and women living in the South.\n\nWithin an inquiry study through a food frequency questionnaire of 6,157 North American women diagnosed with invasive breast cancer between 1993 and 2011 and followed-up through 2018 during a median time of 11.3 years, there are 1,265 deaths.10 Women in the highest versus lowest quartile of adherence to the following four diet quality indices have a lower risk of all-cause mortality: the Healthy Eating Index-2015, Alternative Healthy Eating Index, Alternative Mediterranean Diet, and Dietary Approaches to Stop Hypertension. The values of multivariable-adjusted hazard ratios in terms of these indices are the following: 0.88 (between 0.74 and 1.4 at 95% at 95% confidence interval), 0.82 (between 0.69 and 0.97 at 95% confidence interval), 0.73 (between 0.59 and 0.92 at 95% confidence interval), and 0.78 (between 0.65 and 0.94 at 95% confidence interval).\n\nIn 2023, 297,790 newly registered breast cancer cases are projected to occur in the United States of America.11 The total number of these cases will reach up to 31% of the patients with ten most common malignant diseases. Besides the total number of death, cases due to breast cancer will reach up to 43,170 or to 15% of the patients with ten most common malignant diseases.\n\nBetween 2014 and 2019, 55,465 breast cancer patients at a mean age of 55.7±12.0 years (range, 25 to 97 years) are diagnosed in Kazakhstan based on nationwide large-scale healthcare data from the National Registry.12 Most patients (44.8% of the cases) are aged between 45 and 59 years. Incidence rate varies between 45 per 100,000 population in 2015 and 73 per 100,000 population in 2016 while prevalence rate increases from 304 per 100,000 population in 2014 up to 506 per 100 000 population in 2019. Mortality rates are stable and high in the senile patients aged between 75 and 89 years. Mortality is positively associated with diabetes mellitus (hazard ratio of 1.2; between 1.1% and 2.3 at 95% confidence interval) and negatively associated with arterial hypertension (hazard ratio of 0.42; between 0.4% and 0.5% at 95% confidence interval).\n\nBased on data on breast cancer incidence rate between 1999 and 2020 and breast cancer mortality rate between 1993 and 2021 in South Korea, the results from their projection by fitting a linear regression model indicate that in 2023, there will be 28,851 new cases (22.4% of ten most common malignant diseases) and 2,944 death cases (9.2% of these diseases).13 Crude and age-adjusted (world standard) incidence rates of 111.9 per 100,000 population and 67.7 per 100,000 population as well as crude and age-adjusted (world standard) mortality rates of 11.4 per 100,000 population and 5.7 per 100,000 population, respectively, could be expected.\n\nWithin a hospital-based retrospective cohort study in South Ethiopia, 302 female breast cancer patients diagnosed from 2013 to 2018 are followed-up for a total of 4685.62 person-months.14 Their median survival time is 50.81 months. About 83.4% of them have advanced-stage disease at presentation. The overall survival probability at two and three years is 73.2% and 63.0%, respectively. Independent predictors of mortality are the following: patients residing in rural areas (adjusted hazard ratio of 2.71; between 1.44 and 5.09 at 95% confidence interval), travel time to a health facility ≥7 hours (adjusted hazard ratio of 3.42; between 1.05 and 11.10 at 95% confidence interval), patients presenting within 7-23 months after the onset of symptoms (adjusted hazard ratio of 2.63; between 1.22 and 5.64 at 95% confidence interval), patients presenting more than 23 months after the onset of symptoms (adjusted hazard ratio of 2.37; between 1.00 and 5.59 at 95% confidence interval), advanced stage at presentation (adjusted hazard ratio of 3.01; between 1.05 and 8.59 at 95% confidence interval), and patients having never received chemotherapy (adjusted hazard ratio of 6.69; between 2.20 and 20.30 at 95% confidence interval).\n\nDuring the period from 1999 to 2020, breast cancer mortality rate in South Africa increases from 9.82 per 100,000 to 13.27 per 100,000 at around of 1.4% per annum (between 0.8% and 2.0% at 95% confidence interval; p<0.001).15 Young women aged 30-49 years present with a statistically significant mortality rate increase (by 1.1%-1.8%; p<0.001).\n\nBetween 2009 and 2016, 10,124 deaths from breast cancer are recorded in the Mortality Information System in the city of São Paulo, Brazil, among women aged 20 years and over.16 The following variables are associated with breast cancer mortality: travel time between one and two hours to work (relative risk of 0.97; between 0.93 and 1.00 at 95% credible interval), women being the head of the household (relative risk of 0.97; between 0.94 and 0.99 at 95% credible interval), and deaths from breast cancer in private health institutions (relative risk of 1.04; between 1.00 and 1.07 at 95% credible interval). During the period from 1999 to 2019, there are stable temporal trends of overall mortality coefficients for breast cancer (β=-0.006; between -0.02 and 0.01 at 95% confidence interval) in Passo Fundo, Rio Grande do Sul, Brazil.17 A rising mortality trend is identified in women with up to 7 years of schooling and in older women as well.\n\nThe analysis of data from the Polish National Cancer Registry shows that between 2000 and 2019, a total of 315,278 patients, 2,353 male patients and 312,925 female patients, are diagnosed with breast cancer.18 The age-adjusted five- and ten-year net survival is statistically significantly higher in women than in men (77.33% versus 65.47%; p<0.001). There is a statistically significant increase only in female survival (by 7.32%; p<0.001) between the earliest period (2000-2004) and latest one (2015-2019). The standardized mortality ratios are considerably higher for women than for men (3.35 versus 2.89, respectively).\n\nIn 2019, breast cancer age-standardized incidence rate is statistically significantly higher in Sweden (217.5 per 100 000) than in Crete (58.9 per 100,000) (p<0.001).19 During the period between 2005 and 2019, breast cancer age-standardized mortality rate decreases in Sweden from 25.5 per 100,000 down to 16.8 per 100,000 while it increases in Crete from 22.1 per 100,000 up to 25.3 per 100,000. Since 2015, there is a successive rise of survival rate with a five-year survival rate of 92% in Sweden but a decrease of the survival rate with a five-year survival rate of 85% in Crete.\n\nThe results from a case-referent investigation of 1,571 women in Flanders, Belgium, during the period between 2005 and 2017 indicate that women who have participated in the Flemish population-based mammography screening program introduced in 2001 have a 51% lower risk of breast cancer-specific mortality compared to those who have not (adjusted odds ratio of 0.49; between 0.44 and 0.55 at 95% confidence interval).20\n\nDuring the recent years, there are relatively scanty regional epidemiological investigations dealing with breast cancer in women worldwide. It should be emphasized that the significant differences in terms of the dynamics of breast country incidence, prevalence and mortality rates in single regions in Bulgaria and in other European countries deserve a special attention by the public. The research in this interdisciplinary field accomplished by national and international collectives could shed light on a variety of unsolved issues associated not only with environmental and occupational factors but also with personal life-style improvement.\n\n\nConclusion\n\nWe establish a gradual improvement of the epidemiological parameters of female breast cancer in the region of Varna during the last few years. The performance of regular regional epidemiological research of the most common and socially significant malignant diseases in Bulgaria could contribute to the enhancement not only of the effectiveness and quality of their prevention, but also of their timely diagnosis and adequate complex treatment.\n\nRecent retrospective study was approved by the Ethics Committee of Medical University-Varna, Bulgaria (protocol № 61/30.03.2017) on 30th March 2017 and is in accordance with Declaration of Helsinki, 1964.\n\nDue to the retrospective nature of the study, the need for informed consent of the patients was waived by the committee. This study includes epidemiological analyses concerning patients, that are part of a larger previous study in which the ethics committee approved the use of these data. The data and results presented in this study have not been previously published.", "appendix": "Data availability\n\nFigshare: Social epidemiology of female breast cancer in the Region of Varna-Bulgaria in 2013-2021_data.doc. https://doi.org/10.6084/m9.figshare.25028666. 21\n\nThis project contains the following underlying data:\n\n• Data file 1, type - dataset: Social epidemiology of female breast cancer in the Region of Varna-Bulgaria in 2013-2021_data.doc.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nSince the obligation of Marko Markov Specialized Hospital for Oncological Diseases of Varna to keep the privacy of patients individual data, there are not presented in this retrospective study, but grouped, organised and analysed statistical data for 2017-2021. In case scientists, readers need to access these private individual patients data they should apply by the Ethics Committee of Medical University-Varna, Bulgaria in accordance with Declaration of Helsinki, 1964 and Marko Markov Specialized Hospital for Oncological Diseases of Varna regulatory board.\n\n\nReferences\n\nMustafa M, Abbas K, Alam M, et al.: Molecular pathways and therapeutic targets linked to triple-negative breast cancer (TNBC). Mol. Cell. Biochem. 2023 [cited 2023 Oct 6]; 479: 895–913. Springer. PubMed Abstract \| Publisher Full Text\n\nMubarik S, Wang F, Nadeem AA, et al.: Breast cancer epidemiology and sociodemographic differences in BRICS-plus countries from 1990 to 2019: An age period cohort analysis. SSM - Popul Heal. 2023 Jun 1 [cited 2023 Oct 6]; 22: 101418. Publisher Full Text \| Free Full Text\n\nBencina G, Chami N, Hughes R, et al.: Breast cancer-related mortality in Central and Eastern Europe: years of life lost and productivity costs. J. Med. Econ. 2023; 26(1): 254–261. PubMed Abstract \| Publisher Full Text\n\nTrama A, Stark D, Bozovic-Spasojevic I, et al.: Cancer burden in adolescents and young adults in Europe. ESMO Open. 2023; 8(1): 100744. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNational Oncological Hospital BNCR: Cancer Incidence in Bulgaria, 2014 and 2015.Valerianova Z, Atanasov T, Vukov M, editors. Bulgarian National Cancer Registry. Sofia, Bulgaria: “Paradigma“ 2017; 2017; Vol. XXV. .\n\nUniversity Specialized Hospital for Active Treatment in Oncology. Bulgarian National Cancer Registry.Valerianova Z, Atanasov T, editors. Bulgarian National Cancer Registry. Sofia, Bulgaria: Paradigma; 2020; Vol. XXVI. : 2017. 2017. Reference Source\n\nYaneva G: Breast cancer epidemiology in North-Eastern Bulgaria. Sci Work Union Sci Bulg Plovdiv. 2019; 22: 394–397.\n\nBazzi T, Al-husseini M, Saravolatz L, et al.: Trends in Breast Cancer Incidence and Mortality in the United States From 2004-2018: A Surveillance, Epidemiology, and End Results (SEER)-Based Study. Cureus. 2023.\n\nEllington TD, Henley SJ, Wilson RJ, et al.: Trends in breast cancer mortality by race/ethnicity, age, and US census region, United States ─ 1999-2020. Cancer. 2023; 129(1): 32–38. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHaslam DE, John EM, Knight JA, et al.: Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry. Cancer Epidemiol. Biomarkers Prev. 2023; 32(5): 678–686. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSiegel RL, Miller KD, Wagle NS, et al.: Cancer statistics, 2023. CA Cancer J. Clin. 2023 Jan [cited 2023 Oct 6]; 73(1): 17–48. PubMed Abstract \| Publisher Full Text\n\nMidlenko A, Mussina K, Zhakhina G, et al.: Prevalence, incidence, and mortality rates of breast cancer in Kazakhstan: data from the Unified National Electronic Health System, 2014–2019. Front. Public Health. 2023; 11: 11. Publisher Full Text\n\nJung KW, Kang MJ, Park EH, et al.: Prediction of Cancer Incidence and Mortality in Korea, 2023. Cancer Res. Treat. 2023; 55(2): 400–407. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShita A, Yalew AW, Seife E, et al.: Survival and predictors of breast cancer mortality in South Ethiopia: A retrospective cohort study. PLoS One. 2023; 18(3 March): e0282746. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOlorunfemi G, Libhaber E, Ezechi OC, et al.: Population-based temporal trends and ethnic disparity in breast cancer mortality in South Africa (1999-2018): Joinpoint and age–period–cohort regression analyses. Front. Oncol. 2023; 13: 13. Publisher Full Text\n\nde Aguiar BS , Pellini ACG, Rebolledo EAS, et al.: Intra-urban spatial variability of breast and cervical cancer mortality in the city of São Paulo: analysis of associated factors. Rev. Bras. Epidemiol. 2023; 26: 26. Publisher Full Text\n\nPecinato V, Jacobo A, da Silva SG : Mortality trends of breast and cervical cancer in Passo Fundo, Rio Grande do Sul: an analysis by age and schooling, 1999-2019. Epidemiol. e Serv. Saude. 2022; 31(3). Publisher Full Text\n\nCaetano dos Santos FL, Michalek IM, Wojciechowska U, et al.: Changes in the survival of patients with breast cancer: Poland, 2000–2019. Breast Cancer Res. Treat. 2023; 197(3): 623–631. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoginski M, Sifaki-Pistolla D, Stomby A, et al.: Paradoxes of breast cancer incidence and mortality in two corners of Europe. BMC Cancer. 2022; 22(1): 1123. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDe Troeyer K, Silversmit G, Rosskamp M, et al.: The effect of the Flemish breast cancer screening program on breast cancer-specific mortality: A case-referent study. Cancer Epidemiol. 2023; 82: 102320. Publisher Full Text\n\nYaneva G, Dimitrova T, Tasinov O: Social epidemiology of female breast cancer in the Region of Varna-Bulgaria in 2013-2021_data.doc. [Data]. 2024. Publisher Full Text" }	[ { "id": "331024", "date": "21 Oct 2024", "name": "İbrahim Yıldız", "expertise": [ "Reviewer Expertise İnternal Medicine Specialist and Medical Oncologist" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI have reviewed the article titled “Social Epidemiology of Female Breast Cancer in the Region of Varna-Bulgaria in 2013-2021.” The study provides significant insights into the incidence, prevalence, and mortality rates of breast cancer in the Varna region, offering valuable data for healthcare planning and policy-making. The authors present a thorough analysis of regional trends over an extended period, highlighting the importance of localized epidemiological studies for effective cancer control strategies. However, I believe the manuscript could be further strengthened with a few additional improvements.\nTo enhance the comprehensiveness of the findings, I suggest including a section that compares the results from Varna with national Bulgarian data and, if possible, data from neighboring countries with similar demographic characteristics. This would place the regional findings in a broader context and provide more meaningful insights. Given the importance of screening in detecting breast cancer, it would be beneficial to discuss the current state of breast cancer screening programs in Varna or Bulgaria, along with their impact on incidence and mortality rates. This would highlight the role of screening in cancer prevention and control. Moreover, as genetic predisposition (e.g., BRCA1/BRCA2 mutations) is a known risk factor for breast cancer, it would be useful to include some discussion of genetic factors. Additionally, suggesting future research that explores the genetic components of breast cancer in the region would add depth to the study. Overall, this is a well-organized and informative study, and addressing these points would enhance its clarity and impact.\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/13-1137
https://f1000research.com/articles/13-1134/v1	04 Oct 24	{ "type": "Research Article", "title": "Searching for non-English literature may be unnecessary for HTA Reports", "authors": [ "Elke Hausner", "Sibylle Sturtz", "Sandra Molnar", "Lisa Schell", "Wiebke Sieben", "Stefan Sauerland", "Sibylle Sturtz", "Sandra Molnar", "Lisa Schell", "Wiebke Sieben", "Stefan Sauerland" ], "abstract": "Background Health technology assessment (HTA) reports are based on comprehensive information retrieval. Current standards discourage the use of search restrictions, such as publication date and language. Given limited resources, it was unclear whether the effort invested in screening and translating studies published in languages other than English provided relevant additional information compared with the inclusion of English-language publications alone. We therefore analysed the impact of non-English publications on the conclusions of HTA reports produced by the German HTA agency, the Institute for Quality and Efficiency in Health Care (IQWiG).\n\nMethods We determined whether non-English publications were included in all HTA reports on non-drug interventions and on selected drug interventions (search period: 01/2011 to 08/2018). If at least one non-English publication was included, we assessed for each endpoint whether or not the exclusion of non-English publications changed the conclusion. If a non-English publication did not contain information relevant to the HTA report, we classified the publication as “not relevant”.\n\nResults Of 70 HTA reports, 38 (54%) included 128 non-English publications. In 4 reports (6%) with 50 endpoints investigated in 39 PICO questions, the exclusion of a total of 10 non-English publications led to a change in the conclusions for 13 endpoints (8 PICO questions). This was largely due to the fact that in many cases, non-English publications were the predominant or only literature available, resulting in a lack of analysable data after their exclusion.\n\nConclusions In general, studies published in non-English languages have little influence on the conclusions of HTA reports. For the vast majority of topics, a language restriction to English seems justified. Studies published in non-English languages may be useful in exceptional cases, for example when an intervention is only available in certain countries.", "keywords": [ "Language", "Publication Bias", "Publications", "Retrospective Studies" ], "content": "Introduction\n\nHealth technology assessments (HTAs), which usually include systematic reviews, are based on comprehensive information retrieval requiring the use of multiple information sources.1,2 Current standards discourage the use of search restrictions, such as publication date and language.1,3 This is justified by the assumption that otherwise HTA conclusions could be biased, as studies with statistically significant results are more likely to be published in English-language journals, whereas non-significant results are more likely to be published in journals in languages other than English.4 However, there is now evidence that significant results are increasingly being published in non-English journals.5\n\nIn practice, many systematic reviewers restrict their searches to English-language articles.6,7 The reasons for this are pragmatic: non-English literature is often more difficult to obtain and translation costs are high.8\n\nThe Institute for Quality and Efficiency in Health Care (IQWiG9) is a German HTA agency. In addition to more than 100 HTAs based on dossiers submitted by drug companies, IQWiG conducts around 10-15 other HTAs per year, mostly on non-drug interventions. The HTA reports investigate patient-relevant endpoints or validated surrogate endpoints and may comprise a number of different PICO questions on population, intervention, comparator, and outcomes. If possible, results of single studies are pooled in meta-analyses. The overall certainty of conclusions is graded into 3 levels of increasing certainty (hint, indication or proof of harm or benefit) according to the amount and quality of the available evidence. A detailed overview of IQWiG’s methods is provided in its methods paper.10\n\nIQWiG’s reports are generally based on comprehensive information retrieval. However, it was previously unclear whether it was worthwhile searching for, screening, and translating non-English publications on primary studies, i.e. whether their inclusion influenced the conclusions of the reports.\n\nThe aim of this analysis was to assess the impact of non-English publications on the conclusions of HTA reports.\n\n\nMethods\n\nFollowing an internal protocol, we screened HTA reports (all reports on non-drug interventions published by IQWiG between 06/2007 and 08/2018 and randomly selected reports on drugs published between 09/2011 and 11/2016) for the inclusion of non-English publications. This procedure was not updated to include more recent HTA reports in the present article, as from September 2018 onwards, IQWiG restricted its searches to publications with English or German full texts. We focused on non-drug interventions, as we expected a higher number of non-English publications in this area.\n\nIn order to identify non-English publications, we screened all publications listed in the study pools of the HTA reports. This step was carried out via the EndNote databases of the underlying projects or, for older projects, via the reference lists in the HTA reports. In the next step, the language of the publications was identified using the entries in the bibliographic databases (MEDLINE, Embase). In a few cases this was not possible, so the language was checked using the full text or journal description. Data were extracted by one person and checked by another.\n\nOnly journal publications were included in the analysis, i.e., unpublished reports, conferences abstracts, evidence syntheses, clinical study reports, or registry entries were not considered. For updates of HTA reports, only the newly identified references were taken into account. For all HTA reports that included at least one non-English publication, we analysed whether the exclusion of such publications led to a change in conclusions; this was done separately for each PICO question and, if applicable, for each endpoint using specific categories (Table 1).\n\n\n\n• Non-English study with low weight for PICO\n\n• All studies including non-English publication point into the same direction\n\n• Higher level of evidence compared to non-English publication available\n\n• Amount and quality of the evidence of all studies included in the HTA report was too low for reliable conclusions, regardless of inclusion of non-English publication\n\n• All studies included have unclear clinical relevance\n\n• Diagnostic study without direct relevance for the HTA report\n\n\n\n• Quality of study too low to change conclusion\n\n• A secondary publication in English was included\n\n• No data from non-English publication was used in the HTA report\n\n• Non-English publication was not translated\n\nUsing standardized methods (IQWiG’s methods paper10 and internal guidance), we re-assessed the conclusions for the affected endpoints and PICO questions in the HTA reports. We did not re-analyse HTA reports on diagnostic test accuracy (DTA), as no conclusion on test accuracy endpoints is drawn in such reports.\n\nFor this purpose, the project manager reviewed all reports and assessed the impact of the exclusion of the non-English publication(s). This included the examination of individual studies on a specific endpoint or PICO question, qualitative re-assessments, and, in 3 cases, meta-analyses that had to be recalculated. When in doubt, the project manager consulted with another project manager or statistician.\n\nFor each endpoint, we defined a change in a conclusion due to the exclusion of non-English publications as either an upgrading or downgrading of the certainty of the conclusion or a complete loss of data (no conclusion possible). The effect of the exclusion of non-English publications on conclusions was categorized for each HTA report as follows: Category A: change in the conclusion for a particular endpoint; Category B: no change in the conclusion for a particular endpoint; Category C: the non-English publications do not contain relevant information for the HTA report (e.g. because the amount or quality of the data is too low) and are therefore classified as “not relevant”. The categorization was carried out independently by the project manager and a statistician. Any discrepancies were resolved by consensus between the two.\n\n\nResults\n\n70 eligible HTA reports including 2339 publications were identified30 (Figure 1). Due to the inclusion of only a small number of selected drug reports, the vast majority of the HTA reports (96%) were on non-drug interventions (Table 2).\n\n\n\n• Drug\n\n• Non-drug\n\n○ Diagnostic\n\n○ Screening\n\n○ Treatment\n\n\n\n• Number per report\n\n\n\n• RCTs only\n\n• RCTs + other study designs\n\na In addition, information retrieval for the HTA reports usually included a search of study registries and a check of reference lists of systematic reviews. Furthermore, requests to authors were made, if necessary, and public hearings took place (except for rapid reports).\n\nOf the 70 HTA reports, 32 (46%) included English-language publications only (Table 3). The remaining 38 reports (54%) included 128 non-English publications. These were most commonly published in German, Chinese, French and Spanish (Table 4).\n\na % of all included 2339 publications.\n\nHTA reports with a change in the conclusions (Category A)\n\nThe 4 reports with a change in the conclusions were (short titles):\n\n• A05-18: Tiotropium bromide for chronic obstructive pulmonary disease,11,12\n\n• N14-02: Systemic psychotherapy in adults13,14\n\n• N16-01: Active knee motion devices for anterior cruciate ligament ruptures15,16\n\n• N16-03: Continuous passive motion (CPM) devices after knee or shoulder surgery17,18\n\nFor further details, see Table 5.\n\na 2 publications are available for the Zhang 2006 study: Zhang 2006a and Zhang 2006b.\n\nThese 4 reports investigated 50 endpoints in 39 PICO questions. In 3 out of the 4 reports (A05-18, N14-02, N16-01), the only available publication on a particular endpoint was a non-English publication. The exclusion of the non-English publication led to a change in the conclusion for 13 endpoints in 8 PICO questions (Table 5). For 5 of these endpoints, the conclusion changed from a non-significant effect or an inconclusive result to “no conclusion possible” (due to a lack of data), and for 7 endpoints with previously statistically significant results, no conclusions could be drawn due to lack of data. For 1 endpoint, the conclusion changed from an inconclusive result to a hint of a benefit of the test intervention due to an effect becoming statistically significant (see example below).\n\nOf the 10 studies that influenced the conclusions, 7 were published in Chinese and 3 in German (Table 4).\n\nExample from an HTA report\n\nReport N16-03 investigated the use of continuous passive motion (CPM) devices after knee or shoulder surgery. For the comparison of shoulder devices in combination with physical therapy versus physical therapy alone in patients with rotator cuff rupture, there were 2 studies on the endpoint “pain”, one in English (Garofalo 2010) and one in German (Michael 2005). When both studies were considered, the results for this endpoint were inconsistent (see Figure 2), and therefore no conclusion could be drawn. When Michael 2005 was excluded, there was a hint of a benefit for combination therapy, i.e. the exclusion of non-English literature changed the conclusion.\n\nHTA reports with no change in the conclusions (Category B)\n\nIf the exclusion of non-English publications did not change the conclusions of the HTA report, we identified the reason for this for each endpoint. In most cases, this was because there were several studies for each endpoint with results pointing in the same direction, meaning that the exclusion of a non-English publication had a negligible effect.\n\nExample from an HTA report\n\nReport N09-01 investigated different non-drug local treatments in patients with benign prostatic syndrome. For the comparison of holmium laser therapy (HoLEP) versus standard treatment, 6 studies were included for the endpoint “symptom scores at 3 months”, of which one was in Chinese (Zhang 2007). Neither the result of a single study nor the pooled effect estimate showed a statistically significant effect. Zhang 2007 contributed a weight of 16.1% to the pooled effect estimate (see Figure 3); its exclusion did not change the conclusion.\n\nNon-English publications classified as not relevant (Category C)\n\nFor the non-English publications assigned to Category C, the studies formally met the inclusion criteria of the HTA reports, and were therefore included in the study pool, but were not used in the actual assessment, mainly due to low data quality.\n\n\nDiscussion\n\nOur analysis shows that the exclusion of studies published in non-English languages has only a minor effect on the conclusions of HTA reports. This is consistent with the results of a recent systematic review by Dobrescu et al. on the restriction of systematic reviews of diagnostic or treatment interventions to English-language publications. They found that the inclusion of solely English-language publications led to a change in statistical significance in only 23 out of 259 meta-analyses (9%) and concluded that “the impact of restricting systematic reviews to English-language publications is negligible for most conventional medicine topics”.19 Dobrescu et al.’s article was primarily based on the analysis of Cochrane reviews. Our analysis shows that the results can also be transferred to the context of HTA reports. In our analysis, most studies with an impact on the conclusions of the HTA reports were published in Chinese. This is notable, as the volume of Chinese-language literature is growing rapidly and there have been calls for the inclusion of such publications.20,21 However, their quality has been questioned because of methodological flaws and overly positive results.5\n\nOn the basis of our analysis, it is not possible to identify topics where non-English publications might be relevant. However, it seems reasonable to conduct additional searches for non-English literature if a particular intervention is exclusively or preferentially available in a specific region. For example, the “continuous active motion device” is a German product that is hardly marketed outside Germany. Only 2 studies could be identified for the HTA; both were published by German authors, one in English and one in German.\n\nLanguage restrictions can save time. If an HTA report is being prepared under considerable time pressure, the exclusion of non-English literature should already take place at the level of the search strategy, resulting in a lower number of hits to be screened.\n\nMethods for meta-analysis and for the assessment of study quality have changed over the past decades, which may influence the conclusions of HTA reports. We therefore tried to follow the original methods of the HTA reports included.\n\nOnly a small proportion of HTA reports required a recalculation of results.\n\nAt IQWiG, the analysis presented here led to the restriction of information retrieval in HTA reports to German- and English-language literature from September 2018 onwards. This change in approach is also described in IQWiG’s updated methods paper.10 For the present article, it was therefore not meaningful to update the pool of HTA reports by including HTA reports published by IQWiG after October 2019. An evaluation of current HTA reports from other large HTA agencies shows that they generally use a language restriction in their reports.22–29\n\nWe did not analyse whether the non-English study publications were of lower quality than the English-language ones.\n\nFor 2 reports (D06-01B and D06-01C), we also included evidence syntheses, although this document type was to be excluded. One report (D06-01M) was included although only a preliminary version was available. As the results of these 3 reports did not influence the analysis, they were not subsequently removed from the database. Because only a small number of selected drug reports were included, the vast majority of the HTA reports were on non-drug interventions. Therefore, no conclusive statement can be made about drug reports.\n\n\nConclusions\n\nIn general, studies published in non-English languages have little influence on the conclusions of HTA reports. For the vast majority of topics, a language restriction to English seems justified. Studies published in non-English languages may be useful in exceptional cases, for example when an intervention is only available in certain countries.\n\n\nEthics and consent\n\nEthics and consent are not required.", "appendix": "Data availability\n\nZenodo: Searching for non-English literature may be unnecessary for HTA Reports - supplemental material [Data set]. https://zenodo.org/records/13340928.\n\n▪ Supplementary-material_matrix_V2.xlsx (Data set of extracted references with details of the publication language) 30\n\nData are available under the terms of the Creative Commons Attribution 4.0 International License (CC-BY 4.0).\n\nZenodo: Searching for non-English literature may be unnecessary for HTA Reports - supplemental material [Data set].https://doi.org/10.5281/zenodo.12642960.\n\n▪ Supplementary-material_table.docx (HTA reports with endpoints that resulted in a change in the conclusion (Category A and B) 31\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 Anke Schulz (calculations), Wolfram Groß (data curation), and Natalie McGauran (translation and editing).\n\n\nReferences\n\nLefebvre C, Glanville J, Briscoe S, et al.: Chapter 4: Searching for and selecting studies.2023. [Accessed: 07.02.2024]. Reference Source\n\nEUnetHTA JA3WP6B2-2 Authoring Team: Process of information retrieval for systematic reviews and health technology assessments on clinical effectiveness. Methodological Guidelines.2019. [Accessed: 06.02.2024]. Reference Source\n\nRelevo R, Balshem H: Finding evidence for comparing medical interventions: AHRQ and the Effective Health Care Program. J. Clin. Epidemiol. 2011; 64(11): 1168–1177. PubMed Abstract \| Publisher Full Text\n\nEgger M, Zellweger-Zahner T, Schneider M, et al.: Language bias in randomised controlled trials published in English and German. Lancet. 1997; 350(9074): 326–329. Publisher Full Text\n\nWu T, Li Y, Bian Z, et al.: Randomized trials published in some Chinese journals: how many are randomized? Trials. 2009; 10: 46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJackson JL, Kuriyama A: How Often Do Systematic Reviews Exclude Articles Not Published in English? J. Gen. Intern. Med. 2019; 34(8): 1388–1389. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoffmann F, Allers K, Rombey T, et al.: Nearly 80 systematic reviews were published each day: Observational study on trends in epidemiology and reporting over the years 2000-2019. J. Clin. Epidemiol. 2021; 138: 1–11. PubMed Abstract \| Publisher Full Text\n\nMorrison A, Moulton K, Clark M, et al.: English-Language Restriction When Conducting Systematic Review-based Meta-analyses: Systematic Review of Published Studies.2009. [Accessed: 06.02.2024]. Reference Source\n\nInstitute for Quality and Efficiency for in Health Care: IQWiG.2024. [Accessed: 08.01.2024]. Reference Source\n\nInstitute for Quality and Efficiency for in Health Care: General Methods. [Accessed: 08.01.2024]. Reference Source\n\nInstitut für Qualität und Wirtschaftlichkeit im Gesundheitswesen: Tiotropiumbromid bei COPD; Abschlussbericht.2012. [Accessed: 06.02.2024]. Reference Source\n\nInstitute for Quality and Efficiency in Health Care: Tiotropium bromide for COPD; Executive Summary.2012. [Accessed: 06.02.2024]. Reference Source\n\nInstitut für Qualität und Wirtschaftlichkeit im Gesundheitswesen: Systemische Therapie bei Erwachsenen als Psychotherapieverfahren; Abschlussbericht.2017. [Accessed: 06.02.2024]. Reference Source\n\nInstitute for Quality and Efficiency in Health Care: Systemic therapy in adults as a psychotherapeutic approach; Extract.2017. [Accessed: 06.02.2024]. Reference Source\n\nInstitut für Qualität und Wirtschaftlichkeit im Gesundheitswesen: Aktive Kniebewegungsschienen in der Behandlung von Rupturen des vorderen Kreuzbands; Abschlussbericht.2017. [Accessed: 06.02.2024]. Reference Source\n\nInstitute for Quality and Efficiency in Health Care: Active knee motion devices in the treatment of anterior cruciate ligament ruptures; Extract.2017. [Accessed: 06.02.2024]. Reference Source\n\nInstitut für Qualität und Wirtschaftlichkeit im Gesundheitswesen: Einsatz von motorbetriebenen Bewegungsschienen (CPM) nach Interventionen am Knie- oder am Schultergelenk; Abschlussbericht.2018. [Accessed: 06.02.2024]. Reference Source\n\nInstitute for Quality and Efficiency for in Health Care: Motor-driven continuous passive motion (CPM) devices after interventions in the knee and shoulder joint; Extract.2018. [Accessed: 06.02.2024]. Reference Source\n\nDobrescu AI, Nussbaumer-Streit B, Klerings I, et al.: Restricting evidence syntheses of interventions to English-language publications is a viable methodological shortcut for most medical topics: a systematic review. J. Clin. Epidemiol. 2021; 137: 209–217. PubMed Abstract \| Publisher Full Text\n\nXue J, Chen W, Chen L, et al.: Significant discrepancies were found in pooled estimates of searching with Chinese indexes versus searching with English indexes. J. Clin. Epidemiol. 2016; 70: 246–253. PubMed Abstract \| Publisher Full Text\n\nCohen JF, Korevaar DA, Wang J, et al.: Should we search Chinese biomedical databases when performing systematic reviews? Syst. Rev. 2015; 4(1): 23. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilson M, Wang Z, Dobler CC, et al.: Noninvasive Positive Pressure Ventilation in the Home (with addendum).2020. [Accessed: 06.02.2024]. Reference Source\n\nNational Institute for Health and Care Excellence: Remsima (infliximab biosimilar) for subcutaneous injection for managing Crohn’s disease and ulcerative colitis; Evidence review.2021. [Accessed: 06.02.2024]. Reference Source\n\nNational Institute for Health and Care Excellence: Antimicrobial prescribing: delafloxacin for community-acquired pneumonia; Evidence review.2021. [Accessed: 06.02.2024]. Reference Source\n\nHaute Autorité de santé: Suivi par télésurveillance des patients porteurs d’un moniteur cardiaque implantable.2021. [Accessed: 06.02.2024]. Reference Source\n\nHaute Autorité de santé: Evaluation du parage de plaie de la pulpe par coiffage pulpaire direct.2019. [Accessed: 06.02.2024]. Reference Source\n\nFarrell K, Horton J: Airway Pressure Release Ventilation for Acute Respiratory Distress Syndrome: An Update. Can. J. Health Technol. 2022; 2(9). Publisher Full Text\n\nChou R, Cantor A, Dana T, et al.: Statin Use for the Primary Prevention of Cardiovascular Disease in Adults: A Systematic Review for the U.S. Preventive Services Task Force.2022. [Accessed: 06.02.2024]. Reference Source\n\nBarbara AM, Grobelna A: Real-Time Continuous Glucose Monitoring for People Living With Type 1 Diabetes. Can. J. Health Technol. 2022; 2(8). Publisher Full Text\n\nHausner E: Searching for non-English literature may be unnecessary for HTA Reports - supplemental material. Supplementary-material_matrix_V2. [Data set]. Zenodo. 2024. Reference Source\n\nHausner E: Searching for non-English literature may be unnecessary for HTA Reports - supplemental material. Supplementary-material_table. [Data set]. Zenodo. 2024. Publisher Full Text" }	[ { "id": "332664", "date": "18 Nov 2024", "name": "Knut Sundell", "expertise": [], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDifferent aspects of publication bias (positive outcome bias, time-lag bias, and place-of-publication bias) constitute serious threats to the validity of research synthesis. If research syntheses are based on a biased selection of the available research, there is an increased risk of producing misleading results. Awareness of these types of bias is important for reading systematic reviews and incorporating their findings into clinical practice and decision making.\nThe authors have screened 70 HTA reports from the German HTA agency, the Institute for Quality and Efficiency in Health Care (IQWiG) searching for reports that include non-English articles. If at least one non-English publication was included, the authors assessed whether the exclusion of non-English publications changed the conclusion. Of 70 HTA reports, 38 (54%) included non-English publications. The exclusion of non-English studies has only a minor effect on the conclusions of HTA reports\nThe authors conclude that, (1) in general, studies published in non-English languages have little influence on the conclusions of HTA reports, and (2) For the vast majority of topics, a language restriction to English seems justified.\nThese conclusions seem premature because of possible selection bias. We don’t know if the non-English articles in these reports constitute all relevant articles or a skewed sample (e.g., because of positive outcome biased, ). To be able to conclude that non-English articles have little influence on the report conclusions, the articles need to represent all relevant articles (i.e., no publication bias) which will require an extensive search for grey literature, including non-peer reviewed articles, the types of articles that the authors have excluded (i.e., conferences abstracts, evidence syntheses, clinical study reports, or registry entries).\nThe best we can say about the results is that non-English articles that are included in IQWiG’s reports may have had scant influence on the HTA-reports’ conclusions. This may be a thought-provoking result but hardly one to base policy on including or excluding non-English articles.\nFurthermore, I suggest that the authors discuss the types of bias and their relative importance for the design of the study. The exclusion of non-English publications might be motivated, but the results might still be biased because of positive outcome bias, time-lag bias, place-of-publication bias or other types of bias?\nThere is no motivation for only including the German HTA organization. What are the pros and cons of this choice?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "344994", "date": "14 Dec 2024", "name": "Sonia Garcia Gonzalez-Moral", "expertise": [ "Reviewer Expertise Information retrieval", "systematic reviews", "HTA", "health research methods" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 welcome the opportunity to comment on this paper. With this study the authors have challenged the status quo of current systematic literature review guidelines such as those from Cochrane and health technology assessment methods recommendations for undertaking literature searches such as those recommended by EUneHTA. Such bold move feels justified if one understand the intensity of resource and capacity involved in HTA and so, while I support the rationale for this study and think that this is a good first attempt to breach this topic, in general I do not think that this study boasts the sufficient methodological rigor nor a big enough sample size to draw conclusions that could be generalized to HTA. To start with, the title of this manuscript ‘Searching for non-English literature may be unnecessary for HTA reports’ suggests the opposite of what the authors conclude ‘At IQWiG, the analysis presented here led to the restriction of information retrieval in HTA reports to German- and English-language literature from September 2018 onwards’. I would therefore recommend that the title is revised, contextualizing this study to the needs and experience of the German HTA agency may increase the accuracy of their findings and conclusions. In the Introduction section the authors draw from one single study (Wu et al., 2009) to justify why non-English studies should no longer be searched for in HTA reports. Wu et al. analysed how randomised controlled trials were being reported in the Chinese literature written in Chinese. Their paper seemed to suggest that significant results were being published in languages other than English (in their case Chinese) and that RCTs were often poorly reported in Chinese. However, the authors of this manuscript later in the Discussion counterargue this point by remarking that ‘[…] as the volume of Chinese-language literature is growing rapidly and there have been calls for the inclusion of such publications. However, their quality has been questioned because of methodological flaws and overly positive results.’ Deviating from the point of publication bias and focusing on the quality of the research as a reason for not searching non- English language publications in HTA. While the quality of research is extremely important, there are instruments that deal with that issue within the review process making ‘poor quality’ (according to Wu’s study) not a priory reason for not searching the entire scientific literature written on a particular language such as Chinese. In light of this contradiction the rationale for this study should be reformulated to accurately justify the reasons for not searching non-English papers and always placing these in the context of the German HTA agency. So far, the reasons presented here do not seem to warrant such claim. There are a number of omissions and inaccuracies through the methods section such as the search period in the abstract is not in line with the period reported in the Methods rendering this point unclear. Further, having read the full paper twice, I am still unsure of whether HTA reports of drugs were or not included in their assessment. I think the authors should provide a detailed list of the HTA reports (medicines and non-medicines) that were screened for inclusion in the methods section since these are not their results but the body of data they used for analysis. They should also justify why diagnostic HTA reports would have been included from the start if they were not to be re-analysed in the results. Furthermore, the authors seem to apply the inclusion and exclusion criteria unsystematically when they declare that they only considered journal articles cited in HTA reports but then they present as a limitation that ‘For 2 reports (D06-01B and D06-01C), we also included evidence syntheses, although this document type was to be excluded.’ But fail to provide an explanation as to why such allowance was made. In the results section two random examples are provided of HTA report, can the authors justify why these are explained in more detail and not the others? which criteria led the authors to provide these two examples? This feels selection bias and should be avoided. In the Discussion section authors seem to contradict themselves. They start by saying that ‘the exclusion of studies published in non-English languages has only a minor effect on the conclusions of HTA reports’ At this point it is important to note that the measure of such effect (whether is big or small) is not provided throughout the manuscript nor it is explained how this ‘change in effect’ was estimated, there are no statistical tests and no p values provided making is really difficult to study whether the change, although minor, might or might not have been significant for the results of the HTA report and their future recommendations. The section follows by saying that ‘On the basis of our analysis, it is not possible to identify topics where non-English publications might be relevant.’ This statement seems to contradict what has just been said. And finally, they acknowledge that actually ‘it seems reasonable to conduct additional searches for non-English literature if a particular intervention is exclusively or preferentially available in a specific region’. The latter being a statement which defeats the point of the entire manuscript in its current rationale and supporting evidence. Please fix reference number 1 to reflect the title (Cochrane Handbook for Systematic Reviews of Interventions) of the handbook in with Chapter 4 is included. Table 1 would benefit from including definitions for each of the categories. Figure 1 please include the distribution of the 38 reports as they are allocated to different categories. Table 5. What does EP mean?\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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? No", "responses": [] }, { "id": "344992", "date": "28 Dec 2024", "name": "Tarquin Mittermayr", "expertise": [ "Reviewer Expertise Conducting systematic searches in my position as an Information 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\nI am happy to be invited to write a review on this relevant topic. Whilst the method for assessing the impact of excluding non-english literature on the conclusion of HTA reports is generally explained in a clear and comprehensible manner, Hausner et al fall short of explaining or referencing the internal protocol mentioned in the methods section.\nIt would have also been helpful to either provide an explanation already in this section or refer to the appropriate page (e.g. “please find details on page 8”) in the limitations section as to why no publications after 2018 were considered for this assessment.\nTable 1 would benefit from clearer and more concise information: The same reasons for classifying low quality studies as category B in the classification table (“Amount and quality of the evidence…”) are listed in the explanation of the categories below the table under category C, thus giving room for ambiguous interpretations.\nTable 2 contains the total number of HTA reports included as well as the number per report. It is unclear if the number given for the latter (22.5) is an average, median or a percentage. In consideration of whether providing this number is meaningful, stating just the range of included publications per report might suffice and be more explanatory.\nThe discussion section contains the confusing remark “We did not analyse whether the non-English study publications were of lower quality than the English language ones”. This appears to be contradictory to the explanations given for the classifications in Table 1. Should the contradictory nature of this statement be due to an imprecision in terminology (quality of evidence vs. quality of study publications), this study by Hausner et al would have benefited from performing a qualitative analyses of the publications themselves (in addition to analysing the containing evidence).\nIn an article which argues that excluding non-English literature may have little impact on the overall conclusion of an HTA report, the example from Report N16-03 given in the Results section, where the exclusion of a non-English article led to a change in the conclusion, might sit uncomfortably with systematic evidence based medicine professionals. As graphical this example may be in showing the effect of this exclusion, it also appears to undermine the core argument of this article.\nA revision by the authors of this publication should focus on the coherence of their argumentation on the one hand, and on supporting their methods with more concise examples (e.g. Tables and Figures).\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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1134
https://f1000research.com/articles/13-1133/v1	04 Oct 24	{ "type": "Research Article", "title": "A comparative analysis of the amount of fluoride release, recharge and re-release after uptake in three light-cure orthodontic bonding adhesives – An in-vitro study", "authors": [ "Akankshya Panda", "Ritesh Singla", "Nishu Singla", "Madhumitha Natarajan", "Akankshya Panda", "Ritesh Singla", "Madhumitha Natarajan" ], "abstract": "Background Fluoride-releasing adhesives in orthodontics help protect enamel. The study compared the fluoride release, recharge, and re-release properties of three light-cure orthodontic bonding adhesives: Group A: TransbondTM Plus Color Change, Group B: Waldent Orthobond LC, and Group C: Koden EZ Bond.\n\nMethods The study conducted an in-vitro investigation using 24 maxillary first premolar teeth bonded with one of three fluoride-releasing adhesives after etching. Each sample was placed in artificial saliva, and fluoride release was measured over 60 days using a fluoride electrode. After initial release measurement, specimens were soaked in 1000 ppm fluoride solution for 5 minutes, rinsed, and placed in new containers with distilled water before re-release measurements. Statistical Analysis: One-way ANOVA and Repeated Measures ANOVA tests were used to determine significance, with the Bonferroni posthoc test for further analysis.\n\nResults The fluoride release rate decreased gradually over time for all three groups. The highest fluoride release occurred on Day 1 for all three bonding agents, with a significantly reduced fluoride release by Day 2. Group A exhibited consistent and highest overall fluoride release throughout the 60 days. Group B gradually declined to release fluoride until Day 7, releasing the least fluoride throughout the study. Group C had a higher fluoride release on Day 1 and Day 2 but slowly declined until Day 14. Group B and Group C sharply declined fluoride release by Day 30 and almost negligible amounts on Day 60. All three agents noted enhanced fluoride release post-recharge, with continuous release until day 14. Greater release on days 7 and 14 compared to the initial release in all three groups.\n\nConclusion Transbond Plus Color Change: Consistent high fluoride was released initially and post-recharge. Waldent Orthobond LC: Lower release throughout the study. Koden EZ Bond: High initial release and post-recharge but continuing to decrease until Day 14.", "keywords": [ "Fluoride releasing", "Orthodontic adhesives", "Transbond Plus Color change", "Waldent Orthobond LC", "Koden EZ Bond", "Fluoride recharge" ], "content": "Introduction\n\nOrthodontic treatments, which correct dental misalignments, pose challenges for maintaining oral hygiene and preventing dental caries.1,2 The fluoride-releasing bonding adhesives are crucial in strengthening the enamel, making it more resistant to acid attacks and reducing caries risk.3,4 Fluoride released by the adhesives helps remineralization, allowing the tooth’s decalcified enamel near the brackets to repair itself to some extent by forming fluorapatite crystals that strengthen enamel after being demineralized by acids.5–7 It disrupts bacterial adhesion and colonization, interferes with sugar metabolism by bacteria, and thus reduces acid production, preventing demineralization and caries formation.8 It also helps arrest or reverse incipient carious lesions of enamel.9 The ability of adhesives to recharge fluoride ions from the oral environment to replace lost fluoride and re-release fluoride is essential for ongoing protection. After the initial release and uptake, the fluoride within the adhesive can continue to be released gradually over time, providing a sustained protective effect.10–12\n\nThe mechanisms of releasing, absorbing, and re-releasing fluoride through adhesive bonding are complex and influenced by various factors. Factors such as adhesive composition, filler materials, curing techniques, and environmental conditions influence fluoride release and uptake.13–16 Adhesives with higher concentrations of fluoride-releasing compounds typically offer more protection by releasing higher amounts and longer durations of fluoride. The type, size, and distribution of fillers can also impact the adhesive’s physical properties, including its porosity and the rate at which fluoride is released.17,18 The overall effectiveness of the adhesive in preventing caries can depend on how well the adhesive bonds to the tooth and how well it maintains fluoride release throughout treatment. Understanding how bonding adhesives release, absorb, and re-release fluoride is crucial for orthodontists to choose the right products and implement strategies that enhance both the effectiveness of the orthodontic treatment and prevent caries during orthodontic treatment.\n\nThis study was planned to explore different adhesive formulations under experimental conditions to understand the dynamics of fluoride release and its implications for caries prevention. The study investigated the fluoride release, uptake, and re-release behaviors of three commercially available light-cure orthodontic bonding adhesives: Transbond Plus Color Change, Waldent Orthobond LC, and Koden EZ Bond using McLaughlin Bennett 5.0 brackets by Forestadent. It included in-vitro experiments simulating clinical scenarios to monitor the fluoride release rate from each adhesive over time. The findings aim to compare the three adhesives to see if one offers superior performance regarding fluoride release, uptake, and re-release. These behaviors can significantly impact the effectiveness of caries prevention in orthodontic treatments. The research could improve oral health outcomes for orthodontic patients and provide insights for clinicians and researchers in orthodontics and preventive dentistry.\n\n\nMethods\n\nThis was an in-vitro experiment conducted on 24 extracted first premolar teeth. The research’s permission was acquired from the Ethics Committee of Kasturba Medical College and Kasturba Hospital (IEC-51/2022). Based on a previous study, the sample size of 24 premolar teeth (8 in each group; 3 groups) was determined using power analysis.13 The sample collection process involved obtaining anonymous first premolar teeth from the Department of Oral Surgery, Manipal College of Dental Sciences, Manipal. These teeth were extracted from orthodontic patients who needed these extractions as part of their treatment. Due to the in-vitro nature of the study involving experimentation on anonymized teeth samples, patient consent was waived by the ethical committee.19 Upper first premolars were chosen due to their prevalence in orthodontic extractions, suitability for bracket bonding, and susceptibility to demineralization during orthodontic treatment. The inclusion criteria for the samples were sound crown structure, free of caries and cracks, no developmental defects, and absence of restorations. After extraction, the teeth were carefully handled to avoid damage or contamination. They were cleaned using non-fluoridated pumice and stored in distilled water to prevent dehydration until use. Each tooth was mounted to the cementoenamel junction in cold cure acrylic using a PVC pipe template (19 mm diameter, 25 mm height).\n\nBefore bonding, the buccal surfaces of the upper first premolar teeth were etched with 37% phosphoric acid for 30 seconds to enhance bond strength. Three light cure orthodontic bonding agents were used: Group A: Transbond Plus Color Change, Group B: Waldent Orthobond LC, and Group C: Koden EZ Bond. Brackets (McLaughlin Bennett 5.0 by Forestadent) were positioned and bonded according to the manufacturer’s guidelines for each agent. A thin layer of bonding agent was applied to the bracket base, and the bracket was pressed onto the tooth. Excess adhesive was removed. The brackets were cured using a 3M S10 ELIPAR Light Curing Unit set at 1200 mW/cm2, with 10 seconds of light exposure from the incisal edge and another 10 seconds from the gingival, mesial, or distal edges. The light was positioned close to the bracket base to ensure proper polymerization. Each bracket bonding procedure followed the same standardized protocol to ensure consistency and comparability between the different bonding agents used in the study.\n\nAfter bonding the brackets to etched enamel surfaces, specimens were placed in plastic vials with 5 ml of artificial saliva containing carboxymethyl cellulose to simulate the oral environment. Fluoride release was measured to assess the amount of fluoride ions released from the orthodontic adhesive over time. Fluoride concentration was recorded using an Orion fluoride ion meter with a selective electrode. The electrode, featuring a lanthanum fluoride crystal, measures the potential differences fluoride ions create. To ensure accurate measurements, TISAB was used to provide a uniform ionic strength, adjust pH, and break up fluoride complexes.\n\nSamples and standard solutions were prepared in 100 ml beakers with equal amounts of TISAB, maintaining a total volume of 30 ml. The meter was calibrated using standard fluoride solutions of 0.1 ppm, 1 ppm, and 10 ppm. Initial fluoride release was measured by immersing the electrodes for 3 minutes on days 1, 2, 3, 4, 5, 6, 7, 14, 30, and 60 post-bonding. These measurements are crucial for evaluating the fluoride-releasing capabilities of different orthodontic bonding agents and their potential benefits for caries prevention and enamel remineralization. By monitoring fluoride release over specific intervals, the study aims to determine the efficacy and duration of fluoride release, which is essential for assessing the clinical implications of the bonding agents used in orthodontic treatment.\n\nAfter the initial fluoride release measurements, the specimens undergo fluoride uptake and rerelease to simulate dynamic oral environment exposure. Fluoride Uptake: Specimens were soaked for 5 minutes in a 1000 ppm fluoride solution, rinsed with distilled water, dried, and transferred to new containers with 5 ml of distilled water each time before recording post-recharge measurements. Fluoride Rerelease: Fluoride concentration is measured using a fluoride meter on days 1, 2, 7, 14, 30, and 60 post-immersion. These measurements assess the adhesive’s fluoride uptake capacity, retention, and rerelease patterns, providing insights into their sustained fluoride-releasing potential. This helps evaluate their effectiveness in replenishing fluoride ions, promoting caries prevention, and enamel remineralization during orthodontic treatment.\n\nThe study data was analyzed using the statistical package SPSS 26.0 (SPSS Inc., Chicago, IL). Descriptive statistics was performed to assess the mean and standard deviation of the respective groups. The data’s normality was evaluated using the Shapiro-Wilk test, indicating a normal distribution (P>0.05), allowing for parametric tests. The mean difference between the groups was determined using the ‘One-way ANOVA test’ and within-group analysis by ‘repeated measures of ANOVA test’ followed by the ‘Bonferroni posthoc test.’ The level of significance was set at P<0.05.\n\n\nResults\n\nFluoride released by three light-cured bonding agents (Group A: Transbond Plus Color Change, Group B: Waldent Orthobond LC, Group C: Koden EZ Bond) was analyzed over 60 days using an ion-selective electrode. Repeated Measures ANOVA showed significant differences within each group over time (P<0.05). There was a significant decrease in the release of fluoride levels between all pair days except for Day 2 vs Day 3 in Group A (P>0.05). It was observed that the fluoride release rate decreased gradually for all three groups over time (Figure 1). The highest fluoride release occurred on Day 1 for all three bonding agents, with a significantly decreased fluoride release by Day 2. Group A showed the consistent and highest overall fluoride release compared to the other two groups, gradually reducing over time. Group B gradually declined to release fluoride until Day 7, releasing the least fluoride throughout the study. Group C had a higher fluoride release on Day 1 and Day 2 but continued to decrease until Day 14 (Table S1, Extended data). Group B and Group C sharply declined fluoride release by Day 30 and almost negligible amounts on Day 60.\n\nOn day 1, all three groups exhibited similar fluoride release, with Group C slightly higher and no statistically significant differences. On day 2, Group C exhibited significantly higher fluoride release than Group A and Group B (P<0.0001). From day 3 to day 6, Groups C and A showed similar levels of fluoride release. However, from day 7 onwards, Group A released significantly higher levels of fluoride than Group C. Additionally, starting from day 2, Group A consistently exhibited significantly higher fluoride release than Group B. Group C also demonstrated a significantly higher fluoride release than Group B except on day 60, when there was no significant difference between them (Table S2, Extended data).\n\nWhen the three orthodontic adhesives were recharged with a 1000 ppm NaF solution, the rate of fluoride re-release declined over time, similar to the initial post-bonding release (Figure 2). However, fluoride was increased in all three agents post-recharge compared to the initial release, with the sustained release until Day 14 (Figures 3, 4, and 5). It was observed that Days 7 and 14 showed higher release in all groups after recharging compared to the initial release. Repeated Measures ANOVA showed a significant decrease in fluoride re-release within each group over time (P<0.05) (Table 1). Comparison between the groups revealed that on Day 1, Group C exhibited slightly higher fluoride release than Groups A and B. After that, starting from Day 2, Group A released higher fluoride than the other two groups (Group B and C). On Day 30 and Day 60, Groups B and C had negligible release; Group A had significant release throughout 60 days post-recharge (Table 2).\n\n* P<0.05 is statistically significant.\n\n* P<0.05 is statistically significant (Friedman test & Bonferroni Postthoc test).\n\n\nDiscussion\n\nThe emergence of white spot lesions near orthodontic brackets due to early enamel demineralization is a significant concern for orthodontists.1,2 The effectiveness of standard preventive measures like sealants, topical fluorides, and oral hygiene instructions for orthodontic patients may be limited if the challenges of maintaining oral hygiene with braces are not adequately addressed. Additionally, a study by Mohammed Althagafi found that fluoride pre-treatment before bonding reduces bond strength, increasing bracket debonding and chairside time.20 An ideal preventive system should deliver controlled fluoride release at plaque-prone sites around orthodontic brackets without relying on patient cooperation. Incorporating fluoride-releasing adhesives into orthodontic treatment can thus offer significant benefits in immediate bond strength and long-term enamel protection.21–23\n\nThe protection against demineralization varies with the amount of fluoride released by different bonding materials.13–16 The efficacy of fluoride-releasing materials is influenced by how well they release, recharge, and re-release fluoride, which is affected by the bonding agent’s matrix, size, and shape.17,18 Understanding the fluoride-releasing potential of different bonding adhesives is essential for selecting the most effective materials to protect enamel during orthodontic treatment. This study compares the fluoride-releasing potential of three commercially available light-cure orthodontic bonding adhesives (Transbond Plus Color Change, Waldent Orthobond LC, Koden Ez bond).\n\nThe study revealed that on Day 1, there was a “burst effect” of fluoride release, followed by a gradual decline from Day 2. This pattern was consistent across all three adhesives. Chan DCN et al. and McNeill CJ et al. observed similar patterns in their studies, with significant drops in fluoride release after 24 hours, continuing to decrease over time.24,25 Transbond Plus Color Change exhibited the consistent and highest overall fluoride release throughout the 60 days. Koden Ez bond had the highest fluoride release on Day 1 and Day 2 and a similar release as Transbond Plus Color Change till Day 6 but continued to decrease until Day 14. Waldent Orthobond LC gradually declined to release fluoride until Day 7, releasing the least fluoride throughout the study. Waldent Orthobond LC and Koden Ez bond sharply declined fluoride release by Day 30 and almost negligible amounts on Day 60.\n\nEven though a similar comparison group wasn’t found in other studies, according to similar research, Transbond Plus Color Change Adhesive significantly reduces enamel demineralization around brackets compared to traditional adhesives. It outperforms other adhesive groups in preventing white spot lesions, such as reported by Osama et al. that Transbond Plus Color Change Adhesive was more effective than the conventional adhesive Transbond XT.26 Bhushan R et al. found it more effective than the GC Fuji Ortho LC and Vitremer groups.27 At the same time, Passalini P reported it more effective than Orthodontic Fill Magic.28 On the contrary, in a study by Vittorio Cacciafesta et al., Fuji Ortho LC released the highest amount of fluoride. In contrast, Transbond Plus released negligible amounts of fluoride, among other bracket-bonding adhesives.16\n\nTransbond Plus Color Change adhesive contains fluoro-aluminosilicate glass, which acts as a reservoir for fluoride. The adhesive is hydrophilic, allowing it to perform effectively even in the presence of saliva. The cured, cross-linked structure of Transbond Plus Color Change is designed to be stable, allowing for the controlled release of fluoride over an extended period. As a result, fluoride is steadily released even after the initial application period. This matrix helps to retain fluoride and release it gradually, providing ongoing protection against demineralization.26,29 Waldent Orthobond LC and Koden EZ Bond are relatively new materials and lack extensive documentation on fluoride release, recharge, and re-release capabilities, unlike Transbond Plus Color Change. In the current study, Waldent Orthobond LC may offer competitive bonding strength and performance but might not match the fluoride management features of Transbond Plus Color Change. Koden EZ Bond does offer high initial fluoride release and post-recharge for the first week, continuing to decrease till Day 14.\n\nConsistent with prior research, each bonding agent showed an enhanced recharge level with each additional fluoride treatment, even after aging.29,30 Similarly, the correlation between pre-recharge release levels and post-recharge re-release levels aligns with previous studies.30,31 These results suggest that the rechargeability of these composites is influenced by the availability of sites within the material capable of retaining absorbed fluoride.31,32 Waldent Orthobond LC had the lowest re-release throughout the study. Koden Ez bond exhibited the highest initial release post-recharge but declined sharply after day 2, showing negligible release by day 60. Transbond Plus Color Change had a lower initial release but demonstrated superior recharge and re-release properties, suggesting a greater capacity to uptake and release fluoride over time.26\n\nThe current orthodontic bonding agents are mainly designed for their bonding strength and ease of use. They offered their highest fluoride ion release within the first 24 hours, followed by a low level of long-term fluoride ion release.3,4 Most fluoride-releasing adhesives exhibit low release after 2 months, necessitating sustained release throughout the typical 2-year orthodontic treatment. Therefore, it is recommended to use additional fluoride sources, such as toothpaste and mouthwash, during treatment.10–12 External fluoride sources replace fluoride ions in the resin matrix, effectively recharging the bonding agent. The recharge process depends on exposure concentration, duration, and resin matrix properties.17,18 In this study, bonding adhesives were recharged by dipping samples in 1000 ppm sodium fluoride solution for 5 minutes, simulating daily use of fluoridated toothpaste for 6 months. Periodic re-fluoridation of bonding agents is necessary to replenish utilized fluoride ions and prevent enamel demineralization during orthodontic treatment. This study’s findings align with previous research, emphasizing the importance of continuous lower fluoride levels rather than one-time high-concentration applications.10–12\n\nWhile the current in-vitro study provides valuable preliminary insights into the performance of three bonding agents, its limitations must be considered. The controlled laboratory environment may not fully replicate the complex conditions of an oral environment, which can affect the applicability of the findings. Therefore, further research is necessary to validate and expand upon these results. Conducting in vivo studies with larger sample sizes and incorporating a wider range of bonding materials will offer a more comprehensive understanding of the most effective and practical orthodontic adhesives. Such research will help confirm the initial findings and clarify how these materials perform under real-world conditions.\n\n\nConclusion\n\nAll three orthodontic adhesives showed a significant decrease in fluoride release after day 1, continuing through day 60. After recharging with a 1000 ppm fluoride solution, the fluoride release levels of the adhesives were similar to their initial release. Transbond Plus Color Change Adhesive demonstrated stable and sustained higher fluoride release over a 60-day study period. Although it did not have the highest initial fluoride release or the most robust recharge and re-release capabilities, its balanced combination of these properties and its color-changing feature indicate proper curing, making it the most suitable option for clinical use among the materials studied. Koden Ez Bond adhesive exhibited the highest initial and post-recharge fluoride release but sharply declined by day 30 and almost negligible amounts on Day 60. Waldent Orthobond LC adhesive consistently showed lower fluoride release initially and after recharging than the other adhesives.\n\nThe research’s permission was acquired from the Ethics Committee of Kasturba Medical College and Kasturba Hospital (IEC no.51/2022, Dated 31-12-2022). Due to the in-vitro nature of the study involving experimentation on anonymized teeth samples, patient consent was waived by the ethical committee.19", "appendix": "Data availability\n\nFigshare: A comparative analysis of the amount of fluoride release, recharge, and re-release after uptake in three light-cure orthodontic bonding adhesives – An in-vitro study. https://doi.org/10.6084/m9.figshare.27005521.v1 33\n\nThis project contains the following underlying data:\n\n• Data.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: A comparative analysis of the amount of fluoride release, recharge, and re-release after uptake in three light-cure orthodontic bonding adhesives – An in-vitro study. https://doi.org/10.6084/m9.figshare.27005521.v1 33\n\nThis project contains the following extended data:\n\n• Tables.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\nZachrisson BU, Zachrisson S: Caries incidence and orthodontic treatment with fixed appliances. Eur. J. Oral Sci. 1971 Apr; 79(2): 183–192. Publisher Full Text\n\nMizrahi E: Surface distribution of enamel opacities following orthodontic treatment. Am. J. Orthod. 1983 Oct 1; 84(4): 323–331. PubMed Abstract \| Publisher Full Text\n\nAn JS, Lim BS, Ahn SJ: Managing oral biofilms to avoid enamel demineralization during fixed orthodontic treatment. Korean J. Orthod. 2023 Nov 25; 53(6): 345–357. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRaji SH, Banimostafaee H, Hajizadeh F: Effects of fluoride release from orthodontic bonding materials on nanomechanical properties of the enamel around orthodontic brackets. Dent. Res. J. (Isfahan). 2014 Jan; 11(1): 67–73. PubMed Abstract\n\nØgaard B, Rølla G, Arends J, et al.: Orthodontic appliances and enamel demineralization Part 2. Prevention and treatment of lesions. Am. J. Orthod. Dentofacial Orthop. 1988 Aug 1; 94(2): 123–128. PubMed Abstract \| Publisher Full Text\n\nBenson PE, Parkin N, Dyer F, et al.: Fluorides for preventing early tooth decay (demineralized lesions) during fixed brace treatment. Cochrane Database Syst. Rev. 2019; 2019(11): Art. No.: CD003809. Publisher Full Text\n\nFejerskov O, Thylstrup A, Larsen MJ: Rational use of fluorides in caries prevention. A concept based on possible cariostatic mechanisms. Acta Odontol. Scand. 1981; 39(4): 241–249. Publisher Full Text\n\nRolla G: Effects of fluoride on initiation of plaque formation. Caries Res. 1977 Jan 1; 11(Suppl 1): 243–261. Publisher Full Text\n\nFeatherstone JD: Prevention and reversal of dental caries: role of low-level fluoride. Community Dent. Oral Epidemiol. 1999 Feb; 27(1): 31–40. PubMed Abstract \| Publisher Full Text\n\nLim BS, Lee SJ, Lim YJ, et al.: Effects of periodic fluoride treatment on fluoride ion release from fresh orthodontic adhesives. J. Dent. 2011 Nov; 39(11): 788–794. PubMed Abstract \| Publisher Full Text\n\nAhn SJ, Lee SJ, Lee DY, et al.: Effects of different fluoride recharging protocols on fluoride ion release from various orthodontic adhesives. J. Dent. 2011 Mar; 39(3): 196–201. PubMed Abstract \| Publisher Full Text\n\nBenington PC, Gillgrass TJ, Foye RH, et al.: Daily exposure to fluoride mouth rinse produces sustained fluoride release from orthodontic adhesives in vitro. J. Dent. 2001 Jan; 29(1): 23–29. PubMed Abstract \| Publisher Full Text\n\nBarik AK, Duggal R: Comparative evaluation of fluoride release from chemically cured and light-cured orthodontic bonding agents and surface alteration of enamel: an in vitro study. J. Indian Orthod. Soc. 2020 Jul; 54(3): 233–239. Publisher Full Text\n\nRegalla RR, Jadav C, Babu DA, et al.: Evaluation and comparison of quantity and pattern of fluoride release from orthodontic adhesives: an in vitro study. J. Contemp. Dent. Pract. 2014 Jan 1; 15(1): 99–102. PubMed Abstract \| Publisher Full Text\n\nMonteith VL, Millett DT, Creanor SL, et al.: Fluoride release from orthodontic bonding agents: a comparison of three in vitro models. J. Dent. 1999 Jan; 27(1): 53–61. Publisher Full Text\n\nCacciafesta V, Sfondrini MF, Tagliani P, et al.: In-vitro fluoride release rates from 9 orthodontic bonding adhesives. Am. J. Orthod. Dentofacial Orthop. 2007 Nov; 132(5): 656–662. PubMed Abstract \| Publisher Full Text\n\nXu X, Burgess JO: Compressive strength, fluoride release, and recharge of fluoride-releasing materials. Biomaterials. 2003; 24(14): 2451–2461. PubMed Abstract \| Publisher Full Text\n\nItota T, Carrick TE, Yoshiyama M, et al.: Fluoride release and recharge in giomer, compomer and resin composite. Dent. Mater. 2004; 20: 789–795. PubMed Abstract \| Publisher Full Text\n\nNational Ethical Guidelines for Biomedical and Health Research Involving Human Participants by Indian Council of Medical Research.2017. 978-81-910091-94. Reference Source\n\nAlthagafi NM: Impact of fluoride-releasing orthodontic adhesives on the shear bond strength of orthodontic brackets to eroded enamel following different surface treatment protocols. J. Orthod. Sci. 2022; 11: 3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasdra EK, Huber H, Komposch G: Fluoride released from orthodontic bonding agents alters the enamel surface and inhibits enamel demineralization in vitro. Am. J. Orthod. Dentofacial Orthop. 1996; 109: 466–472. PubMed Abstract \| Publisher Full Text\n\nOggard B, Rezk-Lega F, Ruben J, et al.: Cariostatic effect and fluoride release from a visible light-curing adhesive for bonding of orthodontic brackets. Am. J. Orthod. Dentofacial Orthop. 1992; 101: 303–307. PubMed Abstract \| Publisher Full Text\n\nRogers S, Chadwick B, Treasure E: Fluoride-containing orthodontic adhesives and decalcification in patients with fixed appliances: a systematic review. Am. J. Orthod. Dentofacial Orthop. 2010 Oct; 138(4): 390.e1–390.e8. PubMed Abstract \| Publisher Full Text\n\nChan DCN, Swift EJ, Bishara SE: In vitro evaluation of a Fluoride-releasing orthodontic resin. J. Dent. Res. 1990; 69: 1576–1579. Publisher Full Text\n\nMcNeill CJ, Wiltshire WA, Dawes C, et al.: Fluoride release from new light-cured orthodontic bonding agents. Am. J. Orthod. Dentofacial Orthop. 2001; 120: 392–397. PubMed Abstract \| Publisher Full Text\n\nEissaa OE, El-Shourbagy EM, Ghobashy SA: In vivo effect of a fluoride-releasing adhesive on inhibition of enamel demineralization around orthodontic brackets. Tanta Dent. J. 2013; 10(2): 86–96. Publisher Full Text\n\nBhushan R, Shruti S, Prasanth PS, et al.: Assessment of the Effectiveness of Different Fluoride-releasing Bonding Agents on Prevention of Enamel Demineralization around Orthodontic Bracket: An In Vitro Study. J. Contemp. Dent. Pract. 2021 Oct 1; 22(10): 1130–1134. PubMed Abstract \| Publisher Full Text\n\nPassalini P, Fidalgo TK, Caldeira EM, et al.: Preventive effect of fluoridated orthodontic resins subjected to high cariogenic challenges. Braz. Dent. J. 2010; 21(3): 211–215. PubMed Abstract \| Publisher Full Text\n\nBakhtyar S, Hassan BA: Evaluation of fluoride-releasing and recharging orthodontic adhesive resins: An in vitro study. EDJ. 2021 Feb. 19; 3(2): 126–134. Publisher Full Text Reference Source\n\nDionysopoulos D, Koliniotou-Koumpia E, Helvatzoglou-Antoniades M, et al.: Fluoride release and recharge abilities of contemporary fluoride-containing restorative materials and dental adhesives. Dent. Mater. J. 2013; 32(2): 296–304. PubMed Abstract \| Publisher Full Text\n\nAttar N, Turgut MD: Fluoride release and uptake capacities of fluoride-releasing restorative materials. Oper. Dent. 2003; 28(4): 395–402. PubMed Abstract\n\nAttar N: Onen A Fluoride release and uptake characteristics of aesthetic restorative materials. J. Oral Rehabil. 2002; 29(8): 791–798. PubMed Abstract \| Publisher Full Text\n\nSingla R: A comparative analysis of the amount of fluoride release, recharge, and re-release after uptake in three light-cure orthodontic bonding adhesives – An in-vitro study. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "336725", "date": "25 Nov 2024", "name": "Ganugapanta Vivek Reddy", "expertise": [ "Reviewer Expertise cbct" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDemineralisation around the brackets is a matter of concern ,need to take steps in prevention ,lot of research is going on to reduce it, your efforts to compare gives audience a complete understanding and insight in to material aspects .\nFew clarifications\n1.How was sample size determined per group . 2. Type of curing Used in the study. 3.Reasoning behind selection of material.\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/13-1133
https://f1000research.com/articles/13-601/v1	07 Jun 24	{ "type": "Case Study", "title": "A Case Study on Measuring AI Assistant Competence in Narrative Interviews", "authors": [ "Chitat Chan", "Yunmeng Zhao", "Yunmeng Zhao" ], "abstract": "Abstract*\nBackground Researchers are leading the development of AI designed to conduct interviews. These developments imply that AI's role is expanding from mere data analysis to becoming a tool for social researchers to interact with and comprehend their subjects. Yet, academic discussions have not addressed the potential impacts of AI on narrative interviews. In narrative interviews, the method of collecting data is a collaborative effort. The interviewer also contributes to exploring and shaping the interviewee's story. A compelling narrative interviewer has to display critical skills, such as maintaining a specific questioning order, showing empathy, and helping participants delve into and build their own stories.\n\nMethods This case study configured an OpenAI Assistant on WhatsApp to conduct narrative interviews with a human participant. The participant shared the same story in two distinct conversations: first, following a standard cycle and answering questions earnestly, and second, deliberately sidetracking the assistant from the main interview path as instructed by the researcher, to test how well the metrics could reflect the deliberate differences between different conversations. The AI's performance was evaluated through conversation analysis and specific narrative indicators, focusing on its adherence to the interview structure, empathy, narrative coherence, complexity, and support for human participant agency. The study sought to answer these questions: 1) How can the proposed metrics help us, as social researchers without a technical background, understand the quality of the AI-driven interviews in this study? 2) What do these findings contribute to our discussion on using AI in narrative interviews for social research? 3) What further research could these results inspire?\n\nResults The findings show to what extent the AI maintained structure and adaptability in conversations, illustrating its potential to support personalized, flexible narrative interviews based on specific needs.\n\nConclusions These results suggest that social researchers without a technical background can use observation-based metrics to gauge how well an AI assistant conducts narrative interviews. They also prompt reflection on AI's role in narrative interviews and spark further research.", "keywords": [ "Artificial Intelligence", "Narrative Inquiry", "Qualitative Research", "WhatsApp Interviews", "Conversational AI", "Prompt Engineering", "Digital Research Methodologies" ], "content": "Virtual assistants breaking into narrative research\n\nIn recent years, conversational artificial intelligence (AI), exemplified by Open AI’s ChatGPT, has ushered in a new era of human-machine interaction (Brown et al., 2020; Wei et al., 2021). The transformative potential of these technologies spans a diverse range of applications and capabilities (Adamopoulou & Moussiades, 2020; Bendig et al., 2019; Chan & Li, 2023; Shah et al., 2017; Xu & Zhuang, 2022).\n\nThe integration of generative AI has revolutionized and democratized the process of qualitative data collection, analysis, and interpretation. This technological leap has boosted efficiency and expanded the horizons of narrative inquiry methods (Christou, 2023, 2024; Cohen & Queen, 2023; Lennon et al., 2021; Morgan, 2023). While AI technology has streamlined most narrative analysis processes, capturing nuanced narrative data is also gaining prominence.\n\nSome researchers are now at the forefront of developing AI for interview purposes (Cordero et al., 2022; Han et al., 2021). Commercial entities have also harnessed the power of artificial intelligence (AI) to conduct qualitative customer interviews. These AI tools streamline the process of gathering and analyzing customer feedback (e.g., https://listenlabs.ai/). They can conduct interviews, record responses, and use advanced algorithms to interpret the data, unearthing insights that might otherwise be overlooked. Furthermore, influential bloggers have championed using AI in user interviews, citing its ability to enhance efficiency (e.g., https://www.hotjar.com/blog/ai-user-interviews/). By automating repetitive tasks, AI accelerates the interview process and ensures high precision. Given these advantages, AI-driven narrative interviews are poised to become a significant trend, offering substantial benefits across various industries.\n\nIntroducing customizable generative AI model interfaces, such as ChatGPT Builder and Assistant API, has expanded the possibilities further. It's not only about how computer experts can utilize those AI models but also about how non-experts in computing can adapt these models to meet specific requirements across different contexts (DeVon, 2023; Stallbaumer, 2023; Wang et al., 2023). Such APIs also support complex stepwise instructions and facilitate continuous dialogues, moving beyond simple question-and-answer interactions. These advancements forecast a growing trend where AI becomes essential to how researchers interact with and understand their participants.\n\nThese advancements show that AI is moving beyond just analyzing data in the background; it is becoming a crucial tool for researchers to engage with and understand their participants. This shift is both exciting and challenging. Narrative interviews are complex because they involve interaction, continuity, responsiveness, and deep engagement with participants' stories. In these interviews, the dialogue is about sharing information and jointly creating a story (Chase, 2018; Clandinin, 2007). AI does not merely improve how we analyze these stories; it also transforms how stories are constructed and gathered in the first place.\n\nHowever, academic discussions have not explored how AI could enable or limit narrative interviews. As conversational AI continues to evolve, researchers and industry experts have proposed various metrics to assess the performance of AI assistants (Katic et al., 2024; Sharma, 2020; Xu & Jiang, 2024). Existing literature primarily measures the overall technical performance of dialogue systems, such as response time, language proficiency, repetitions, and human-likeness (Deriu et al., 2021; Finch & Choi, 2020; Lee et al., 2023), instead of focusing on the micro-level performance at the conversational level. Assessing the overall competence of language models is essential in overall technical development, but they do not evaluate AI assistants’ performance in interview contexts. Some researchers have provided practical measures at the conversation level; for example, Concannon and Tomalin (2023) suggest using an Empathy Scale for Human–Computer Communication, based on raters using a Likert scale to assess the textual content of conversations. This instrument is relevant and valuable, but empathy is just one of the domains in narrative interviews. Other areas also need to be addressed to ensure the quality of narrative data.\n\nAgainst this backdrop, exploring and discussing how we can assess AI's role in narrative interviews is crucial. This exploration is critical to understanding how AI can enhance or compromise the depth and quality of narrative data and what this means for future technological advancements.\n\n\nWhy do assistants' interview skills matter and what are these skills?\n\nDialogue is not just about exchanging information but also about building a story collaboratively. The qualitative inquiry approach is deeply rooted in constructivist and social constructionist worldviews, which suggest that reality is constructed through social interactions and discursive contexts (Abkhezr et al., 2020; Denicolo et al., 2016). Participants engaging in meaningful conversations during interviews can contribute to reality construction and reflection (Gergen, 2001; Shotter, 1993). As such, narrative inquiry generally assumes a more active role for interview participants in which their “active narrativity” (Gubrium et al., 2012, p. 28) is highlighted.\n\nFirst, narrative interviewers need to be sensitive to the sequence of questioning. A narrative necessarily implies a sequence and consequence of events, and different questioning sequences, in principle, yield different results (Riessman, 2008; Riessman & Quinney, 2005). Unlike self-report questionnaires that see each question as an independent item and sometimes can be randomly arranged, narrative interviews involve a dialogic process that assumes a continual unfolding of the participant’s story. Even though qualitative research typically favors open-ended questions, interviewers need to guide the conversation to stay focused on the specific topic of inquiry. In some therapeutic contexts, the sequence or scaffolding of the questions is even conceived as a key to therapeutic effects (Duvall & Béres, 2011; White, 2007).\n\nSecond, narrative interviewers need to demonstrate empathy. Rather than merely factual descriptions, participants’ narrative productions are considered an active practice of data production in data collection contexts, and narrative inquirers must be able to exercise this “active narrativity” (Chase, 2018; Clandinin, 2007). As such, the narrative inquirer’s “capacity to be empathic, nonjudgmental, concerned, tolerant, and emotionally responsive” (Josselson, 2007, p. 539) is prioritized. This method fosters an environment where participants can actively contribute to knowledge production.\n\nThird, narrative interviewers need to facilitate participants in exploring and constructing meanings, and they also need to balance their agency and participant agency in such a process. Participants’ voices reflect the diversity of their narratives and the many ways they can author and re-author themselves. In short, narrative interviews involve both the research participants and the inquirer’s agency (Gubrium et al., 2012, p. 33), and such a methodological characteristic also blurs the boundary between inquiry and intervention (Abkhezr et al., 2020). This balancing act requires interviewers to be attentive and adaptive, intervening gently to steer the conversation back on track when necessary without stifling the participant's natural flow of expression.\n\nIn sum, the form of data collection in a narrative interview is a collaborative production. When conducting a narrative interview, the interviewer also partly constructs the interviewee’s narrative. As such, to competently conduct narrative interviews, the interviewer should be able to:\n\n• Follow a particular questioning sequence while remaining adaptable.\n\n• Demonstrate empathy.\n\n• Facilitate participants’ exploration and construction of meanings while avoiding domination.\n\nThis brief review of narrative inquirer capabilities is not comprehensive. The abovementioned competencies were chosen to inform our case study, which is mainly heuristic. In this study, we configured an AI Assistant and assessed its competence in narrative interviews, referring to the abovementioned competencies.\n\n\nConversation analysis and competence metrics\n\nThis study suggested using conversation analysis and some selected narrative variables to measure AI’s competencies in narrative interviews. Conversation analysis is a method used in sociology, linguistics, and communication studies to analyze the structure and patterns of interaction in everyday spoken conversations. It focuses on how people manage and organize spoken interaction and how they produce and interpret conversation in social contexts (Liddicoat, 2021). The units of conversation analysis can be the entire conversation and individual utterances in the conversation. Researchers can use humans or machines for textual coding based on specific rubrics. It is a kind of observation-based rating, commonly utilizing the Likert scale to assess textual data systematically. The following metrics were chosen primarily for their simplicity and to facilitate testing and demonstration:\n\nWe assigned a progression score to each utterance based on its intended progression stage referencing a specific conversation plan. This measure is adapted from the sequential analysis used in therapy research, which assesses the sequence of conversation utterances (Au-yeung, 2023; Chan et al., 2020; Connor et al., 2009; Moran et al., 2005; Ramey et al., 2009). It assumes that an utterance at any point is a response to the utterance preceding it, and the analysis is to plot the progression throughout the conversation. A higher score does not mean better or more advanced; it just shows the order of the utterances and whether they follow the sequence. This study recorded and organized all the utterances from the interview conversations in a spreadsheet. These utterances were arranged in rows, each representing an utterance unit that could be tagged with a progression score. We also used this scoring system to calculate average progression scores over specific time intervals and to support data visualization.\n\nWe assigned an empathys core to the assistant in an interview conversation based on an overall interpretation of the conversation. In the realm of human-machine communication, the capacity to foster a sense of empathy is primarily accomplished through linguistic conduct. Although there is a scarcity of studies exploring the use of language to exhibit and react to emotions empathetically, Concannon and Tomalin (2023) seek to bridge this gap by showcasing how an analysis of empathetic response tactics can be used to measure empathy. The empathy level score utilized in this study draws inspiration from the affective item of the Empathy Scale for Human-Computer Communication, as proposed by Concannon and Tomalin (2023). The scale used in this study is grounded on an observation-based rating that employs a Likert scale to evaluate the textual content of dialogues. This metric gauges the assistant's ability to exhibit concern, compassion, or empathy that resonates with the user's emotional intensity or tone. This is typically achieved through empathetic language, expressions of comprehension, or supportive feedback that acknowledges and validates the user's emotions.\n\nTo what extent participants have explored and constructed meaning in narrative interviews is complex and multi-dimensional, this study contended that a set of independent yet interrelated metrics can reflect it. These metrics include the human participant's level of agency, the coherence of the conversation content, the complexity of the content, and the meaning-making in the conversation.\n\nIn this study, we assigned an agency score to the human participant in an interview conversation based on an overall interpretation of the conversation. Human agency refers to the capacity of individuals to act independently and make their own free choices. It is the power that enables individuals to think, act, and make decisions on their own. It is essential to assess the interviewee’s agency in narrative interview contexts because it provides insights into how well the interviewee is allowed to express their thoughts, influence the direction of the conversation, and contribute to the narrative. Understanding the level of agency can help evaluate the effectiveness of the interview process and the quality of the data collected. This measure is adapted from the agency item in the narrative identity measure proposed by Adler et al. (2017). Originally, it referred to the degree to which the narrative protagonist could initiate changes independently, exert some control over their experiences, and influence their own life. In our study, we assessed the extent to which the participant (interviewee) could exert control throughout their conversation with the assistant, such as asking for clarifications, suggesting new topics, and requesting corrections. However, agency alone does not directly imply positivity. Rejecting and sidetracking can also be ways of exercising agency, so it does not directly mean high quality. Therefore, it must be interpreted in conjunction with measures from other metrics.\n\nWe assigned a coherence score to the interview conversation based on an overall interpretation of the conversation. Coherence refers to the logical and consistent interconnection of ideas in a text. It originally refers to the degree to which the narrator situates the characters of their story and their actions in a specific context, the story follows a temporal sequence of goal-oriented actions that are culturally recognized, emotions are clearly expressed in support of the point of the narrative, and the narrative is integrated into more prominent life themes and meanings. In this study, we assessed the degree to which the participant (interviewee) situated elements in their interview conversation with the AI assistant coherently and to what extent their utterances could be integrated into more prominent themes and meanings coherently. Assessing the coherence of conversation texts in narrative interview contexts is worthwhile because it reflects the outcomes of constructive interactions. This measure is adapted from the coherence item in the narrative identity measure suggested by Adler et al. (2017). However, coherence alone cannot guarantee the quality of the narrative. A simple, single-minded story can be very coherent but does not directly imply high quality. Therefore, it needs to be interpreted in conjunction with measures from other metrics.\n\nWe assigned a complexity score to the interview conversation based on an overall interpretation of the conversation. Complexity refers to the degree of variation and intricacy within the conversation. Assessing the complexity of conversation texts is worthwhile because it reflects the outcomes of interactions. This measure is adapted from the complexity item in the narrative identity measure suggested by Adler et al. (2017). It originally refers to the degree of engagement in narrative processing, as shown by depth of thought and nuance, such as seeing a variety of perspectives or emotions. In this study, we assessed the participant's (interviewee's) degree of engagement in their conversation with the assistant, as shown by depth of thought and nuance, as well as a variety of perspectives or emotions. However, complexity alone does not directly imply positivity. Sidetracking to different topics can make a conversation very complex, but it does not directly mean high quality. Therefore, it has to be interpreted in conjunction with measures from other metrics.\n\nWe assigned a meaning-making score to the interview conversation based on an overall interpretation of the conversation. Meaning-making refers to how individuals interpret and make sense of life events, relationships, and their self-concept. Evaluating the interviewee's process of constructing meaning in narrative interview settings is valuable as it offers deep insights into their comprehension and the narratives they articulate. This measure is adapted from the meaning-making item in the narrative identity measure developed by Adler et al. (2017). It originally refers to the degree to which the protagonist learns something or gleans a message from an event. In this study, we assessed the degree to which the participant (interviewee) has developed ideas and themes in response to the assistant’s questions. Measures from the abovementioned metrics, such as agency level, coherence, and complexity, should be interpreted alongside this meaning-making score.\n\n\nA case study\n\nAs social researchers without a technical background, we were able to configure an assistant using OpenAI’s Assistants API (Application Interface) (https://platform.openai.com/) using its GPT-4 model. It is worthwhile to note that this Assistant API differs from the highly user-friendly ChatGPT, as it offers more robust features tailored for developers, and this API can enable us to deploy chatbots on websites and various messaging platforms, offering flexibility and user accessibility without relying on OpenAI’s user interface. OpenAI Assistants API allows users to set long, stepwise, and systematic instructions for the assistant on the back end. All these can be done without coding, using the Playground on OpenAI.\n\nWe deployed our Assistant on WhatsApp. Using WhatsApp is good for several reasons. First and foremost, the use of WhatsApp in research is widely discussed as it can potentially enhance communication and collaboration outside traditional lab settings (Gasaymeh, 2017; Suárez-Lantarón et al., 2022). Second, many people are familiar with WhatsApp, so chatting with an assistant does not require them to pick up new skills. Third, WhatsApp keeps messages safe and private, so chats are secured. Fourth, users can get quick replies and support when using an AI assistant because the interaction is immediate and yet asynchronous, chatting with that assistant anytime and anywhere.\n\nIn a way, WhatsApp acts merely as a shell or user interface, while our settings on cloud-based service platforms control the actual automation. We ran our simple Python file on a cloud service platform. In this study, we used Replit (https://replit.com/), a dynamic, user-friendly software creation platform that caters to a broad spectrum of developers with various tools and features. Through Replit, we could access third-party AI models, such as OpenAI’s Assistants API. In this project, the Python file sent requests to and received responses from OpenAI’s Assistants API. The source code can be provided upon request. We connect the files on Replit to WhatsApp through a service platform called ManyChat (https://manychat.com/), which lets users build and manage chatbots for messaging apps like WhatsApp (and many others).\n\nThis research adopted a structured conversational framework that prompted participants to engage thoroughly with their personal stories, fostering a deeper self-reflection and integration of insights. The framework used in this study was partially informed by narrative therapy (Au-yeung, 2023; Chan, 2012, 2023; Chan et al., 2020; Chan et al., 2012; Ramey et al., 2009; Ramey et al., 2010; White, 2007).\n\nIn this study, the conversation plan involves unfolding details and elaborating connections. It then invited the participant to propose a name based on inductive reflection and explore deeper core values. The stages are as follows: 1. Orientation, 2. Unfolding, 3. Naming, 4. Explaining, 5. Exploring core values, 6. Aspirations, and 7. Closing. Instructions for the AI, specifically the interview guide, are available in the published dataset (Chan, 2024). We designed this conversation plan specifically for its manageable complexity – making the interview not too simple but not too complicated – so it can facilitate our testing. Unlike more superficial, disjointed question-and-answer dialogues, this conversation plan enables us to explore continuity and interview skills. Our goal is to evaluate the assistant's compliance with these instructions effectively. An in-depth theoretical discussion of interview strategies falls outside the scope of this study.\n\nIn this study, we tested and demonstrated these metrics with a single case. Focusing on a single participant allowed the researcher to delve deeply into the content at an utterance level, observing the dynamics between the AI and the human participant. This depth provides detailed insights that might be missed in studies with multiple participants. A single-case study can also help review and fine-tune the suggested metrics during development.\n\nWe engaged a postgraduate-level student for an AI-facilitated narrative interview to discuss her cultural adaptation and academic challenges in Hong Kong. The researcher designed an AI assistant to conduct the interview, enabling the student to respond independently. This single case was selected for its availability and to maximize the depth of analysis in the conversations while avoiding premature scaling of the research application. The primary aim of these conversations was not to delve into the nuances of cultural adaptation but to determine whether observable indicators could effectively assess the AI assistant's role and competence in narrative interviews. This technical testing was part of a research project that received approval from the Research Ethics Committee of Hong Kong Baptist University, under reference number REC/23-24/0301.\n\nThe student shared the same story in this study in two distinct conversations. Full interview transcripts are available in Chan (2024). She followed a standard cycle in the first round, answering questions earnestly as directed. In the second conversation, she was instructed by the researcher to intentionally spend more time discussing various events related to her issue and sidetrack the assistant from the main interview path. These two versions were developed for research purposes. The first was designed to be serious, while the second was deliberately non-cooperative. We intentionally crafted these differences and tested how well the metrics could capture and reflect these variations.\n\nThe case study aimed to answer the following questions:\n\n1. How can the proposed metrics help us, as social researchers without a technical background, understand the quality of the AI-driven interviews in this study?\n\n2. What do these findings contribute to our discussion on using AI in narrative interviews for social research?\n\n3. What further research could these results inspire?\n\n\nData analysis method\n\nWe collected the data for the study via the AI assistant who conducted the narrative interviews via WhatsApp on 2024-01-17. The assistant engaged with the participant, prompted her to unfold her narratives, and recorded the conversation. The participant interacted with the assistant asynchronously, which allowed her to respond at her own pace.\n\nTo evaluate progression in asynchronous conversations, we used sequence numbers to represent the development of the dialogues. We also used a proportional timeline, dividing the conversation into 4 equal quarters based on the number of utterances instead of actual time. This approach accounts for the varying lengths of conversations. For example, in a story with 100 utterances, each quarter consists of 25 utterances, with the first 25 as Quarter 1 and the last 25 as Quarter 4.\n\nThe utterances during these interviews were then organized using a spreadsheet for detailed tagging that was conducted on 2024-05-14. The above-mentioned competence metrics were applied.\n\nIn this study, a human research assistant manually assigned the progression score to indicate the stage reflected by each conversation utterance, and the researcher also used ChatGPT4 to tag each utterance based on the operational definitions noted earlier. We used 1 for utterances about orientation, 2 for unfolding story episodes, and so on. We also assigned a score of 0.5 for utterances that do not fit any of these categories, such as misunderstandings, irrelevant comments, or getting sidetracked (see Table 1).\n\nA human research assistant tagged the interview text manually for other variables (empathy, meaning-making, agency, coherence, and complexity). The principal researcher also used ChatGPT4 to assess each conversation based on the same metrics (i.e., we uploaded the conversation scripts to ChatGPT and asked it to rate). We used a 5-point Likert scale, ranging from “not at all demonstrated” to “extensively demonstrated,” to indicate the level of each measure. We highlighted specific dialogue examples from the conversations to support such assessments.\n\nTo check the consistency of the ratings, we carried out simple inter-rater reliability tests between the results from manual tagging and machine tagging. The human research assistant and ChatGPT4 tagged the two conversations on 2024-05-14, respectively, using the same set of metrics. The differences will be reported in the Results section. The principal researcher compared the results, and differences were reviewed until all disagreements were resolved.\n\n\nResults\n\nAdherence to the conversation plan can be assessed by utterance sequence analysis. In the utterance sequence analysis of Conversation 1, there were discrepancies in 5 out of 54 utterances, which means approximately 90.74% agreement. After reviewing, the researcher agreed with the AI's categorization for 2 cases and the human's categorization for 3 cases. In the utterance sequence analysis of Conversation 2, 5 out of 84 utterances had discrepancies, showing about 94.05% agreement. Here, the researcher agreed with the AI's categorization for 3 cases and the human's for 2 cases. These consistencies indicated that the progression score metric is sufficiently clear for use by both machines and humans.\n\nThe analysis indicated the progression scores across various time intervals in two separate conversations, offering quantitative insights into how well the AI assistant adhered to the expected 7-step progression plan during narrative interviews. Table 2 shows a consistent increase in progression scores from Quarter 1 to Quarter 4 in both conversations, indicating that the conversations advanced methodically through the planned stages. In Conversation 1, the progression scores of the Assistant move from 1.71 to 6.17, and in Conversation 2, from 1.56 to 6.00, reflecting a structured and coherent unfolding of the narrative as intended by the conversation plan. Similar patterns were observed in the participant progression scores.\n\nIt is worth noting that participants' progression scores consistently align with the assistant's across various intervals, although the assistant's scores are typically a bit higher. For example, during Quarter 2 of Conversation 1, the assistant scored 2.64, while the participant scored 2.14 on average. Similar patterns of discrepancy were observed in Conversation 2 and at different time quarters. This consistent variance indicates that the assistant frequently leads by posing questions that advance the conversation to the next stage, resulting in higher progression scores.\n\nNotably, the AI assistant demonstrated flexibility within this structure, as evidenced by slightly varying scores at similar stages across different conversations. This variability implies that while the assistant followed the predefined conversational path, it also adapted responses based on the participant's input, maintaining a balance between following the planned sequence and responding dynamically to the flow of the conversation. This shows the assistant's ability to effectively manage structured narrative interviews, aligning closely with the progression expectations while integrating the necessary responsiveness to participant interactions.\n\nAs a kind of quantified measure, the progression scores can facilitate data visualization that presents such similarities and differences. In simple line charts, we depicted the progression of the conversation utterances of the AI assistant and the human participant in the two conversations. This simple visualization allows the general patterns of these conversations to be easily observed and compared. For example, the progressions of the assistant and the participant in the conversations are almost synchronous, demonstrating an upward development (see Figure 1 and Figure 2). However, the general progression pattern of Conversation 1 (see Figure 1) differs from that of Conversation 2 (see Figure 2). The lines in Conversation 1 (Figure 1) rise evenly and gradually. In contrast, the lines in Conversation 2 (Figure 2) remain relatively flat in Quarter 1 and become steeper in Quarters 2 and 3 due to a sudden topic change and subsequent return to the original conversation track.\n\nThe empathy level score can tell us the level based on interactions and conversation wordings. Regarding the rating, the research assistant and ChatGPT4 agreed in their assessments, implying that the empathy metric is sufficiently clear for use by both machines and humans. In Conversation 1, the assistant scored 4 out of 5 in empathy. The assistant consistently demonstrates concern and understanding, actively inviting the participant to share her experiences and showing appreciation for her stories. In Conversation 2, the assistant also scored 4 out of 5 in empathy (see Table 3).\n\nThe assistant maintained consistent empathy throughout, clarifying and assisting the participant in her storytelling. For instance, the assistant's use of metaphor examples to help the participant articulate her experiences indicates a high degree of empathetic engagement. Here are some examples of utterances from the assistant, extracted from the conversations, that reflect its empathetic capabilities:\n\nIt's heartwarming to hear about your interaction with people from different backgrounds during the celebration\n\nThat's a wonderful story! It's heartwarming to hear about your interaction with people from different backgrounds during the celebration. Sharing traditions and capturing those moments must have been a rich cultural exchange. Do you have more story episodes that are similar or related to those you have already talked about? Or would you like to take a break before continuing?\n\nCertainly! Considering your experiences, here are a few metaphors to consider: 1. A cultural mosaic where each piece represents a different culture or festival that comes together to create a vibrant picture of life here. 2. A bridge symbolizing the connections you've built between people of different backgrounds and your family, blending the new with the familiar. 3. A tapestry weaving together threads of different traditions, celebrations, and friendships you've experienced here. Remember, these are just suggestions to spark your imagination. Feel free to choose one that resonates with you or propose your own metaphor. What do you think?\n\nThe construction of meanings in narrative interviews is complex and multi-dimensional, reflected by a series of independent yet interrelated metrics. These metrics include the human participant's level of agency, the meaning-making in the conversation, the coherence of the content, and the complexity of the content (see Table 3). In the rating, the human research assistant and ChatGPT4 mostly agreed on all these metrics, except that there was a disagreement on coherence in Conversation 2, where the human research assistant gave a score of 2 and ChatGPT4 gave a score of 3. After reviewing this, the principal researcher sided with ChatGPT4's score.\n\nIn Conversation 1, the Level of Agency of the human participant scored 3. The participant sometimes exercises control over the direction of the conversation, such as asserting, “I’d like to share more experiences,” yet often follows the assistant's lead. This balance indicates a moderate level of agency, where the participant neither dominates the conversation nor remains passive. In Conversation 2, the Level of Agency of the human participant scored 4, even higher than Conversation 1. Here, the participant displays a high level of agency, initiating new topics, requesting clarifications, and directing and side-tracking the conversation flow with statements like, “Can I share other stories?” and “Let’s move back.”\n\nIn Conversation 1, the Level of Coherence scored 4. The participant's narrative is coherent, featuring a clear sequence and contextual understanding. They situate their experiences within broader themes of cultural exchange and personal growth, as illustrated when discussing the Christmas celebrations and interactions during the Mid-Autumn Festival. In Conversation 2, the Level of Coherence scored 3. The conversation maintains moderate coherence, with the participant providing context for their experiences. Nonetheless, some narrative elements, such as an abrupt shift to discuss a news piece about North Korea, disrupt the narrative flow and context.\n\nIn Conversation 1, the Level of Complexity scored 3. The participant expresses various emotions and thoughts, reflecting on their interactions and cultural exchanges. While the conversation includes depth, it occasionally lacks the exploration of conflicting or challenging aspects of their experiences, which would indicate a higher level of complexity. In Conversation 2, the Level of Complexity scored 2. The participant's stories are engaging but lack depth compared to other discussions. A straightforward recounting of experiences somewhat limits the complexity without much reflection on conflicting perspectives or emotional nuances.\n\nIn Conversation 1, the Level of Meaning-Making scored 4. The participant actively engages in meaning-making, recounting events and reflecting on their significance, exemplified when comparing Hong Kong to a “lively global village” and discussing how their experiences influence their adaptability and cultural inclusiveness. In Conversation 2, the Level of Meaning-Making scored 3. The participant's reflections show moderate meaning-making, with some exploration of the significance of their experiences. However, the conversation occasionally reverts to mere descriptions, not delving deeper into the meanings behind these experiences.\n\nOverall, these metrics help illustrate to what extent the conversations are co-constructed by both the human participant and the assistant. The dialogue excerpt below (from Conversation 1) illustrates the dynamic interplay between the AI assistant and the human participant.\n\nThis simple dialogue segment exemplifies the dynamic interplay between the AI assistant and the human participant, demonstrating how meanings are co-constructed through their interactions. Initially, the AI recognized and respects the participant's request for a break, showing responsiveness to the participant's immediate needs. Upon the participant's return, the AI seamlessly guided the conversation forward and suggested a summary of past discussions. Such interactions illustrate the AI's role in structuring the dialogue.\n\nThe assistant then helps the participant to reflect deeper on their experiences by introducing the concept of using metaphors. This is not merely a suggestion but a collaborative effort to frame the participant's experiences meaningfully and relatable. When the participant asks for metaphor suggestions, the AI provides several tailored options that resonate with the participant's experiences. This prompts the participant to think creatively and select a metaphor reflecting her perspective, culminating in “Living in a lively global village.”\n\nSubsequently, the AI validates the participant's chosen metaphor and encourages further elaboration, which leads the participant to describe their experiences in Hong Kong in more detail. This back-and-forth interaction shows how the AI and the human together construct a more nuanced understanding of the participant's life and experiences.\n\nFinally, the dialogue culminates with a story about cultural exchange during Christmas, which illustrates how the participant has internalized the metaphor of a “global village.” This story further enriches the metaphor by adding layers of cultural interaction and learning, facilitated by the participant's narrative prompted by the AI's guiding questions.\n\nOverall, the dialogue demonstrates a collaborative construction of meaning, where both the human and the AI contribute dynamically to the unfolding narrative, each influencing and enhancing the other's contributions to develop a deeper understanding of the human participant's experiences.\n\n\nDiscussion\n\nBefore discussing the potential of assessing the performance of generative AI-based assistants in narrative interviews, it is crucial to recognize the limitations of this study. First, the primary goal of this case study was to explore ideas and stimulate discussion rather than to conduct rigorous experiments. Consequently, it does not assess the effectiveness of assessment tools in a traditional experimental setup. Second, the conversation analysis method used here struggles with long speeches. While a single long speech that is made up of many complex parts might not be effectively analyzed as one unit, breaking it down into smaller utterances also reveals challenges, especially for lengthy dialogues. However, such extended dialogues are uncommon in platforms like WhatsApp, where the typical brevity of messages somewhat lessens these issues. Third, this study was a pilot test conducted using economical or free software on a small scale. The technical setup, which utilized readily available services like Replit and ManyChat, might not be suitable for large-scale data collection that requires simultaneous access by multiple participants. There is a significant need to enhance data management and scalability, potentially through integration with advanced cloud storage solutions to support broader participation and collaboration. Despite these limitations, exploring the potential and challenges of using metrics to assess AI competencies in narrative interviews is worthwhile.\n\nAs conversational AI evolves, researchers and industry experts have proposed various metrics to evaluate AI assistants; however, existing literature mainly focuses on broad technical aspects of dialogue systems—such as response time, language proficiency, repetitions, and human-likeness (Deriu et al., 2021; Finch & Choi, 2020; Lee et al., 2023) — rather than on the detailed impacts at the conversational level. The case study reported in this article demonstrated that it is possible for social researchers without a technical background to use observation-based metrics to assess to what extent an AI assistant can guide conversations, adhere to structured steps, and gather required information in a narrative format.\n\nIn this study, the AI assistant can maintain organization while being adaptable in intelligent and coherent conversations. It efficiently managed the conversations sequentially, showing that it may help support self-directed, adaptable narrative interviews tailored to individual needs. If an AI assistant consistently maintains high quality across interviews by adhering strictly to prescribed standards, that assistant will be valuable in large-scale studies where consistency is crucial for ensuring reliable and replicable results.\n\nHowever, the findings also revealed the AI assistant's shortcomings in conducting narrative interviews, prompting researchers to explore methods to assess and improve AI performance in such contexts. Notably, the scores for meaning-making and complexity were lower than those for other metrics, indicating a need for the AI to handle follow-up questions better. This issue could be addressed through improvements in prompt design, suggesting more tailored and context-aware interactions. Additionally, further advancements in language model development may be necessary to enhance AI's ability to understand and generate more complex and nuanced responses. These steps are essential for ensuring that AI systems can effectively replicate the depth of human conversation and interaction in narrative interviews.\n\nThe study employed a range of metrics—including progression, empathy, meaning-making, agency, coherence, and complexity—to assess the quality of interviews conducted by the AI. These metrics assess selected aspects of the interview process, underscoring the AI's role as a facilitator in narrative interviews. They can serve as preliminary tools to ensure that the quality of interaction remains high and aligns with the objectives of narrative inquiry. Nonetheless, further improvements are necessary, such as refining these metrics and expanding the evaluation criteria to encompass additional interactive elements.\n\nChallenges accompany opportunities. Although AI can manage the structural elements of narrative interviews, it also prompts important questions about interviewers' essential, constitutive role in these settings (Abkhezr et al., 2020; Gubrium et al., 2012). In our case, where the interviewer is an AI, these questions become even more compelling and complex.\n\nFirst, narrative interviewing is a collaborative and co-authoring process (Abkhezr et al., 2020; Gubrium et al., 2012). As conversations progressed, participants deepened their thoughts, transforming the interaction from simple data collection into a meaningful construction process. Notably, the AI's role in initially constructing narrative data underscores the constitutive nature of the interview process, a phenomenon also observed with human interviewers. Technological developments suggest that AI is likely to evolve beyond simple backend analysis and become a fundamental component in how researchers initially engage with and understand their participants. This transformation brings new opportunities and challenges as AI begins to influence the shaping of raw data from the outset, potentially redefining the meaning of narrative research. As AI shapes how raw data are formed from the beginning, researchers are presented with enhanced efficiencies and fresh challenges. This transformation underscores the need for researchers to be adept in traditional research skills and navigating AI technologies.\n\nDue to its efficiency and convenience, social researchers may increasingly adopt AI. This trend highlights a shift in the research landscape, where the potential for scalable data collection and analysis often outweighs traditional concerns about the depth and nuance typically provided by human interviewers. Consequently, the question may not be whether AI can be a competent narrative interviewer but whether researchers can effectively control its performance. The real challenge lies in enhancing and monitoring AI's capabilities to match the richness of human interactions, ensuring that the quality of insights is not compromised.\n\nSecond, the trend of customizable generative AI assistants (DeVon, 2023; Stallbaumer, 2023; Wang et al., 2023) may imply that the performance of AI assistants may rely on the human researchers’ ability to set instruction prompts as well as the AI models themselves. Integrating AI assistants in narrative interviews represents a significant advance in research methodologies, providing an accessible gateway for scholars from non-technical fields like arts and social sciences. The initial setup of the AI assistant is code-free and straightforward, allowing researchers to configure basic settings and outline the chatbot’s conversational strategy without any programming knowledge. This accessibility lets scholars focus on the content and quality of the interviews rather than the complexities of technology. As AI technology evolves, it is expected to become increasingly user-friendly, further lowering barriers for all researchers, regardless of their technical skills. The evolution towards customizable AI and user-friendly model platforms suggests the pivotal concern shifts toward who configures the AI assistant and how it enables or limits functions, thereby shaping the narrative data.\n\nThird, the development of large language models is unevenly distributed, and AI language model development reveals significant disparities in sociopolitical contexts (Campolo & Crawford, 2020; Navigli et al., 2023). Currently, most advancements primarily benefit English and Putonghua speakers, leaving speakers of other languages with less sophisticated tools. This disparity underscores the importance of developing AI capabilities for a wider range of languages to ensure inclusivity and accuracy in global research contexts. For example, the study's reliance on the English version of the GPT-4 model in a predominantly Cantonese-speaking region like Hong Kong highlights existing challenges. AI models such as GPT, Google Gemini, and Baidu’s ERNIE Bot often struggle with the nuances of Cantonese, impacting the accuracy and effectiveness of translations and data interpretation. This underscores the necessity for researchers to assess and understand the limitations and capabilities of these AI models within specific linguistic contexts. Thus, while the quality of customizable AI assistants partly relies on the prompt engineering of human researchers, sociocultural forces also shape the training models behind AI's front end. Consequently, that means researchers need to participate in, or at least pay attention to, AI model developments. Engaging with these developments will be crucial for conducting accurate, inclusive, and compelling research within the evolving landscape of research methodologies.\n\nAs conversational AI evolves, various metrics have been proposed to evaluate AI assistants. While existing literature mainly focuses on broad technical aspects like response time and language proficiency (Deriu et al., 2021; Finch & Choi, 2020; Lee et al., 2023), our study illustrates the feasibility of developing and applying metrics that assess AI performance at the conversational level. This has sparked further research into refining and expanding these metrics and their applications:\n\nFirst, there is a clear need for more refined metrics to capture human-AI interactions' nuanced aspects more accurately. Given this trend, the real challenge becomes ensuring that AI interviews can retain the richness of human interactions without compromising the quality of insights. This raises important questions about the competencies of AI tools and the metrics used to evaluate them. Current metrics in the literature tend to be highly technical and computation-based, which may not fully capture the nuances of narrative inquiry. This suggests a need to review and develop new, relevant, and valid metrics that can effectively assess the quality of AI-facilitated narrative interviews in social research contexts.\n\nSecond, although the inter-rater reliability tests conducted in this case study indicated that these metrics are sufficiently clear for use by either machines or humans, there is still room for improving their precision, particularly in the finer nuances of conversational analysis, which could further refine the accuracy of both manual and automated assessments. Fortunately, the direction for enhancement appears feasible and promising, with ongoing advancements in AI and computational linguistics providing robust tools and methodologies to support these improvements. By investing in these areas, we can significantly boost the reliability and utility of these metrics in diverse research and application settings.\n\nThird, metrics are discipline-specific, with different types of narrative interviews across disciplines. This variability implies a wide range of application scenarios and research gaps waiting for further exploration. For example, in customer interactions, metrics such as empathy and progression are essential for training AI to handle inquiries and complaints effectively, ensuring customer satisfaction. In therapy, the ability of AI to engage in empathetic dialogue and promote meaning-making is invaluable. In educational environments, it is essential to ensure AI's ability to guide students through learning materials coherently and engagingly. In Human Resources, AI applications for conducting initial interviews can ensure potential candidates have meaningful and respected interactions, which can improve recruitment processes and enhance candidate satisfaction.\n\nFourth, these metrics can be used to create programs that automatically analyze and suggest regular improvements. Clearly defined metrics play a crucial role in advancing machine learning applications, particularly in automating tagging and analysis processes. Clear metrics establish standardized criteria that machines can use to evaluate and categorize data consistently. In the context of AI interviews, for example, metrics, like coherence and empathy levels provide specific, measurable standards that AI systems, can learn to recognize and apply. Once AI systems are trained on these standardized metrics, they can automatically analyze large volumes of data much faster than human analysts. With robust metrics, AI systems can scale their analysis capabilities without a proportional increase in human oversight. This scalability is crucial for large-scale studies or applications where the volume of data would be unmanageable for human teams alone.\n\nFifth, it highlights the need for interdisciplinary collaborations in AI development. Including insights from psychology, linguistics, and social sciences could lead to more sophisticated AI systems better tuned to human narrative complexities. Further research should explore how to expand interdisciplinary collaboration. There is a significant opportunity to integrate input from narrative researchers into the design of AI assistants and the development of evaluation metrics. By involving experts in narrative methods, AI developers can enhance the capability of AI tools to handle complex, nuanced interactions and improve the fidelity of data collected in narrative inquiries. This collaborative approach could lead to more sophisticated AI systems that are better equipped to meet the needs of diverse research fields and methodologies.\n\nOverall, using narrative interview competence metrics to assess AI performance highlights both the potential for transformation and the need to address the complexities introduced by AI technologies. These enhancements and collaborative efforts could improve the efficacy and accuracy of AI in conducting narrative interviews, setting new standards in the field of qualitative research.\n\n\nConcluding remarks\n\nAs we venture further into the evolving landscape of narrative research with AI, it's essential to consider the broader implications of these technologies, not only for enhancing the mechanics of data collection but also for redefining the very essence of qualitative social inquiry.\n\nIntegrating AI in narrative interviews is not just about leveraging a tool; it's about stepping into a partnership where AI contributes to the narrative construction process. This partnership challenges us to rethink our traditional roles and methodologies in research. As AI takes on a more constitutive role in narrative creation, it shifts from a mere facilitator to an active participant in the dialogue. This transformation opens many avenues for deeper engagement with participants' stories.\n\nEmbracing AI in narrative research also demands continuous improvement and refinement of AI performance metrics. These should aim to capture the nuances of human-AI interaction more accurately without compromising the richness of narrative data. Additionally, it is crucial to engage interdisciplinary expertise in developing these metrics and AI systems. By incorporating insights from fields such as psychology, linguistics, and social sciences, AI tools can be better tailored to meet the diverse needs of narrative research.\n\nIn conclusion, the integration of AI into narrative interviews is not merely an advancement in technology, but it may be a paradigm shift in the research landscape. It challenges us to reimagine the possibilities of narrative inquiry, pushing the boundaries of what it means to capture and interpret human experiences. As we continue to explore this frontier, our focus should not only be on developing AI tools but also on refining our understanding of the complex, iterative dance between humans and machine, ensuring that each step forward is taken with thoughtful consideration of its impact on the narrative fabric of human life.\n\nThis study was part of a research project that received approval from the Research Ethics Committee of Hong Kong Baptist University, under reference number REC/23-24/0385 (approval date: April 2, 2024). All participants were aged 18 or above, they provided written informed consent prior to their participation in the study, ensuring they understood the purpose of the research, how their data would be used, and their rights to confidentiality and withdrawal at any time.", "appendix": "Data availability\n\nDANS: Transcript of a Conversation Between a Customized AI and Human Users, https://doi.org/10.17026/SS/KCPEDX (Chan, 2024)\n\nData is available under the terms of CC By 4.0\n\nDANS: Transcript of a Conversation Between a Customized AI and Human Users, https://doi.org/10.17026/SS/KCPEDX (Chan, 2024)\n\nThis Project contains the following underlying data:\n\n• instructions_for_the_AI.docx\n\nData is available under the terms of CC By 4.0\n\n\nAcknowledgments\n\nGrammar checks and language suggestions were supported by Grammarly and ChatGPT4.\n\n\nReferences\n\nAbkhezr P, McMahon M, Campbell M, et al.: Exploring the boundary between narrative research and narrative intervention Implications of participating in narrative inquiry for young people with refugee backgrounds. Narrative inquiry: NI. 2020; 30: 316–342. Publisher Full Text\n\nAdamopoulou E, Moussiades L: Chatbots: History, technology, and applications. Machine Learning with Applications. 2020; 2: 100006. Publisher Full Text\n\nAdler JM, Dunlop WL, Fivush R, et al.: Research Methods for Studying Narrative Identity:A Primer. Soc. Psychol. Personal. Sci. 2017; 8: 519–527. Publisher Full Text\n\nAu-yeung H: Visualising narrative practice with a 5-level scaffolding lens: An illustrative case study. China Journal of Social Work. 2023; 16: 18–29. Publisher Full Text\n\nBendig E, Erb B, Schulze-Thuesing L, et al.: The next generation: chatbots in clinical psychology and psychotherapy to foster mental health – a scoping review. Verhaltenstherapie. 2019; 29: 266–280. Publisher Full Text\n\nBrown T, Mann B, Ryder N, et al.: Language models are few-shot learners. Adv. Neural Inf. Proces. Syst. 2020; 33: 1877–1901. Reference Source\n\nCampolo A, Crawford K: Enchanted determinism: Power without responsibility in artificial intelligence. Engag. Sci. Technol. Soc. 2020; 6: 1–19. Publisher Full Text\n\nChan C: Narrative practice with youth: A heuristic case study on a youth-centre drama workshop. J. Soc. Work. Pract. 2012; 26: 197–214. Publisher Full Text\n\nChan C: Digital technologies and evolving narrative practice: an autoethnographic study. China Journal of Social Work. 2023; 16: 83–99. Publisher Full Text\n\nChan C: Transcript of a Conversation Between a Customized AI and Human Users (Version 3) [transcripts]. DANS Data Station Social Sciences and Humanities; 2024. Publisher Full Text\n\nChan C, Au-yeung H, Chiu W, et al.: Indicators for assessing intervention fidelity of narrative practice: A heuristic review of the concept of scaffolding in White (2007). Journal of Systemic Therapies. 2020; 39(3): 77–90. Publisher Full Text\n\nChan C, Li F: Developing a natural language-based AI-chatbot for social work training: an illustrative case study. China Journal of Social Work. 2023; 16: 121–136. Publisher Full Text\n\nChan C, Ngai K-H, Wong C-K: Using photographs in narrative therapy to externalize the problem: A substance abuse case. Journal of Systemic Therapies. 2012; 31(2): 1–20. Publisher Full Text\n\nChase SE: Narrative inquiry: Toward theoretical and methodological maturity. The Sage handbook of qualitative research. 2018; Vol. 5: pp. 546–560.\n\nChristou P: How to Use Artificial Intelligence (AI) as a Resource, ow Methodological and Analysis Tool in Qualitative Research?. Qual. Rep. 2023; 28: 1968–1980. Publisher Full Text\n\nChristou P: Thematic Analysis through Artificial Intelligence (AI). Qual. Rep. 2024; 29: 560–576. Publisher Full Text\n\nClandinin DJ: Handbook of Narrative Inquiry: Mapping a Methodology.2007. Publisher Full Text\n\nCohen S, Queen D: Generative artificial intelligence community of practice for research. Int. Wound J. 2023; 20: 1817–1818. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConcannon S, Tomalin M: Measuring perceived empathy in dialogue systems. AI & Soc. 2023. Publisher Full Text\n\nConnor M, Fletcher I, Salmon P: The analysis of verbal interaction sequences in dyadic clinical communication: A review of methods. Patient Educ. Couns. 2009; 75: 169–177. PubMed Abstract \| Publisher Full Text Reference Source\n\nCordero J, Barba-Guaman L, Guamán F: Use of chatbots for customer service in MSMEs. Applied Computing and Informatics. 2022. Publisher Full Text\n\nDenicolo P, Long T, Bradley-Cole K: Constructivist approaches and research methods: A practical guide to exploring personal meanings. Sage; 2016.\n\nDeriu J, Rodrigo A, Otegi A, et al.: Survey on evaluation methods for dialogue systems. Artif. Intell. Rev. 2021; 54: 755–810. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeVon C: You can now build your own version of ChatGPT—here’s what to know. CNBC. 2023, 2023-11-11. Reference Source\n\nDuvall J, Béres L: Innovations in narrative therapy: Connecting practice, training, and research. W.W. Norton; 2011.\n\nFinch SE, Choi JD: Towards unified dialogue system evaluation: A comprehensive analysis of current evaluation protocols. arXiv preprint arXiv:2006.06110. 2020.\n\nGasaymeh A-MM: University students use of WhatsApp and their perceptions regarding its possible integration into their education. Global J. Comp. Sci. Technol. 2017; 17: 1–9.\n\nGergen KJ: Social construction in context. London: Sage Publications; 2001.\n\nGubrium JF, Holstein JA, Marvasti A, et al.: The SAGE Handbook of Interview Research: The Complexity of the Craft. Thousand Oaks: SAGE Publications; 2012.\n\nHan X, Zhou M, Turner MJ, et al.: Designing effective interview chatbots: Automatic chatbot profiling and design suggestion generation for chatbot debugging. Proceedings of the 2021 CHI Conference on Human Factors in Computing Systems. 2021; 1–15.\n\nJosselson R: The ethical attitude in narrative research: Principles and practicalities.Clandinin DJ, editor. Handbook of Narrative Inquiry: Mapping a Methodology. SAGE; 2007; pp. 537–566. Publisher Full Text\n\nKatic MA, Miletic E, Candrlic S: Performance analysis of virtual assistants: A case study based on the Croatian language. INTED2024 Proceedings. 2024; 7305–7315.\n\nLee M, Srivastava M, Hardy A, et al.: Evaluating human-language model interaction. arXiv preprint arXiv:2212.09746. 2023.\n\nLennon RP, Fraleigh R, Van Scoy LJ, et al.: Developing and testing an automated qualitative assistant (AQUA) to support qualitative analysis. Family medicine and community health. 2021; 9: e001287. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiddicoat AJ: An introduction to conversation analysis. Bloomsbury Publishing; 2021.\n\nMoran G, Diamond GM, Diamond GS: The relational reframe and parents' problem constructions in attachment-based family therapy. Psychother. Res. 2005; 15: 226–235. PubMed Abstract \| Publisher Full Text\n\nMorgan DL: Exploring the use of artificial intelligence for qualitative data analysis: The case of ChatGPT. Int J Qual Methods. 2023; 22: 16094069231211248. Publisher Full Text\n\nNavigli R, Conia S, Ross B: Biases in large language models: origins, inventory, and discussion. ACM Journal of Data and Information Quality. 2023; 15: 1–21. Publisher Full Text\n\nRamey HL, Tarulli D, Frijters JC, et al.: A sequential analysis of externalizing in narrative therapy with children. Contemp. Fam. Ther. 2009; 31: 262–279. Publisher Full Text\n\nRamey HL, Young K, Tarulli D: Scaffolding and concept formation in narrative therapy: A qualitative research report. Journal of Systemic Therapies. 2010; 29(4): 74–91. Publisher Full Text\n\nRiessman CK: Narrative methods for the human sciences. Sage Publications; 2008.\n\nRiessman CK, Quinney L: Narrative in social work: A critical review. Qual. Soc. Work. 2005; 4: 391–412. Publisher Full Text\n\nShah R, Lahoti S, Lavanya K: An intelligent chat-bot using natural language processing. International Journal of Engineering Research. 2017; 6: 281–286. Publisher Full Text\n\nSharma V: Measure your virtual assistant performance.2020, 2020-07-19. Reference SourceReference Source\n\nShotter J: Cultural politics of everyday life: social constructionism, rhetoric and knowing of the third kind. Toronto: University of Toronto Press; 1993.\n\nStallbaumer C: Introducing Microsoft Copilot Studio and new features in Copilot for Microsoft 365.2023, 2023-11-15. Retrieved 2023-11-20. Reference Source\n\nSuárez-Lantarón B, Deocano-Ruíz Y, García-Perales N, et al.: The educational use of WhatsApp. Sustainability. 2022; 14: 10510. Publisher Full Text\n\nWang J, Shi E, Yu S, et al.: Prompt engineering for healthcare: Methodologies and applications. arXiv preprint arXiv:2304.14670. 2023.\n\nWei J, Bosma M, Zhao VY, et al.: Finetuned language models are zero-shot learners. arXiv preprint arXiv:2109.01652. 2021.\n\nWhite M: Maps of narrative practice. W.W. Norton; 2007.\n\nXu B, Zhuang Z: Survey on psychotherapy chatbots. Concurrency and Computation: Practice and Experience. 2022; 34: e6170. Publisher Full Text\n\nXu Z, Jiang J: Multi-dimensional Evaluation of Empathetic Dialog Responses. arXiv preprint arXiv:2402.11409. 2024." }	[ { "id": "298274", "date": "26 Jul 2024", "name": "Jonathan Singer", "expertise": [ "Reviewer Expertise Youth suicide prevention", "qualitative research", "technology and social work education/practice" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 addresses an interesting and important topic. My comments are focused on clarifying certain details to enhance the paper’s clarity and coherence, rather than critiquing its main idea, which I find compelling but somewhat unclear in its current form. Despite reading through the entire paper multiple times, I struggled to fully grasp key parts. Reorganizing the literature review, introducing a clear “Methods” section, and streamlining the manuscript would greatly improve its readability.\nLiterature Review The literature review begins by emphasizing the potential of AI in narrative interviewing, but it would benefit from first defining and describing what narrative interviewing entails. The enthusiastic discussion of AI, including references to “influential bloggers,” feels more promotional than academic, especially since it turns out to be an advertisement for a for-profit company selling narrative interviewing tools. To strengthen the paper, I recommend moving the definitions of key terms like “narrative interviewing” and “conversation analysis” to the beginning of the literature review. Additionally, information from paragraph 5 and the section “Why do assistant’s interview skills matter” should be relocated to the start to provide important context early on.\nThe language in the literature review occasionally seems exaggerated and inconsistent. For instance, the statement that AI is “becoming a crucial tool for researchers” feels overstated without supporting evidence. Furthermore, it appears contradictory to claim that AI improves analysis while also stating that academics have not “explored how AI could enable or limit narrative interviews.” Clarifying these points and providing supporting evidence will strengthen the argument.\nThere are also some statements that seem unnecessary and detract from the narrative flow, such as “This brief review of narrative inquirer capabilities is not comprehensive.” Removing such remarks can streamline the text and improve readability.\nMethods Section Introducing a “Methods” header before discussing competence metrics would improve the manuscript’s structure. The justification for the competence metrics needs to be clearer. Rather than stating that “The following metrics were chosen primarily for their simplicity and to facilitate testing and demonstration,” it would be helpful to explain the rationale behind selecting these specific metrics and whether they are based on existing frameworks or newly developed by the authors.\nScores: The authors identified six scores but did not talk about how those scores were established, the scales, or anything else about them. Specifically:\nCompetence 1: The explanation of how progression scores are assigned is vague. There is no clear description of the criteria used to determine the progression stage of each utterance. This lack of specificity makes it difficult to understand the validity and reliability of the scoring system. The method’s reliance on previous studies (Au-yeung, 2023; Chan et al., 2020; Connor et al., 2009; Moran et al., 2005; Ramey et al., 2009) without providing a detailed explanation or adaptation process is problematic. It would be helpful to have a more thorough, but not necessarily long explanation of how these methodologies are applied to the current study.\nRelatedly, the sequential analysis method from therapy research may not be directly applicable to narrative interviews conducted by AI. If this method was developed from narrative interviews, then say so. There are therapy approaches like CBT or behavioral therapies that have structured, goal-oriented sessions. ABFT is task oriented, but still provides the therapist structure. Narrative interviews, from your description, are more open-ended, possibly more like Rogerian or supportive therapy sessions. The adaptation of this method needs more rigorous justification.\nI was also unclear how and why a higher score isn’t better, and also why you calculated average progression scores over time. How does this score help us to understand how good AI is doing?\nCompetence 2: Is there empirical validation or psychometric testing of the empathy scale? If so, please provide that information for the reader. I would like more information about why a Likert scale is used for empathy, especially since the previous competence argued that higher scores were not necessarily better. That does not seem to be the case with this scale.\nCompetence 3: I didn’t understand the use of the word “Domination” in the subheader. You introduce multiple metrics (agency, coherence, complexity, and meaning-making) without clearly explaining how they are operationalized. Each one of these needs to be defined and the reader needs measurement criteria for each metric, especially since the previous two measures apparently used different scales. For example, the authors say that measuring “agency” cannot be done in isolation, but there is no description of how the scores or definitions of the other measures are used to understand or measure agency. Indeed, it seems that if the concepts in Competence 3 are interrelated, might there be a way to discuss the measures as a coherent package, rather than individual scales?\nThe description of the Case study has many strengths, including the innovative use of ChatGPT to create a chatbot that the researchers would otherwise have not been able to program, highlighting the value of deploying the chatbot on WhatsApp, clearly defining the seven stages, and the ingenuity of having the postgraduate have two conversations – one genuine and one combative. The major limitation of the description of the case study is that it seems to be disconnected from the measures. I know that you provide results in the results section, but it would be helpful to have notes about how each section connects to the measures.\nData Analysis Method and Data Collection Section I was unclear about the context in which the postgrad was having the WhatsApp conversations. Was this in a lab? Were the researchers observing? Was this in private? I didn’t understand why the conversation was divided into four equal quarters. i.e. The choice of four quarters seems arbitrary. I know that it makes it easy to analyze by utterances rather than time, but it seems to miss the importance of space and silence in a narrative interview.\nThe process for manually assigning progression scores is not clearly defined. There is no description of the criteria used by the human research assistant to assign these scores, which raises concerns about the subjectivity and consistency of the ratings. Is there any research on using LLMs or ChatGPT specifically to assigning scores to narrative interviews? If so, it would be good to cite that here.\nResults The agreement between the human research assistant and ChatGPT4 on most metrics in and of itself is encouraging for researchers interested in using LLMs.\nIn finding 2, what distinguishes a 3 from a 4? This is part of my ongoing concern about the paper’s lack of clarity with the measures.\nThe disagreement on coherence in Conversation 2 highlights the need for clear criteria. The authors wrote, “In the rating, the human research assistant and ChatGPT4 mostly agreed on all these metrics, except that there was a disagreement on coherence in Conversation 2, where the human research assistant gave a score of 2 and ChatGPT4 gave a score of 3. After reviewing this, the principal researcher sided with ChatGPT4's score.” The manuscript should detail the specific aspects that led to different ratings and the rationale for siding with ChatGPT4’s score. Especially in these early days of using LLMs for analysis, this kind of transparency will be instructive as well as increase trustworthiness of the analysis.\nDiscussion I thought it was interesting that there were challenges with long speeches in conversation analysis. Even though WhatsApp tends to have shorter exchanges, what are some potential solutions or alternative methods to address these challenges, especially since narrative interviews often involve extended dialogue. I’m thinking specifically about qualitative researchers who are interested in using this for more traditional open-ended narrative interviews, not on WhatsApp. Perhaps this is part of an expanded discussion on the scalability of this type of AI use.\nI agree that there need to be more refined metrics (and some of my critiques of this paper are in line with that call).\nHow would you propose to improve interrater reliability? Again, are there computational linguists who have looked into human/LLM IRR?\nAfter reading through the discussion a few times, I still didn’t have a good understanding of the differences between conversations 1 and 2. For example, in the results section you noted differences in agency, coherence and complexity. Why did the participant exhibit higher agency in Conversation 2? What factors contributed to the lower coherence and complexity in Conversation 2? If you discussed this and I missed it, my apologies.\nFinal note:\nI hope this feedback is helpful. I typically do not review manuscripts until I fully understand both the spirit and letter of the manuscript, but I am providing this feedback in response to the editor’s request for a timely review\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Partly", "responses": [ { "c_id": "12380", "date": "04 Oct 2024", "name": "Chitat CHAN", "role": "Author Response", "response": "Responding to Jonathan Singer, Loyola University Chicago, Chicago, Illinois, USA Literature Review The literature review begins by emphasizing the potential of AI in narrative interviewing, but it would benefit from first defining and describing what narrative interviewing entails. The enthusiastic discussion of AI, including references to “influential bloggers,” feels more promotional than academic, especially since it turns out to be an advertisement for a for-profit company selling narrative interviewing tools. To strengthen the paper, I recommend moving the definitions of key terms like “narrative interviewing” and “conversation analysis” to the beginning of the literature review. Additionally, information from paragraph 5 and the section “Why do assistant’s interview skills matter” should be relocated to the start to provide important context early on. Response: The literature review part was entirely reorganized. The revised manuscript now includes a more structured literature review. It has been significantly reframed to focus on the democratization of AI chatbots and the emerging trend of customizable AI, which opens new opportunities across various fields, including social work. These advancements enable non-technical users to develop and tailor AI tools for specific applications. As there is limited research on how social workers, especially those with minimal coding experience, can instruct and evaluate AI assistants to conduct narrative interviews, the study investigates this aspect. The role of narrative interviews is instrumental, serving as a case to explore possibilities and provide feedback within a broader context. This sets a clear foundation before discussing the role of AI in narrative interviewing. The language in the literature review occasionally seems exaggerated and inconsistent. For instance, the statement that AI is “becoming a crucial tool for researchers” feels overstated without supporting evidence. Furthermore, it appears contradictory to claim that AI improves analysis while also stating that academics have not “explored how AI could enable or limit narrative interviews.” Clarifying these points and providing supporting evidence will strengthen the argument. Response: Improved clarity and exaggeration removed. The revised manuscript moderates such language and focuses on informed claims. It highlights the exploratory nature of the study and emphasizes the use of rubrics as tools for qualitative assessment rather than making broad claims about AI’s capabilities. There are also some statements that seem unnecessary and detract from the narrative flow, such as “This brief review of narrative inquirer capabilities is not comprehensive.” Removing such remarks can streamline the text and improve readability. Response: In the revised manuscript, we eliminated remarks such as “This brief review of narrative inquirer capabilities is not comprehensive” to streamline the text and enhance the overall clarity. Methods Section Introducing a “Methods” header before discussing competence metrics would improve the manuscript’s structure. The justification for the competence metrics needs to be clearer. Rather than stating that “The following metrics were chosen primarily for their simplicity and to facilitate testing and demonstration,” it would be helpful to explain the rationale behind selecting these specific metrics and whether they are based on existing frameworks or newly developed by the authors. Scores: The authors identified six scores but did not talk about how those scores were established, the scales, or anything else about them. Specifically: Competence 1: The explanation of how progression scores are assigned is vague. There is no clear description of the criteria used to determine the progression stage of each utterance. This lack of specificity makes it difficult to understand the validity and reliability of the scoring system. The method’s reliance on previous studies (Au-yeung, 2023; Chan et al., 2020; Connor et al., 2009; Moran et al., 2005; Ramey et al., 2009) without providing a detailed explanation or adaptation process is problematic. It would be helpful to have a more thorough, but not necessarily long explanation of how these methodologies are applied to the current study. Relatedly, the sequential analysis method from therapy research may not be directly applicable to narrative interviews conducted by AI. If this method was developed from narrative interviews, then say so. There are therapy approaches like CBT or behavioral therapies that have structured, goal-oriented sessions. ABFT is task oriented, but still provides the therapist structure. Narrative interviews, from your description, are more open-ended, possibly more like Rogerian or supportive therapy sessions. The adaptation of this method needs more rigorous justification. I was also unclear how and why a higher score isn’t better, and also why you calculated average progression scores over time. How does this score help us to understand how good AI is doing? Competence 2: Is there empirical validation or psychometric testing of the empathy scale? If so, please provide that information for the reader. I would like more information about why a Likert scale is used for empathy, especially since the previous competence argued that higher scores were not necessarily better. That does not seem to be the case with this scale. Competence 3: I didn’t understand the use of the word “Domination” in the subheader. You introduce multiple metrics (agency, coherence, complexity, and meaning-making) without clearly explaining how they are operationalized. Each one of these needs to be defined and the reader needs measurement criteria for each metric, especially since the previous two measures apparently used different scales. For example, the authors say that measuring “agency” cannot be done in isolation, but there is no description of how the scores or definitions of the other measures are used to understand or measure agency. Indeed, it seems that if the concepts in Competence 3 are interrelated, might there be a way to discuss the measures as a coherent package, rather than individual scales? The description of the Case study has many strengths, including the innovative use of ChatGPT to create a chatbot that the researchers would otherwise have not been able to program, highlighting the value of deploying the chatbot on WhatsApp, clearly defining the seven stages, and the ingenuity of having the postgraduate have two conversations – one genuine and one combative. The major limitation of the description of the case study is that it seems to be disconnected from the measures. I know that you provide results in the results section, but it would be helpful to have notes about how each section connects to the measures. Response: We have reframed the entire methodology. The manuscript now features a \"Methods\" section that explains the autoethnographic approach and the use of rubrics for assessing fidelity and empathy in the AI assistant’s performance. These rubrics provide a qualitative assessment framework that captures the nuances of narrative interviews, reflecting a shift from objective measurement to qualitative assessment aimed at enriching the exploration and discussion. The revised manuscript provides a detailed explanation of how rubrics are used primarily for assessing fidelity and empathy and introduces sequential analysis (and progression scores) to visualize how the conversations aligned with intended plans. The rubrics are the key assessment tools, while the sequential analysis serves more as an illustration. This revised approach emphasizes understanding the context and content of interactions rather than reducing them to numerical scores. Data Analysis Method and Data Collection Section I was unclear about the context in which the postgrad was having the WhatsApp conversations. Was this in a lab? Were the researchers observing? Was this in private? I didn’t understand why the conversation was divided into four equal quarters. i.e. The choice of four quarters seems arbitrary. I know that it makes it easy to analyze by utterances rather than time, but it seems to miss the importance of space and silence in a narrative interview. The process for manually assigning progression scores is not clearly defined. There is no description of the criteria used by the human research assistant to assign these scores, which raises concerns about the subjectivity and consistency of the ratings. Is there any research on using LLMs or ChatGPT specifically to assigning scores to narrative interviews? If so, it would be good to cite that here. Response: The WhatsApp conversation took place in private. We have reframed the entire methodology. The manuscript now features a \"Methods\" section that explains the autoethnographic approach and the use of rubrics for assessing fidelity and empathy in the AI assistant’s performance. The progression scores were primarily instrumental in the visualizations. We used a proportional timeline approach, dividing the conversation into four equal quarters based on the number of utterances instead of actual time, which allows us to account for varying lengths of conversations. For manually assigning progression, the first author and third authors tagged conversations independently, then reviewed and discussed until all disagreements were resolved, which helped ensure reliable and accurate evaluation. The rubrics developed for this study are specifically tailored for narrative interviews and are more flexible than structured, goal-oriented therapy methods. The therapy orientation was de-emphasized. Narrative therapy references were cited because the questioning skills in narrative therapy are useful and help inspire narrative interviews (e.g., creating metaphors). This adaptation is detailed in the methodology section, aligning with the open-ended nature of AI-mediated narrative interviews. Results The agreement between the human research assistant and ChatGPT4 on most metrics in and of itself is encouraging for researchers interested in using LLMs. In finding 2, what distinguishes a 3 from a 4? This is part of my ongoing concern about the paper’s lack of clarity with the measures. The disagreement on coherence in Conversation 2 highlights the need for clear criteria. The authors wrote, “In the rating, the human research assistant and ChatGPT4 mostly agreed on all these metrics, except that there was a disagreement on coherence in Conversation 2, where the human research assistant gave a score of 2 and ChatGPT4 gave a score of 3. After reviewing this, the principal researcher sided with ChatGPT4's score.” The manuscript should detail the specific aspects that led to different ratings and the rationale for siding with ChatGPT4’s score. Especially in these early days of using LLMs for analysis, this kind of transparency will be instructive as well as increase trustworthiness of the analysis. Response: We have completely restructured the methodology. The manuscript now includes a Methods section that explains the autoethnographic approach and the use of rubrics to assess fidelity and empathy in the AI assistant’s performance. We omitted the section on AI tagging, as it no longer aligns with the revised methodology. The rationale for conducting two conversations, as explained in the updated manuscript, was to better assess the extent to which the chatbot maintains similar levels of adherence and fidelity across different contexts, even when the conversation veers off track. Discussion I thought it was interesting that there were challenges with long speeches in conversation analysis. Even though WhatsApp tends to have shorter exchanges, what are some potential solutions or alternative methods to address these challenges, especially since narrative interviews often involve extended dialogue. I’m thinking specifically about qualitative researchers who are interested in using this for more traditional open-ended narrative interviews, not on WhatsApp. Perhaps this is part of an expanded discussion on the scalability of this type of AI use. I agree that there need to be more refined metrics (and some of my critiques of this paper are in line with that call). How would you propose to improve interrater reliability? Again, are there computational linguists who have looked into human/LLM IRR? After reading through the discussion a few times, I still didn’t have a good understanding of the differences between conversations 1 and 2. For example, in the results section you noted differences in agency, coherence and complexity. Why did the participant exhibit higher agency in Conversation 2? What factors contributed to the lower coherence and complexity in Conversation 2? If you discussed this and I missed it, my apologies. Response: We have thoroughly restructured the methodology. The revised manuscript adopts an autoethnographic approach and uses rubrics to assess fidelity and empathy in the AI assistant’s performance. These rubrics provide a qualitative framework that captures the nuances of narrative interviews, shifting the focus from objective measurement to a qualitative assessment aimed at deepening exploration and discussion. As such, interrater reliability is no longer a focus in the revised version. The manuscript explains how rubrics are used to assess fidelity and empathy, while sequential analysis and progression scores visually represent how conversations aligned with the intended plans. The rubrics serve as the primary assessment tools, with sequential analysis as an illustration. This approach emphasizes understanding the context and content of interactions rather than reducing them to numerical scores. The revised methodology aims to explore whether an OpenAI Assistant can be effectively instructed by social workers with minimal coding experience, if the chatbot’s performance can be assessed using simple observation-based rubrics, and how these findings contribute to the broader discussion on democratizing AI in specialized fields like social work. Final note: I hope this feedback is helpful. I typically do not review manuscripts until I fully understand both the spirit and letter of the manuscript, but I am providing this feedback in response to the editor’s request for a timely review Response: We are very thankful for the insightful comments and appreciate the feedback provided. We also want to sincerely apologize, as we were aware that the first version of the manuscript was not fully mature and had several gaps. We recognize that it lacked clarity in several areas, and we are grateful for the opportunity to address those issues. In response, we have completely rewritten the article using the same dataset, but with a more refined focus and clearer articulation of the research aims. This study explores how AI chatbots, particularly those powered by GPT-4, can be applied in social work for conducting narrative interviews. Through an autoethnographic case study approach, social work researchers with limited technical expertise developed and tested an AI chatbot on WhatsApp. The chatbot adhered to a structured interview plan while also demonstrating empathetic engagement with participants. While the AI performed well in maintaining dialogue and showing empathy, challenges were identified in replicating human skills within an AI framework. The study concludes that AI tools can indeed be tailored by social workers to support narrative interviews, though further research is essential to fully address the nuanced needs of the field. Our key focus remains on democratizing AI and empowering domain experts, like social workers, to use these tools effectively. This research enriches the ongoing discussion by exploring the feasibility of AI in specialized fields and emphasizes the importance of interdisciplinary collaboration in developing robust assessment tools to enhance AI implementation." } ] }, { "id": "298273", "date": "15 Aug 2024", "name": "Neil Ballantyne", "expertise": [ "Reviewer Expertise social work", "human service technology", "artificial intelliegence", "qualitative research." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis single-subject case study examines the performance of an AI assistant conducting a narrative, text-based interview with a single human participant using the WhatsApp messaging app.\nThe researchers designed the AI assistant using OpenAI’s Assistants API with the GPT-4 model. The interview was conducted twice under two different conditions. During the first, the human participant was instructed to cooperate with the AI assistant, and during the second, they were instructed to be disruptive, attempting to sidetrack the AI assistant in response to questions.\nTo assess the performance of the AI assistant on the specific and complex task of narrative-based interviewing, the researchers designed criteria and measures that, based on a review of the narrative interview literature, they deemed to be relevant and valid measures of performance. They devised and applied measures addressing different dimensions of the narrative interview, including interview structure, empathy, narrative coherence, complexity, and support for the agency of the human participant.\nA human research assistant and ChatGPT 4 assessed the interview data using these measures, and the results were compared using an inter-rater reliability test. The principal researcher reviewed the results and resolved any disagreements.\nStrengths of the study\nThe researchers are to be commended for devising an imaginative research design to study a complex area of human-computer interaction in a subject area (the application of generative AI to qualitative interviewing) that is both highly topical and deeply controversial. The design of the AI assistant and its deployment on WhatsApp seems to have been well considered, and the limitations imposed by this short exchange, text-based platform are recognised. The criteria for selecting the key measures to assess narrative interview performance, drawn from the literature identified, makes sense. However, a whole paper could have been written on this aspect alone.\nMain areas for improvement\nBe clear about research questions and primary focus\nA lot is going on in this study, and the description and rationale for key design choices are sometimes unclear. The problem begins with the abstract and the research questions, where there seems to be slippage between a focus on evaluating the performance of the AI assistant and evaluating the validity and inter-rater reliability of the measures constructed. The first research question asks:\nHow can the proposed metrics help us, as social researchers without a technical background, understand the quality of the AI-driven interviews in this study?\n\nIn my view, RQ1 would be better focussed on assessing the validity and reliability of the measures selected for evaluating the performance of the AI assistant. This needs to be established before an actual performance assessment of the AI assistant is made. Establishing inter-rater reliability of the measures would be a part of that task.\nHowever, this raises the question of why the researchers decided to have only two raters, one human and the other a GenAI. The comparison is interesting but muddies the waters. This machine versus human rater aspect of the study was a surprise since it was not signalled in the abstract, introduction or research questions. A comparison between the ratings made by a GenAI and human raters would be far more interesting once we had established human inter-rater reliability, which could have been achieved with only a few more humans in the frame.\nEstablish from the outset that this is a pilot study\nThe title and the abstract refer to the study as a case study, albeit one with a single participant, giving the reader the impression of a significant, in-depth exploration of a phenomenon. However, in the section on limitations, the authors describe the study as a pilot study and state that the primary goal “was to explore ideas and stimulate discussion rather than to conduct rigorous experiments”.\n\nI recommend that the abstract and introduction be rewritten to reflect this stance. However, this does beg the question as to whether the paper might be better construed as a working paper for feedback and discussion than as a substantive academic article. The paper is very provocative and stimulating in terms of the issues it raises but inconclusive as an assessment of the utility of an AI assistant for narrative interviews.\nOther areas for improvement\nA balanced approach to the literature and the claims made\nThe literature review is interesting and includes many relevant articles, but the articles selected and the authors’ comments are prone to over-accentuate the potential of a technology that is still emergent. The application of GenAI to qualitative research is deeply contested in the mainstream literature on qualitative methodology, making it hard to concur with the authors’ views that:\nThe integration of generative AI has revolutionized and democratized the process of qualitative data collection, analysis, and interpretation. This technological leap has boosted efficiency and expanded the horizons of narrative inquiry methods.\nThe authors can improve the literature review by recognising GenAI's emergent nature and the fact that many scholars in the mainstream qualitative research field have strong reservations about its applicability and ethical concerns about its use.\nOther issues\nThere are several places in the text where the authors’ explanations of the methods used are a little too opaque. For example, the explanation about the progression scores was helpful but left me puzzled about how this was practically implemented. An example might help.\nAlso, in the findings, the authors highlight that the participant exhibited higher agency during conversation two, which is surely explained by the instruction given to the participant to try to throw the interviewer off track. If that isn’t the explanation, a fuller account as to why not would be helpful.\nOverall\n\nI want to encourage the authors to continue their exploration of the use of GenAI in qualitative research, and I believe that this is a very useful working paper that raises many pertinent issues. Responding to the comments above might help to improve the structure and flow of the paper, but the research design issues cannot be remedied without conducting a completely new study. It is for that reason I decided not to recommend the paper for indexing.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Partly", "responses": [ { "c_id": "12381", "date": "04 Oct 2024", "name": "Chitat CHAN", "role": "Author Response", "response": "//Main areas for improvement Be clear about research questions and primary focus A lot is going on in this study, and the description and rationale for key design choices are sometimes unclear. The problem begins with the abstract and the research questions, where there seems to be slippage between a focus on evaluating the performance of the AI assistant and evaluating the validity and inter-rater reliability of the measures constructed. The first research question asks: How can the proposed metrics help us, as social researchers without a technical background, understand the quality of the AI-driven interviews in this study? In my view, RQ1 would be better focussed on assessing the validity and reliability of the measures selected for evaluating the performance of the AI assistant. This needs to be established before an actual performance assessment of the AI assistant is made. Establishing inter-rater reliability of the measures would be a part of that task. However, this raises the question of why the researchers decided to have only two raters, one human and the other a GenAI. The comparison is interesting but muddies the waters. This machine versus human rater aspect of the study was a surprise since it was not signalled in the abstract, introduction or research questions. A comparison between the ratings made by a GenAI and human raters would be far more interesting once we had established human inter-rater reliability, which could have been achieved with only a few more humans in the frame.// Response: The research questions and focus have been entirely reformulated. The revised manuscript now distinguishes its objectives. It focuses on the democratization of AI chatbots and the emerging trend of customizable AI, which has opened new opportunities across various fields, including social work. The study explores how social workers, particularly those with minimal coding experience, can instruct and evaluate AI assistants to conduct narrative interviews. The role of narrative interviews is used as a case to explore possibilities and provide feedback within a broader context. The emphasis is on qualitative assessment rather than quantitative measurement, aligning with the exploratory nature of the study. //Establish from the outset that this is a pilot study The title and the abstract refer to the study as a case study, albeit one with a single participant, giving the reader the impression of a significant, in-depth exploration of a phenomenon. However, in the section on limitations, the authors describe the study as a pilot study and state that the primary goal “was to explore ideas and stimulate discussion rather than to conduct rigorous experiments”. I recommend that the abstract and introduction be rewritten to reflect this stance. However, this does beg the question as to whether the paper might be better construed as a working paper for feedback and discussion than as a substantive academic article. The paper is very provocative and stimulating in terms of the issues it raises but inconclusive as an assessment of the utility of an AI assistant for narrative interviews.// Response: The pilot and exploratory nature of the study is emphasized. The revised abstract and introduction explicitly state that the study is exploratory and serves as a pilot to stimulate discussion about the use of AI in social work. The manuscript now clearly outlines its objectives, focusing on the democratization of AI chatbots and the emerging trend of customizable AI. The study is qualitative and concerned with the extent to which domain knowledge experts can participate in instructing and assessing AI chatbots. //Other areas for improvement A balanced approach to the literature and the claims made The literature review is interesting and includes many relevant articles, but the articles selected and the authors’ comments are prone to over-accentuate the potential of a technology that is still emergent. The application of GenAI to qualitative research is deeply contested in the mainstream literature on qualitative methodology, making it hard to concur with the authors’ views that: The integration of generative AI has revolutionized and democratized the process of qualitative data collection, analysis, and interpretation. This technological leap has boosted efficiency and expanded the horizons of narrative inquiry methods. The authors can improve the literature review by recognising GenAI's emergent nature and the fact that many scholars in the mainstream qualitative research field have strong reservations about its applicability and ethical concerns about its use.// Response: The literature review has been revised to acknowledge the democratization of AI chatbots and the emerging trend of customizable AI, which opens new opportunities across various fields, including social work. It addresses limitations alongside potential benefits. The discussion part addresses these limitations, noting that the study focused exclusively on OpenAI's product and that findings may not be generalizable to AI tools from other companies. While many principles and challenges identified here could apply broadly to other AI systems, variations in technology and implementation could lead to different outcomes. The introduction of AI tools into practice also brings considerations such as navigating risk management, data privacy, and the uneven development of language models across diverse sociocultural landscapes. While these challenges are important and have been extensively explored by others, the study focuses on exploring how social workers can expand their skill sets and rethink their expertise to engage actively with AI technologies. //Other issues There are several places in the text where the authors’ explanations of the methods used are a little too opaque. For example, the explanation about the progression scores was helpful but left me puzzled about how this was practically implemented. An example might help. Also, in the findings, the authors highlight that the participant exhibited higher agency during conversation two, which is surely explained by the instruction given to the participant to try to throw the interviewer off track. If that isn’t the explanation, a fuller account as to why not would be helpful.// Response: The revised manuscript provides clearer explanations of the methods used. It explains that the study is autoethnographic, reflecting personal experiences and using rubrics for assessing fidelity and empathy in the AI assistant’s performance. Examples of conversation transcripts are included to illustrate these qualitative assessments, emphasizing the depth and context of interactions rather than mere numerical data. We also enhanced clarity in findings. It was noted that some findings, like the participant exhibiting higher agency, were not well-explained. In the revised discussion, the measure of agency has been removed and integrated into the discussion about empathy and a deeper exploration of meanings. This approach aligns with the study’s focus on qualitative assessment and provides a clearer understanding of the findings. //Overall I want to encourage the authors to continue their exploration of the use of GenAI in qualitative research, and I believe that this is a very useful working paper that raises many pertinent issues. Responding to the comments above might help to improve the structure and flow of the paper, but the research design issues cannot be remedied without conducting a completely new study. It is for that reason I decided not to recommend the paper for indexing.// *Response: We are very grateful for the thoughtful and constructive comments provided. We deeply appreciate the feedback, especially regarding the areas for improvement and the suggestion to frame the study as a pilot. These insights were particularly helpful in guiding us toward a more focused and balanced approach. We also want to acknowledge that the first version of the manuscript had several gaps, and we sincerely apologize for any confusion this may have caused. We recognize that the clarity and direction of the paper needed refinement, and we are thankful for the opportunity to improve. In response, we have rewritten the article using the same dataset but with a more refined focus, especially clarifying the research aims and scope. The revised study explores how AI chatbots, particularly GPT-4, can be applied in social work for conducting narrative interviews. Using an autoethnographic case study approach, social work researchers developed and tested an AI chatbot on WhatsApp. The chatbot followed a structured interview plan and demonstrated empathy, though challenges in replicating human skills within AI were noted. The study concludes that social workers can tailor AI tools for narrative interviews, but further research is needed to address the field's complexities. Our focus remains on democratizing AI and empowering social workers to use these tools effectively while emphasizing the need for interdisciplinary collaboration in developing robust assessment tools." } ] } ]	1	https://f1000research.com/articles/13-601
https://f1000research.com/articles/13-360/v1	23 Apr 24	{ "type": "Method Article", "title": "High-speed camera system for efficient monitoring of invasive plant species along roadways", "authors": [ "Mads Dyrmann", "Søren Kelstrup Skovsen", "Peter Hviid Christiansen", "Mikkel Fly Kragh", "Anders Krogh Mortensen", "Søren Kelstrup Skovsen", "Peter Hviid Christiansen", "Mikkel Fly Kragh", "Anders Krogh Mortensen" ], "abstract": "Invasive plant species pose ecological threats to native ecosystems, particularly in areas adjacent to roadways, considering that roadways represent lengthy corridors through which invasive species can propagate. Traditional manual survey methods for monitoring invasive plants are labor-intensive and limited in coverage. This paper introduces a high-speed camera system, named CamAlien, designed to be mounted on vehicles for efficient invasive plant species monitoring along roadways. The camera system captures high-quality images at rapid intervals, to monitor the full roadside when following traffic speed. The system utilizes a global shutter sensor to reduce distortion and geotagging for precise localistion. The camera system makes it possible to collect extensive data sets, which can be used for a digital library of the invasive species and their locations, but also subsequent training of machine learning algorithms for automated species recognition.", "keywords": [ "high-speed camera", "invasive plant species", "roadside monitoring" ], "content": "Introduction\n\nInvasive plant species have emerged as a significant ecological concern due to their adverse impacts on native ecosystems (Gentili et al., 2021). Roadways and their adjacent areas provide a corridor for the rapid spread of invasive plants (Okimura et al., 2016; Lembrechts et al., 2014). Consequently, the development of effective monitoring tools and methodologies is essential for identifying and managing these invasive species, thereby mitigating their ecological consequences.\n\nTraditionally, identifying and mapping invasive plants relied on manual observations and record-keeping. However, conducting thorough surveillance poses challenges due to expansive road networks and vast land areas. To effectively spot these invasive plants, a trained individual must be transported at a pace that allow the person to recognizing them, a task often unattainable when driving at normal speeds on highways. Additionally, due to the varying flowering times among different species, revisiting the same areas multiple times throughout a growing season becomes a necessity.\n\nIn order to address the challenges associated with intensive monitoring of roadside areas and enhance the effectiveness of monitoring invasive plant species along roadways, we propose a high-speed camera specifically designed for mounting on vehicles. By utilizing the existing infrastructure of vehicles traversing road networks, such a camera can maximize the spatial coverage and minimize resource requirements, making invasive plant monitoring more cost-effective and time-efficient.\n\nOther studies have previously focused on automatic monitoring of invasive plant species and investigation of ecological change. Pinzani and Ceschin (2023) engage in monitoring invasive plants along the road network. For this, they use smartphone cameras, as a cheap means of collecting images with geolocation. In their study, they focus on three invasive species in the Tuscany region (central Italy) and they conclude that “Reproducibility, accessibility, and expeditiousness make the SMP [smartphone-monitoring, ed.] method easily exportable, widely usable, and adaptable to different environmental contexts and geographical areas” (Pinzani and Ceschin, 2023, p. 8). Likewise, Surya (2023) demonstrates that a smartphone camera mounted on a bike, can be used for monitoring knotweed plants from a bicycle. Depauw et al. (2022) review the use of ground-based photos in biodiversity and community ecology, phenology, global change ecology and landscape ecology. They find that photography can fundamentally contribute to the understanding of ecosystem responses and that the use of time-lapse cameras may provide an alternative for time consuming observational field studies. However, the right camera technology is not enough, as investments must also be made in proper data handling and analysis.\n\nThis paper presents the design, capabilities, and performance of the proposed high-speed camera equipment. We emphasize the importance of capturing high-quality images while maintaining the necessary speed for effective monitoring. The proposed camera design aims to enhance the frequency and scalability of invasive plant monitoring, providing valuable insights for ecologists engaged in ecological restoration and invasive species management programs. The camera system, named CamAlien, is presently undergoing testing in 11 countries across Europe and its surrounding regions.\n\nThe subsequent sections of this paper delve into the technical aspects of the camera design, including its hardware specifications, software, and mounting on vehicles. We also present sample images from field trials conducted along selected road sections, demonstrating the image quality of the camera system when used at high speed for invasive alien plant species detection. Finally, we discuss the future directions of this technology in the context of invasive alien species monitoring.\n\n\nCamera system overview\n\nThe following sections provide an overview of the camera hardware and software. Figure 1 shows the camera system mounted on the boot lid of a car using a universal mount. The camera system is enclosed and rainproof, but it is recommended to take pictures only in dry weather, as diffraction from rain on the lens can significantly reduce the image quality.\n\nOne of the main components of the system is the camera module itself. An important consideration in designing the camera module is the image sensor. The image sensor must be sensitive enough to allow for a short shutter time, minimizing motion blur when driving at high speeds. If the shutter speed is too long, it effectively reduces the horizontal resolution in the image, making object recognition more challenging. Another factor in selecting a camera sensor is whether to use a rolling or global shutter sensor. Traditional rolling shutter sensors, commonly found in consumer cameras, can introduce distortions in fast-moving scenes by sequentially capturing different parts of the image frame. In contrast, a global shutter sensor captures the entire image simultaneously, eliminating rolling shutter artifacts and ensuring accurate scene rendering. This feature is crucial when capturing images at high speeds, such as when monitoring invasive alien plant species along roads from a moving vehicle, as it maintains image integrity and enables reliable analysis and species identification. We have opted to use a camera module from Lucid Vision Labs, featuring an IMX545 global shutter sensor from Sony Semiconductor. This sensor has a size of 1/1.1\" and boasts a resolution of 12.28 megapixels. We chose this resolution based on a previous study that demonstrated the capability of detecting frequently occurring invasive species along Danish motorways using a 12 megapixel sensor and a 46° horizontal field of view (Dyrmann et al., 2021). Opting for a higher resolution with the same field of view would necessitate a shorter shutter time, potentially leading to increased image noise. Additionally, it would demand a higher bandwidth from the camera to the storage device. Therefore, resolution represents a trade-off between having enough detail for recognizing invasive alien plants and minimizing image noise.\n\nThe lens is important in the design of a camera system, as it influences the image clarity, image distortion, and field of view. The focus distance must also be suited to the distance to the plants. These plants can establish themselves on the road’s periphery, often left partially untouched, unless the vegetation interferes with traffic safety. The distance from the camera to the vegetation and the car’s speed are vital factors for determining the appropriate focal length, shutter speed, and image sampling rate. The camera can be rotated, but for monitoring the road side, it would typically be pointed perpendicular to the travel direction so that it points directly towards the road side. Therefore, the following estimates are based on this camera orientation. If the camera was mounted with a different orientation, it would have less demands on fast exposure. The estimated distance from the camera to the invasive plants at the roadside is 7 meters. Danish motorways typically feature an emergency zone of around 3 meters and at least 1.5 meters vegetation free space (Madsen et al., 2018), but often more. Moreover, the distance from the vehicle to the emergency zone is approximately 1 meter. The camera system is designed to capture images at a rate of up to 10 frames per second, with each frame having a resolution of 12 megapixels. This frame rate combined with a 12 mm lens (Computar V1226-MPZ) that provides a 50° horizontal field of view allows for coverage of the full roadside at a working distance greater than 3.85 meter, when the vehicle is traveling at 130 km/h. The camera needs to function effectively under various lighting conditions since the images solely rely on natural illumination. To ensure uniform lighting across the images, it is essential to continually adapt the camera’s exposure time and gain according to the intensity of sunlight. Consequently, the camera’s settings are configured to prioritize adjusting the exposure time based on the driving speed, so that motion blur is avoided. If additional illumination is still required, the camera will increase the analog gain. It is important to note that both the exposure time and the driving speed impact the sharpness in the images through motion blur, whereas the analog gain adds ISO (International Organization for Standardization) noise. Due to the optical Bayer filter on the camera sensor, the perceived motion blur in the RGB image is approximately half of the theoretical counterpart. Figure 2 illustrates the correlation between exposure time, driving speed, and perceived motion blur, assuming a camera-to-object distance of 7 meters. When driving 130 km/h the maximum perceived blur is less than three pixels, which we consider to be low considering a horizontal resolution of the image of 4096 pixels.\n\nDue to the reliance on natural light, the exposure time in use will depend on the factors such as time of day, weather and season.\n\nA typical use case for a camera system like this is to build a digital library of detected invasive plant species. Since the camera can capture 10 images per second, it can be an infeasible task to review the images afterwards and identify the invasive plants, whether for direct registration purposes or to create training data for automatic detection.\n\nTo facilitate the subsequent annotation of images, we propose a physical remote control shown in Figure 3, that allows marking the locations of invasive plants during recording. When a button on the remote control is pressed, a tag is written into the file name of the images, making it easy to later retrieve the image sequences containing invasive plant species. The remote control also enables starting and stopping the recording, checking the system’s status via LEDs, and turning off the camera system.\n\nAccurate spatial information is crucial for effective monitoring and management of invasive plant species. To ensure precise geolocation data, the camera system is equipped with a GNSS (Global Navigation Satellite System) module (U-blox NEO-7M). This module combines localization from GPS (Global Positioning System), GLONASS (Global’naya Navigatsionnaya Sputnikovaya Sistema), and Galileo, to determine the accurate position and time of each image. By geotagging the images, we enable spatial mapping of invasive species distributions and facilitate spatial analysis, aiding in targeted management strategies and accurate assessment of spread patterns. The GNSS module logs the full road stretch traveled, so it is also possible to see where data has been collected but no invasive planets have been observed.\n\nWhen mounted on the car, the system is powered from the car’s 12 V auxiliary power outlet, i.e., the cigarette lighter socket. Although all of the internal components of the camera system are designed to run at 12 V, the supplied voltage from the car can fluctuate significantly while in operation. During normal operation, the car generator will increase the supply voltage to approximately 13.8 V. The starter motor, however, leads to momentarily voltage drops of 1–2 volts when in use, causing the internal components to turn off if powered directly. To manage these expected fluctuations, as well as vehicles with a 24 V electrical system, a DC-DC converter (Supernight DC310-8 40to12v6a) has been integrated into the camera system. This guarantees a stable 13.8 V internal power supply, provided that the outer supply is in the range of 8–40 V. To keep the system from overheating during summer temperatures, a high static pressure fan (Sanyo Denki 9GV0412P3G03) is mounted on the downfacing intake within the system enclosure. While the downfacing intake and exhaust prevent liquids from entering the system, a replaceable air-filter within the intake keeps out dust and other unwanted materials.\n\nTo facilitate remote access to the system, the camera has a 4G modem (ZTE MF833U1). When an active SIM card is inserted, the system automatically connects to a remote server when powered on. This allows the system to report online statistics such as road coverage, system health, remaining storage space, etc. Moreover, in areas with adequate internet reception, recorded images may be transferred in real time to a centralized server.\n\nTo ensure physical compatibility with a wide range of vehicles, the camera system is designed to be mounted on the boot lid using an adjustable rack (Buzzrack Beetle) as shown in Figure 4. The rack provides a secure and stable platform for attaching the camera equipment, allowing it to be easily installed and removed without causing any damage to the vehicle. The remainder of the system is based on 30×30 mm extruded aluminum frames to ensure a light and durable system. The camera sensor is mounted on a slidable arm that allows the camera sensor to be positioned up to 60 cm closer to the roadside. Using a provided vertical extension arm, the slidable arm can be angled freely up- or downwards, providing vertical adjustments of the camera sensor of up to ±45 cm. To support accurate orientation of the images, the camera sensor is mounted onto the slidable arm with a series of joints that give additional 3 degrees of freedom, corresponding to adjustments of yaw, pitch, and roll. This flexibility enables comprehensive coverage of the road environment across diverse car models, ensuring the same data quality for accurate species identification and monitoring.\n\nTwo cushioned bars are adjusted and positioned onto the boot lid, where six straps are holding the system in place.\n\nThe processing unit of the system includes an Intel NUC12WSHi5 compute element with the Ubuntu operating system that is connected to the camera, the GNSS module, the modem, and the remote controller. Figure 5 illustrates with a flowchart how different components of the system are connected, and how images flow from the camera, through the memory (RAM) and an internal queue, and are finally stored at an external SSD. The communication between components is handled with the Robot Operating System (ROS) (Stanford Artificial Intelligence Laboratory et al.). At system startup, the camera driver configures the camera, ensuring that images are taken at the desired frame rate and shutter speed. It then receives and decodes images in real time, adds metadata in terms of timestamp and geotags, and streams the images to the web interface (if a user is connected) and a temporary image buffer. The buffer allows the user to record images for a configured number of seconds back in time, when a button is pressed in either the web interface or with the physical remote controller. When recording is active, raw images are stored on a fast internal NVME disk. From here, they are anonymized asynchronously using an AI model (YOLO) that automatically detects and removes people, bikes, and vehicles from the images. Finally, the anonymized images are stored to an external SSD.\n\nWhile the remote control provides a simple and easy-to-use interface to the camera system, the web interface provides a more complex, flexible and detailed interface to the camera system. The two main features of the web interface are the live video stream from the camera system’s internal image buffer and the status field (Figure 6, left). The live video stream allows the user to preview the images as real-time feedback of the image content and field of view, allowing the user to quickly adjust the camera position and orientation. The status field provides timestamped human-readable status messages, which elaborates the remote control’s status LEDs, e.g. software failure, overheating, and disk utilization. This enables the user to more quickly solve the problem at hand.\n\nLeft: live video stream from the camera system, buttons for triggering the camera and enabling continuous recording, length of image queue and stored images, and status window. Right: GNSS info (position and speed), and system information (disk utilization, temperatures, and CPU and memory load).\n\nBetween the two main features, two counters show the number of images in the image queue on the internal disk and the stored images on the external disk (Figure 6, left), allowing the user to assess whether images are stored while recording, and if the camera system is still off-loading images to the external disk after a long day of recording.\n\nIn addition, the web interface displays current GNSS information and computer stats such as disk usage, CPU and camera temperature (Figure 6, right) and allows the user to trigger the camera, enable continuous recording, and shutdown the camera system.\n\nThe web interface was implemented using standard ROS packages and Javascript libraries to ensure compatibility with the rest of the system and easy scalability on the user’s device(s), respectively.\n\n\nSample images\n\nThe following section contains sample images from the camera while driving. Figure 7 shows a sequence of three images that were acquired from a motorway near Aarhus in Denmark. The images were taken while the vehicle was traveling at 107 km/h and demonstrates a horizontal overlap of 61% at the start of the roadside. In the images, you can see that even objects that are close to the camera are sharp and it is possible to recognize the various plant species. The frame rate can also be set to match the driving speed so that the overlap between images is always 1/3 of the image width. Figure 8 shows an example of the automatic masking of vehicles.\n\nThe images overlap, which ensures full coverage of the roadside and it is possible to recognize the plant species.\n\n\nConclusion\n\nInvasive plant species present a pressing ecological challenge. Traditional monitoring methods have inherent limitations in coverage, timeliness and resources. This paper details the technical aspects and challenges of a high-speed, vehicle mountable camera system, that is designed for registering invasive plant species along roadways. So far, a total of 11 equivalent systems are currently being used and validated in 11 different countries. The data from such a camera system can provide an overview of the temporal and spatial distribution of invasive species, which can bring greater insight into how invasive plant species spread along roads. However, the data collected through a camera system like this possesses a dual purpose. Not only does it offer insights into invasive species dynamics, but it can also play a role in training advanced machine-learning algorithms, which could subsequently automate the time-consuming process of species recognition.\n\nIn combination with automated plant species recognition, this camera system paves the way for large scale cross country monitoring of invasive species spread.", "appendix": "Data availablility\n\n251 images from a test drive in July 2023 can be found in the following Zenodo repository: https://doi.org/10.5281/zenodo.10292599.\n\nAll images are acquired when driving on highways with speeds >100 km/h.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nGentili R, Schaffner U, Martinoli A, et al.: Invasive alien species and biodiversity: impacts and management. Biodiversity. 2021; 22(1–2): 1–3. Publisher Full Text\n\nOkimura T, Koide D, Mori AS: Differential processes underlying the roadside distributions of native and alien plant assemblages. Biodiversity and Conservation. May 2016; 25(5): 995–1009. 1572-9710. Publisher Full Text\n\nLembrechts JJ, Milbau A, Nijs I: Alien roadside species more easily invade alpine than lowland plant communities in a subarctic mountain ecosystem. PLoS One. Feb 2014; 9(2): e89664. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPinzani L, Ceschin S: Smart (phone)-monitoring (spm): An efficient and accessible method for tracking alien plant species. Sustainability. 2023; 15(12): 2071-1050. Publisher Full Text Reference Source\n\nSurya S: Detection of Japanese Knotweed Beside the Road using Deep Learning. NL: University of Twente; 2023. PhD thesis. Reference Source\n\nDepauw L, Blondeel H, De Lombaerde E, et al.: The use of photos to investigate ecological change. Journal of Ecology. 2022; 110: 1220–1236. Publisher Full Text Reference Source\n\nDyrmann M, Mortensen AK, Linneberg L, et al.: Camera assisted roadside monitoring for invasive alien plant species using deep learning. Sensors. 2021; 21(18): 1424-8220. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMadsen EB, Bach U, Larsen U, et al.: Tværprofiler i Åbent Land. Anlæg og Planlægning. Vejdirektoratet.2018.\n\nStanford Artificial Intelligence Laboratory et al.: Robotic operating system.Reference Source" }	[ { "id": "280723", "date": "20 Jun 2024", "name": "Simona Ceschin", "expertise": [ "Reviewer Expertise Botany", "Floristic Studies", "Biodiversity Monitoring", "Biological Invasion", "R Statistical Package", "Ecology and 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\nI suggest that the authors clarify on some technical aspects noted in the text of the Article. In particular: the inability for the camera to monitor both sides of the roadway at the same time; the distance at which the camera works best in relation to the width of the various European roads; the possible presence of a second operator to use remote control; The internal memory capabilities of the system.\nI suggest that the authors better expand the economic and technical limitations for the reproducibility of the method in other countries both in terms of the availability and cost of the instrumentation used and in terms of its applicability to different environmental and vegetation contexts (e.g. forests, areas with sparse or herbaceous vegetation).\nI personally found this article interesting and well balanced. I therefore only request some clarifications and minor modifications that could improve the understanding of the study. In general, the English language and punctuation should be revised to ensure that an international audience can clearly understand your text.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\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? Yes", "responses": [ { "c_id": "12479", "date": "04 Oct 2024", "name": "Mads Dyrmann", "role": "Author Response", "response": "Thank you for your thorough review. We agree with your points and have therefore updated the article to address and clarify the issues. Regarding adding an extra camera module, it is possible from a technical perspective. It would however affect the development cost and fill the memory faster. Furthermore, annotation would become more cumbersome, as the passenger annotating with the remote control would have to monitor both sides of the road simultaneously." } ] }, { "id": "300995", "date": "17 Jul 2024", "name": "Daniel M Jenkins", "expertise": [ "Reviewer Expertise Sensors and instrumentation" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript provides a fairly straightforward technical description of a vehicle mounted camera system to record images of invasive plants along roadsides during travel. The work represents a significant amount of thought and engineering development to improve the efficiency for data collection, ensuring adequate resolution and speed to ensure complete coverage / overlap capturing a roadside scene. A key advance includes dynamic controls from a web interface, enabling a user to selectively capture specific scenes (reducing unnecessary storage, and effort for subsequent use in AI training or manual recording of target plant census / distribution), and automated control of shutter speed based on GNSS estimate of vehicle speed to minimize motion blur and ensure adequate frame rates. The considerations for design / selection of the optical components / characteristics is comprehensive and systematic. Interestingly the system includes an asynchronous AI engine to automatically “anonymize” people, vehicles, and bicycles recognized in images recorded into permanent external storage- this feels unnecessarily cumbersome for the intended application but an admirable feature to include nevertheless (it’s not clear to me whether privacy laws in Europe or elsewhere would require this for the intended application). It would be really helpful to publish at least some aspects of source code for the system, though I don’t assume that is a requirement for the journal and I understand this would make it more difficult to commercialize the technology for broader deployment (and I assume that is not a requirement for publication in this journal). Overall this writing is very succinct and represents a relatively comprehensive engineering description that would be very useful for the proposed application (I would be personally interested in using it in my own research), and the authors articulate sound reasoning for deploying the technology on a vehicle mounted system. I have only a handful of suggestions for improvement:\nOverall the writing is clear and concise, but there are a handful of issues with English grammar, notably in verb tenses in the second paragraph of the introduction. In the introduction, it would be helpful to include a citation, and / or specific examples of plants where the flowering status is critical for invasive plant ID / differentiation (such that revisiting sites on a regular basis would be necessary for definitive identification) For justification of the specifications of the imaging sensor (description of the camera module), the authors use a systematic approach to ensure that resolution is adequate for identification of invasive plants, with global high speed shutter sufficient to prevent motion blur at the desired resolution (due to the moving vehicle). I think it would be helpful to refer more specifically to some of these design / operating constraints earlier in the manuscript (i.e. the tradeoffs between vehicle speed, shutter speed, and image blur in Figure 2, within the section on image sensor selection), though for the patient reader this probably isn’t critical.\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? 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? Yes", "responses": [ { "c_id": "12480", "date": "04 Oct 2024", "name": "Mads Dyrmann", "role": "Author Response", "response": "Thank you very much for your review and interest in the system. We would like to capture the same species throughout a growing season to obtain the greatest possible variation within each species, which will contribute to the robustness of the AI models that are to be trained to recognize the species. For example, we would not expect a model to be able to recognize Lupinus polyphyllus in bloom if it has only been trained on wilted examples. This has been added to the introduction. We have also added a brief description of the size of objects and considerations regarding ground sampling distance to the section on \"Recording, coverage and field of view considerations. I hope this clarifies our considerations when designing the system." } ] }, { "id": "300993", "date": "22 Jul 2024", "name": "Lorenzo Palazzetti", "expertise": [ "Reviewer Expertise 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\nThe authors investigated the possibility of monitoring invasive plant species using a high-speed camera system mounted on the back of a vehicle. They provided a detailed description of the entire system, including its components and insights into the quality of the collected images. Additionally, they introduced a client-server service to store, anonymize, and geotag the images in real-time relying on an internet connection.\nI list below my main concerns:\nThe authors proposed a system for monitoring invasive plant species along roadways, claiming that it can address the issues of traditional monitoring systems, which are labor-intensive and highly dependent on human effort. While their system moves towards automated monitoring, their solution still requires a driver to traverse multiple roads to cover a large area, and a human operator must (at least) annotate the images after the ride to establish the basis for a machine learning model. Although the latter task can be shortened by leveraging the output of the remote controller, there remains a huge amount of data to process. Additionally, the proposed remote controller necessitates actions to be performed during the ride, making the task human-centered and time-consuming once again. Please discuss possible solutions to these challenges and clarify the role and usage of the remote controller in the system. The authors introduced a remote controller for marking potential areas. From my understanding, this process is performed in real-time during a ride, and it may represent a potential issue for the accuracy of the entire system. The authors have to discuss the accuracy and the precision of this approach (i.e., how many marked locations were correct and how many were positive locations the operator missed) and eventually propose mitigation strategies. The authors provided in Figure 2 an interesting analysis of the correlation between exposure time, speed, and perceived blurriness. Since perceived blurriness inside an image may vary according to the observer, the authors should provide more details on how they derived this indicator. Since the system traces the movements of the vehicle on which the camera is mounted, potential privacy issues may arise. The authors have to discuss potential solutions to anonymize the vehicle's movements and protection against eavesdropping.\n\nIs the rationale for developing the new method (or application) clearly explained? Partly\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? No source data required\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "12481", "date": "04 Oct 2024", "name": "Mads Dyrmann", "role": "Author Response", "response": "Thank you for your review. We have reviewed your comments and addressed them in an updated version of the article. Regarding your point 2, we do not have a measure for how many invasive plants an operator overlook and how timely they press the annotation button. To ensure that the invasive plants are actually recorded, we have built a buffer into the camera that ensures images are saved already one second before the button is pressed. However, while building the image library, we do not see it as critical if some invasive plants are overlooked and the button is not pressed, as long as these non-annotated images are not included in the dataset as examples of areas without invasive plants. Regarding point 3, we have considered blur under the assumption that the image is in focus and the lens is ideally sharp. Blur occurs when the camera is in motion during exposure. We report perceived pixel blur, as the blur occurs before the image is demosaiced, which reduces the observed blur through interpolation. I hope this clarifies our considerations when designing the system." } ] } ]	1	https://f1000research.com/articles/13-360
https://f1000research.com/articles/13-789/v1	11 Jul 24	{ "type": "Brief Report", "title": "Occurrence of pathogenic Candida species in artisanal cheeses from Boyacá, Colombia, including fluconazole resistant isolates", "authors": [ "Zilpa Adriana Sánchez Quitian", "Guisell Mariana Pérez Rozo", "Carolina Firacative", "Zilpa Adriana Sánchez Quitian", "Guisell Mariana Pérez Rozo" ], "abstract": "Yeasts are widely known for their application in food production, but also because of their clinical significance. As human pathogens, several species of yeasts, mainly of the genus Candida, are responsible for a great number of life-threatening infections. The occurrence of yeasts in cheeses, including pathogenic species, has been largely studied, yet the antifungal susceptibility of these microorganisms is rarely reported. Here, we identified the species and determined the antifungal susceptibility profile of 45 Candida isolates recovered from artisanal cheeses from 20 cities in Boyacá, Colombia. Among the species, Candida lambica (28.9%) prevailed, followed by Candida krusei (24.4%), Candida kefyr (22.2%), Candida lusitaniae (11.1%), Candida inconspicua (6.7%) Candida parapsilosis (4.4%) and Candida guillermondii (2.2%). Notably, all seven species have been globally reported, to a greater or lesser extent, to cause fungemia and other invasive infections with high mortality rates. Remarkably, most isolates of C. lambica C. krusei, C. inconspicua and C. parapsilosis were resistant to fluconazole, one of the most common drugs to treat candidiasis. Our findings highlight the importance of exploring the ecological niches of pathogenic yeasts, together with their antifungal susceptibility, considering that the emergence of resistance in non-commensal opportunistic pathogens poses a serious threat to public health.", "keywords": [ "antifungal", "antimicrobial resistance", "artisanal cheeses", "Candida", "fluconazole" ], "content": "Introduction\n\nThe importance of yeasts is highlighted by their application in food production, as these fungi play a vital role in fermentation (Maicas 2020). However, the clinical significance of yeasts has also been clearly established, considering that these microorganisms, as human pathogens, are able to cause life-threatening infections, particularly among older patients and those with an underlying serious condition associated with medical interventions, comorbidities or immunosuppression (Firacative 2020). Moreover, as antifungal resistance emerges in several species of colonizing and environmental yeasts, management and treatment challenges for the infections that they cause also appear, which represents an even major problem to public health (Fisher et al. 2022). Among the most prominent disease-causing fungi are the ascomycetous yeasts of the genus Candida, which are responsible for the majority of cases of invasive fungal infection in hospital settings in the world, with some species having acquired or intrinsic resistance to commonly used antifungal drugs (Bongomin et al. 2017; Lamoth et al. 2018).\n\nGiven that several species of yeasts are frequently found not only in raw milk but also in surfaces and material related with cheese production, handling and manufacturing, the occurrence of these microorganisms in artisanal cheeses is broadly known (Minervini et al. 2001; Mounier et al. 2006). In addition, the implications of the presence of a particular species of yeasts in these dairy products have been widely investigated, since some species can positively contribute to the characteristic taste and flavour of cheeses, while other species can spoil the product, causing off-flavours, softening, and bad odours, among others undesirable signs of spoilage (Minervini et al. 2001; Suzzi et al. 2003; Fadda et al. 2004; Bintsis 2021). Interestingly, from the diverse assortment of yeast species that can be present in artisanal cheeses, not only species of Candida have been found, but also of the genera Geotrichum, Pichia, Rhodotorula, Saccharomyces and Trichosporon, which, albeit uncommon, are increasingly causing severe disease in humans (Bintsis 2021; Chen et al. 2021; Gil et al. 2023).\n\nWhile the instances of invasive yeast infections potentially acquired from food exposure and consumption are infrequent, these may be progressively observed, given that several emerging pathogenic yeasts species are commonly recovered from various environmental sources, including food, rather than from the normal mycobiota of humans (Cooper Jr. 2010; Benedict et al. 2016). In Candida bloodstream infections (BSI), particularly, the gut has been suggested as the main source of endogenous acquisition, and although atypical Candida species are not usually part of the gastrointestinal mycobiota, these yeasts could be transient members of the gut, acquired during feeding (Nucci Marcio and Anaissie 2001; Auchtung et al. 2018).\n\nAs the number of patients at-risk for fungal infections increases, there is a concurrent dramatic upsurge in the number of known opportunistic fungal species that are able to cause disease. Therefore, studies like ours addressed to explore part of the wide diversity of ecological niches of human pathogenic yeasts are helpful to provide further insights into the distribution and expansion of these microorganisms. Moreover, to our knowledge, this is the first study establishing not only the occurrence but also the antifungal susceptibility of clinically relevant Candida species recovered from artisanal cheeses, with the identification of resistant isolates, mainly to fluconazole. Our study contributes to the little information regarding the epidemiology, ecology and antifungal susceptibility profiles of Candida lambica, Candida krusei, Candida kefyr, Candida lusitaniae, Candida inconspicua, Candida parapsilosis and Candida guillermondii, two of which are part of the recently issued World Health Organization (WHO) fungal priority pathogens list (WHO 2022).\n\n\nMethods\n\nForty-five isolates of Candida species previously recovered from 29 artisanal cheeses in 20 cities in Boyacá, Colombia (Figure 1) and belonging to the Collection of Fungi and Microorganisms of Universidad de Boyacá (UBCHM), were studied. A unique isolate of Candida was recovered from 15 cheeses, while two different isolates were recovered from 12 cheeses and three different isolates from two cheeses. Isolates were identified by matrix-assisted laser desorption/ionization time-off-flight (MALDI-TOF) mass spectrometry using the MALDI Biotyper® (Bruker Daltonics Inc., Germany).\n\nIsolates were kept at -80 °C in 2 ml of 10% ultra-pure glycerol (Thermo Fisher Scientific, catalogue number 15514011) and were cultured in Sabouraud dextrose agar (SDA) (BD DIFCO, catalogue number 210950) at 35 °C for 24 h prior to the experiments.\n\nThe colorimetric broth microdilution test, Sensititre® YeastOne® (Thermo Fisher Scientific, catalogue number YO9), was used to determine the susceptibility of the isolates to anidulafungin (AND), micafungin (MF), caspofungin (CAS), 5-fluorocytosine (FC), posaconazole (PZ), voriconazole (VOR), itraconazole (IZ), fluconazole (FZ) and amphotericin B (AB), which are lyophilized in each plate, following the manufacturer’s instructions. In brief, each isolate was grown on SDA for 24 h at 35 °C. Subsequently, a yeast inoculum was prepared, per isolate, in 5 ml of sterile water and adjusted to the 0.5 McFarland standard (1-5 × 106 cells/ml). From this cell suspension, 20 μl were mixed thoroughly with 11 ml of YeastOne® inoculum broth (Thermo Fisher Scientific, catalogue number Y3462) to obtain a final concentration of 1.8-9 × 103 cells/ml. From the last suspension, 100 μl were served into each well of a Sensititre® YeastOne® plate. Plates were sealed and incubated at 35 °C for 24 h. Minimum inhibitory concentration (MIC) values were defined as the lowest concentration of each antifungal that prevented the development of a pink or fuchsia colour, this is, the first blue well (no growth) for amphotericin B, or the first purple well (growth inhibition) or blue well (no growth) for echinocandins, 5-fluorocytosine and azoles (Espinel-Ingroff et al. 1999). The quality control strains of Candida krusei ATCC® 6258 and Candida parapsilosis ATCC® 22019 were used following the M27M44S guideline of the Clinical and Laboratory Standards Institute (CLSI) (CLSI 2022).\n\nSusceptible or resistant isolates to certain antifungal drug were identified, when available, with the clinical breakpoints per species of Candida and per drug, as established by the CLSI and other studies on the antifungal susceptibility of rare yeasts (Borman et al. 2019; CLSI 2022). Per species of Candida with five or more isolates, and per antifungal drug, the frequency of MIC values was determined and the geometric mean MIC was calculated. Using the Mann–Whitney test, the differences in MIC values between species were established, per antifungal drug, with the software GraphPad Prism 9 (https://www.graphpad.com/, La Jolla, CA, USA). p-values <0.05 were considered statistically significant.\n\n\nResults\n\nAmong the 45 isolates included in this study, seven species of Candida were identified. From these, C. lambica (Pichia fermentans) was the most common species, with 13 (28.9%) isolates, followed by C. krusei (Pichia kudriavzevii) with 11 (24.4%), C. kefyr (Kluyveromyces marxianus) with 10 (22.2%), C. lusitaniae (Clavispora lusitaniae) with five (11.1%), C. inconspicua with three (6.7%), C. parapsilosis with two (4.4%) and C. guillermondii (Meyerozyma guilliermondii) with one (2.2%) isolate. From 10 cheeses with two isolates and the two cheeses with three isolates, two different species of Candida were identified. The occurrence of the species did not differ depending on the city.\n\nEven though all seven species recovered from artisanal cheeses have been reported as human pathogens, C. parapsilosis, C. krusei and C. guillermondii are of major clinical relevance, as they are responsible for larger proportions of cases of candidemia and other forms of invasive candidiasis in different countries around the world (Table 1). To a lesser extent, C. lusitaniae, C. kefyr, C. inconspicua and C. lambica have been identified causing disease in humans.\n\n1 Medium and\n\n2 high priority in the World Health Organization fungal priority pathogens list (WHO 2022).\n\nThe majority of Candida isolates from this study were susceptible to the echinocandins tested, to most azoles and to amphotericin B, according to the CLSI breakpoints and other studies (Borman et al. 2019; CLSI 2022) (Table 2). However, 12 isolates (92.3%) of C. lambica, the most common species recovered, 10 (90.9%) of C. krusei, two (66.7%) of C. inconspicua and two (100%) of C. parapsilosis were resistant (R) to fluconazole (MIC ≥16 μg/ml) (Figure 1). In addition, the 10 fluconazole resistant isolates of C. krusei had concomitantly decreased susceptibility to 5-fluorocytosine (MIC ≥8 μg/ml). Intermediate susceptibility to 5-fluorocytosine (MIC = 16 μg/ml) was as well identified in one (10%) isolate of C. kefyr (Pfaller et al. 2002). Notably, fluconazole resistant isolates were identified in 16 (80%) of the 20 studied cities in Boyacá.\n\n1 The modal MIC for each distribution is underlined. Resistant isolates are in bold.\n\n2 AND: anidulafungin; MF: Micafungin; CAS: caspofungin; FC: 5-fluorocytosine; PZ: Posaconazole; VOR: Voriconazole; IZ: Itraconazole; FZ: Fluconazole; AB: Amphotericin-B.\n\n3 GM: Geometric mean in μg/ml calculated with five or more isolates.\n\nWhen comparing the geometric mean MIC among C. lambica, C. krusei, C. kefyr and C. lusitaniae, per antifungal tested (Table 2), it was possible to establish that C. krusei was less susceptible to caspofungin, micafungin and 5-fluorocytosine than C. lambica, C. kefyr and C. lusitaniae (p < 0.05). Additionally, both C. lambica and C. krusei were less susceptible to anidulafungin and all azoles than C. kefyr and C. lusitaniae (p < 0.05). The susceptibility of the studied isolates to amphotericin B did not differ depending on these four species of Candida, with all studied isolates being susceptible to this polyene.\n\n\nDiscussion\n\nThe identification of nonclinical reservoirs of human pathogenic yeasts is of upmost importance, since these might serve as a source of transmission and dissemination of invasive disease. In fact, the full contribution of the environmental reservoirs of Candida species to the well documented shifting epidemiology of candidiasis worldwide, remains largely uncharacterized (Lamoth et al. 2018). Here, we not only describe the occurrence of pathogenic Candida species from artisanal cheeses, but we also report the identification of about 60% of the isolates with resistance to fluconazole, some of them with concomitant reduced susceptibility to 5-fluorocytosine.\n\nIn our study, C. lambica was recovered in almost a third of samples, which is not surprising as this species was firstly isolated from butter milk in The Netherlands and since, it has been commonly encountered in different dairy products such as hard and white-brined cheeses as well as in fermented food (Kurtzman et al. 2011; Bintsis 2021). Even though there have been very few cases of human disease by C. lambica, this yeast has been able to cause fungemia, which is one of the most severe manifestations of invasive candidiasis, with high mortality rates (Pfaller and Diekema 2004; Vervaeke et al. 2008; Noni et al. 2020). Moreover, the resistance to fluconazole that characterises the isolates of this species, which agrees with our findings, could hinder treatment and lead to an inappropriate management, hence to a poor prognosis in patients with these infections (Borman et al. 2019).\n\nC. krusei, which has emerged in the last years as a significant opportunistic pathogen affecting patients with hematologic malignancies and transplant recipients worldwide (Pfaller et al. 2008; Jamiu et al. 2021), was also commonly found in artisanal cheeses, as reported previously (Wanderley et al. 2013; Banjara et al. 2015). In Colombia, C. krusei is the fifth most common Candida species causing BSI, accounting for about 2.2% of all cases, as occurring worldwide (Pfaller and Diekema 2004; Cortes et al. 2020). Importantly, C. krusei has intrinsic resistance to fluconazole, as found in our isolates, reduced susceptibility to 5-fluorocytosine and is rapidly developing acquired resistance to other antifungal drugs, making it a multidrug-resistant pathogen, very difficult to treat (Pfaller et al. 2002; Pfaller et al. 2008).\n\nAnother emerging pathogen causing BSI in patients with blood cancer is C. kefyr (Reuter et al. 2005; Dufresne et al. 2014), which accounted for about 23% of isolates recovered from our artisanal cheeses. In a global study of candidemia, C. kefyr was the nineth most prevalent species of Candida, causing 0.16% of all cases (Pfaller and Diekema 2004), and its incidence was suggested to be influenced by exogenous exposure to yogurt and other milk products (Dufresne et al. 2014). Even though the ecology of this yeast is not fully understood, C. kefyr has been occasionally recovered from blue-veined cheeses and other dairy foods, as well as from fruits, plant material and even plastic devices (Kurtzman et al. 2011; Dufresne et al. 2014; Bintsis 2021). While resistance to antifungals is not common in C. kefyr, we report an isolate with intermediate susceptibility to 5-fluorocytosine, which emphasises the importance of monitoring the emergence of antifungal resistance in uncommon species (Pfaller et al. 2002).\n\nRecovered from semi-hard, white brined and other cheeses, as well as from agave leaves (Wanderley et al. 2013; Bintsis 2021), C. lusitaniae was the fourth most common species recovered in our study. Known for its low susceptibility to fluconazole and amphotericin B, and its ability to acquire antifungal drug resistance within days of treatment, this Candida species has been recognized as a human pathogen for more than four decades (Scott et al. 2023; Angiolella et al. 2024). In fact, in a global surveillance, C. lusitaniae accounted for about 1.1% of all the cases of candidemia, affecting mainly immunocompromised patients with underlying malignancies (Pfaller and Diekema 2004).\n\nCommonly recovered from lactic products, including milk, cheeses, or butter (Minervini et al. 2001; Suzzi et al. 2003; Bintsis 2021), C. inconspicua is a species that has been rarely recovered from clinical samples. Accounting for less than 0.05% of all cases of candidemia globally (Pfaller and Diekema 2004), this yeast, together with other rare yeast species, shared the traits of being the cause of invasive infections and having high MIC values to fluconazole and azole derivatives (Perez-Hansen et al. 2019), which difficult management.\n\nWhile C. parapsilosis has been isolated from cheeses and milk products (Suzzi et al. 2003; Wanderley et al. 2013; Banjara et al. 2015; Fröhlich-Wyder et al. 2019), as reported herein, its relevance lies in the role of this species in healthcare. In Australia, Malaysia, and many countries of Europe and Latin America, including Colombia, C. parapsilosis is the second most important opportunistic pathogenic yeast, after Candida albicans, associated with intrahospital transmission, targeting neonates, immunosuppressed and patients with indwelling catheters (Pfaller and Diekema 2004; Nucci et al. 2013; Pappas et al. 2018; Arendrup et al. 2023; Hernández-Pabón et al. 2024). Remarkably, fluconazole and voriconazole cross-resistance has been described in C. parapsilosis, therefore, affected patients should be treated ideally with an echinocandin, which many times are unavailable in resource-limited countries (Cornely et al. 2012). Together with C. krusei, which was placed in the medium priority group, C. parapsilosis is in the high priority group of the WHO fungal priority pathogens list, highlighting the need to focus attention on the perceived public health importance of these species (WHO 2022).\n\nC. guillermondii, which is most often associated with onychomycosis, is the fourth most frequent species causing invasive fungal infection in critically ill patients in Argentina, Honduras and Venezuela, fifth in Colombia (Nucci et al. 2013) and the seventh cause of BSI by Candida species globally (Pfaller and Diekema 2004). Unfortunately, resistance to amphotericin B, fluconazole and itraconazole, associated with treatment failure, and reduced susceptibility to several other classes of antifungals have been reported in C. guillermondii isolates (Pfaller et al. 2006). Although no specific clinical or environmental sources for infection have been identified, C. guillermondii may be transmitted from patient to patient in the hospital, particularly among those with intravascular foreign bodies (Pfaller et al. 2006).\n\nThe emergence of uncommon, yet resistant, pathogenic Candida species could be due to the selective pressure caused for a larger use of azole derivatives, particularly fluconazole, not only as antifungal prophylaxis but also as empirical therapeutics (Pfaller and Diekema 2004). Given its low cost and low toxicity, fluconazole remains one of the most commonly prescribed antifungal drugs against candidemia and candidiasis (Cornely et al. 2012). Moreover, the use of azoles as fungicides in agriculture, which can contribute to the appearance of antifungal-resistance in nature, is widely documented (CDC 2019).\n\nThe rise of species that are in addition resistant to other class of antifungals, including polyenes, flucytosine and echinocandins, makes these microorganisms multidrug-resistant, as it is the case of C. krusei, C. lusitaniae, and C. guillermondii, among the Candida species reported here, which further increases the risk for human health. Therefore, early detection, including the identification of environmental sources and exogenous exposure, as well as accurate species identification, are crucial to contribute to infection control. Our study provides important data on the occurrence of pathogenic Candida species recovered from artisanal cheeses and on the antifungal susceptibility of these, which until now is rather limited.", "appendix": "Data availability\n\nUnderlying data is deposited in Figshare: Occurrence of pathogenic Candida species in artisanal cheeses from Boyacá, Colombia, including fluconazole resistant isolates. Doi: https://doi.org/10.6084/m9.figshare.26093389 (Sánchez-Quitian et al. 2024).\n\nThis project contains the following underlying data:\n\n- Raw Data.xlsx (antifungal susceptibility testing (AST) data for each isolate and per species with characteristics of each isolate).\n\n- Figure 1 (Map with the isolates).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors thank Claudia Parra from Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, for allowing the use of the MALDI-TOF. We also thank Óscar Perdomo, professor at Universidad de Boyacá, for his collaboration in the construction of the map.\n\n\nReferences\n\nAngiolella L, Rojas F, Giammarino A, et al.: Identification of Virulence Factors in Isolates of Candida haemulonii, Candida albicans and Clavispora lusitaniae with Low Susceptibility and Resistance to Fluconazole and Amphotericin B. Microorganisms. 2024; 12(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArendrup MC, Arikan-Akdagli S, Jorgensen KM, et al.: European candidaemia is characterised by notable differential epidemiology and susceptibility pattern: Results from the ECMM Candida III study. J. Infect. 2023; 87(5): 428–437. PubMed Abstract \| Publisher Full Text\n\nAuchtung TA, Fofanova TY, Stewart CJ, et al.: Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. mSphere. 2018; 3(2). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBanjara N, Suhr MJ, Hallen-Adams HE: Diversity of yeast and mold species from a variety of cheese types. Curr. Microbiol. 2015; 70(6): 792–800. PubMed Abstract \| Publisher Full Text\n\nBenedict K, Chiller TM, Mody RK: Invasive Fungal Infections Acquired from Contaminated Food or Nutritional Supplements: A Review of the Literature. Foodborne Pathog. Dis. 2016; 13(7): 343–349. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBintsis T: Yeasts in different types of cheese. AIMS Microbiol. 2021; 7(4): 447–470. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBongomin F, Gago S, Oladele RO, et al.: Global and multi-national prevalence of fungal diseases-estimate precision. J. Fungi (Basel). 2017; 3(4). Publisher Full Text\n\nBorman AM, Muller J, Walsh-Quantick J, et al.: Fluconazole Resistance in Isolates of Uncommon Pathogenic Yeast Species from the United Kingdom. Antimicrob. Agents Chemother. 2019; 63(8). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCDC: Antibiotic resistance threats in the United States USA: 2019. [accessed 2022 10/06/2022]. Reference Source\n\nChen SC, Perfect J, Colombo AL, et al.: Global guideline for the diagnosis and management of rare yeast infections: an initiative of the ECMM in cooperation with ISHAM and ASM. Lancet Infect. Dis. 2021; 21(12): e375–e386. PubMed Abstract \| Publisher Full Text\n\nmCLSI: Performance Standards for Antifungal Susceptibility Testing of Yeasts. CLSI supplement M27M44S. Third ed.Wayne, PA, USA: Clinical and Laboratory Standards Institute; 2022.\n\nCooper CR Jr.: Chapter 2, Yeasts Pathogenic to Humans.Kurtzman C, Fell JW, Boekhout T, editors. The Yeast: a Taxonomic Study. 5th ed.Amsterdam, The Netherlands: Elsevier; 2010; pp. 9–19.\n\nCornely OA, Bassetti M, Calandra T, et al.: ESCMID* guideline for the diagnosis and management of Candida diseases 2012: non-neutropenic adult patients. Clin. Microbiol. Infect. 2012; 18 Suppl 7: 19–37. PubMed Abstract \| Publisher Full Text\n\nCortes JA, Ruiz JF, Melgarejo-Moreno LN, et al.: Candidemia in Colombia. Biomedica. 2020; 40(1): 195–207. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDufresne SF, Marr KA, Sydnor E, et al.: Epidemiology of Candida kefyr in patients with hematologic malignancies. J. Clin. Microbiol. 2014; 52(6): 1830–1837. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEspinel-Ingroff A, Pfaller M, Messer SA, et al.: Multicenter comparison of the sensititre YeastOne Colorimetric Antifungal Panel with the National Committee for Clinical Laboratory standards M27-A reference method for testing clinical isolates of common and emerging Candida spp., Cryptococcus spp., and other yeasts and yeast-like organisms. J. Clin. Microbiol. 1999; 37(3): 591–595. PubMed Abstract \| Publisher Full Text\n\nFadda ME, Mossa V, Pisano MB, et al.: Occurrence and characterization of yeasts isolated from artisanal Fiore Sardo cheese. Int. J. Food Microbiol. 2004; 95(1): 51–59. PubMed Abstract \| Publisher Full Text\n\nFiracative C: Invasive fungal disease in humans: are we aware of the real impact? Mem. Inst. Oswaldo Cruz. 2020; 115: e200430. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFisher MC, Alastruey-Izquierdo A, Berman J, et al.: Tackling the emerging threat of antifungal resistance to human health. Nat. Rev. Microbiol. 2022; 20: 557–571. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFröhlich-Wyder M-T, Arias-Roth E, Jakob E: Cheese yeasts. Yeast 2019; 36(3): 129–141. Publisher Full Text\n\nGil O, Hernandez-Pabon JC, Tabares B, et al.: Rare Yeasts in Latin America: Uncommon Yet Meaningful. J. Fungi (Basel). 2023; 9(7). Publisher Full Text\n\nHernández-Pabón JC, Tabares B, Gil Ó, et al.: Candida Non-albicans and Non-auris Causing Invasive Candidiasis in a Fourth-Level Hospital in Colombia: Epidemiology, Antifungal Susceptibility, and Genetic Diversity. Journal of Fungi. 2024; 10(5): 326. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJamiu AT, Albertyn J, Sebolai OM, et al.: Update on Candida krusei, a potential multidrug-resistant pathogen. Med. Mycol. 2021; 59(1): 14–30. PubMed Abstract \| Publisher Full Text\n\nKurtzman CP, Fell JW, Boekhout T: The Yeasts, a Taxonomic Study. 5th ed.Elsevier; 2011; vol. 2. .\n\nLamoth F, Lockhart SR, Berkow EL, et al.: Changes in the epidemiological landscape of invasive candidiasis. J. Antimicrob. Chemother. 2018; 73(suppl_1): i4–i13. PubMed Abstract \| Publisher Full Text\n\nMaicas S: The Role of Yeasts in Fermentation Processes. Microorganisms. 2020; 8(8). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMinervini F, Montagna MT, Spilotros G, et al.: Survey on mycoflora of cow and buffalo dairy products from Southern Italy. Int. J. Food Microbiol. 2001; 69(1-2): 141–146. PubMed Abstract \| Publisher Full Text\n\nMounier J, Goerges S, Gelsomino R, et al.: Sources of the adventitious microflora of a smear-ripened cheese. J. Appl. Microbiol. 2006; 101(3): 668–681. PubMed Abstract \| Publisher Full Text\n\nNoni M, Stathi A, Velegraki A, et al.: Rare Invasive Yeast Infections in Greek Neonates and Children, a Retrospective 12-Year Study. J. Fungi (Basel). 2020; 6(4). Publisher Full Text\n\nNucci M, Anaissie E: Revisiting the Source of Candidemia: Skin or Gut? Clin. Infect. Dis. 2001; 33(12): 1959–1967. Publisher Full Text\n\nNucci M, Queiroz-Telles F, Alvarado-Matute T, et al.: Epidemiology of candidemia in Latin America: a laboratory-based survey. PLoS One. 2013; 8(3): e59373. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPappas PG, Lionakis MS, Arendrup MC, et al.: Invasive candidiasis. Nat. Rev. Dis. Prim. 2018; 4(1): 18026. Publisher Full Text\n\nPerez-Hansen A, Lass-Florl C, Lackner M, et al.: Antifungal susceptibility profiles of rare ascomycetous yeasts. J. Antimicrob. Chemother. 2019; 74(9): 2649–2656. Publisher Full Text\n\nPfaller MA, Diekema DJ: Twelve years of fluconazole in clinical practice: global trends in species distribution and fluconazole susceptibility of bloodstream isolates of Candida. Clin. Microbiol. Infect. 2004; 10: 11–23. PubMed Abstract \| Publisher Full Text\n\nPfaller MA, Diekema DJ, Gibbs DL, et al.: Candida krusei, a multidrug-resistant opportunistic fungal pathogen: geographic and temporal trends from the ARTEMIS DISK Antifungal Surveillance Program, 2001 to 2005. J. Clin. Microbiol. 2008; 46(2): 515–521. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPfaller MA, Diekema DJ, Mendez M, et al.: Candida guilliermondii, an opportunistic fungal pathogen with decreased susceptibility to fluconazole: geographic and temporal trends from the ARTEMIS DISK antifungal surveillance program. J. Clin. Microbiol. 2006; 44(10): 3551–3556. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPfaller MA, Messer SA, Boyken L, et al.: In vitro activities of 5-fluorocytosine against 8,803 clinical isolates of Candida spp.: global assessment of primary resistance using National Committee for Clinical Laboratory Standards susceptibility testing methods. Antimicrob. Agents Chemother. 2002; 46(11): 3518–3521. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReuter CW, Morgan MA, Bange FC, et al.: Candida kefyr as an emerging pathogen causing nosocomial bloodstream infections in neutropenic leukemia patients. Clin. Infect. Dis. 2005; 41(9): 1365–1366. PubMed Abstract \| Publisher Full Text\n\nSánchez-Quitian ZA, Pérez-Rozo GM, Firacative C: Underlying data in: Occurrence of pathogenic Candida species in artisanal cheeses from Boyacá, Colombia, including fluconazole resistant isolates. figshare 2024. Publisher Full Text\n\nScott NE, Edwin Erayil S, Kline SE, et al.: Rapid Evolution of Multidrug Resistance in a Candida lusitaniae Infection during Micafungin Monotherapy. Antimicrob. Agents Chemother. 2023; 67(8): e0054323. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSuzzi G, Schirone M, Martuscelli M, et al.: Yeasts associated with Manteca. FEMS Yeast Res. 2003; 3(2): 159–166. PubMed Abstract \| Publisher Full Text\n\nVervaeke S, Vandamme K, Boone E, et al.: A case of Candida lambica fungemia misidentified as Candida krusei in an intravenous drug abuser. Med. Mycol. 2008; 46(8): 853–856. PubMed Abstract \| Publisher Full Text\n\nWanderley LAS, Bianchin A, Teo CRPA, et al.: Occurrence and pathogenicity of Candida spp. in unpasteurized cheese. Revista Brasileira de Biociências: Brazilian Journal of Biosciences. 2013; 11(2 (abr/jun 2013)): 145–148.\n\nWHO: Organization WH, editor. WHO fungal priority pathogens list to guide research, development and public health action. Geneva: World Health Organization; 2022." }	[ { "id": "316495", "date": "29 Aug 2024", "name": "Anastasia Spiliopoulou", "expertise": [ "Reviewer Expertise Medical microbiology", "Mycology", "Antimicrobial resistance", "Host-pathogen interactions" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript, authors have studied the presence of Candida isolates in artisanal cheeses produced in Boyaca, Colombia. Their findings are quite interesting as they isolated species such as Candida parapsilosis and C. krusei, that are quite commonly isolated in invasive Candida human infections as well as other species, such as C. kefyr, C. guillermondii, C. lusitaniae etc that are more uncommonly encountered. It is well known that in many cases the source of candidiasis is the intestinal and colonization of certain Candida spp has been associated with invasive infections in certain patient groups. Moreover, antifungal resistance has spread in livestock farming, a finding that raises great concern. All these aspects are nicely presented and discussed in this work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not 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": "12329", "date": "30 Aug 2024", "name": "Carolina Firacative", "role": "Author Response", "response": "Thanks to the reviewer for the time to read and evaluate our manuscript and for each of the valuable comments." } ] }, { "id": "316497", "date": "16 Sep 2024", "name": "Maria Helena Figueiredo-Carvalho", "expertise": [ "Reviewer Expertise Medical mycology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 manuscript submitted by Sánchez Quitian ZA, Pérez Rozo GM, and Firacative C which evaluated the occurrence of pathogenic Candida species in artisanal cheeses from Boyacá, Colombia, including fluconazole-resistant isolates. The manuscript was written clearly and objectively. However, some modifications are necessary.\nTitle Occurrence of pathogenic Candida species in artisanal cheeses from Boyacá, Colombia, including fluconazole-resistant isolates. Suggest Yeast\nAbstract …Remarkably, most isolates of C. lambica C. krusei, C. inconspicua and C. parapsilosis were resistant to fluconazole, one of the most common drugs to treat candidiasis. Suggest Remove the species C. krusei. This species is intrinsically resistant to fluconazole. Review all yeast species nomenclature. Kidd SE., 2023 [Ref-1] or MycoBank\nCurrent name Pichia fermentans Previous name Candida lambica\nPichia kudriavzevii (Candida krusei)….\nKeywords antifungal, antimicrobial resistance, artisanal cheeses, Candida, fluconazole. Suggest Yeast species or Candida, Pichia, Meyrozyma, Clavispora, Kluyveromyces\nIntroduction: … Our study contributes to the little information regarding the epidemiology, ecology and antifungal susceptibility profiles of Candida lambica, Candida krusei, Candida kefyr, Candida lusitaniae, Candida inconspicua, Candida parapsilosis and Candida guillermondii, two of which are part of the recently issued World Health Organization (WHO) fungal priority pathogens list (WHO 2022). Suggest Candida parapsilosis and Pichia kudrizvzeveii (Candida krusei) hight and media priority group, respectively.\nMethods Isolates Figure 1. Distribution of pathogenic Candida species recovered from artisanal cheeses in Boyacá, Colombia. Suggest Distribution of pathogenic Yeast species recovered from artisanal cheeses in Boyacá, Colombia.\nAntifungal susceptibility testing Was the antifungal test conducted in duplicate? Resistant isolates were found. Pichia kudrizvzeveii (Candida krusei) is intrinsically resistant to fluconazole. However, in your study, one isolate was sensitive.\nResults …Among the 45 isolates included in this study, seven species of Candida were identified. From these, C. lambica (Pichia fermentans) was the most common species, with 13 (28.9%) isolates, followed by C. krusei (Pichia kudriavzevii) with 11 (24.4%), C. kefyr (Kluyveromyces marxianus) with 10 (22.2%), C. lusitaniae (Clavispora lusitaniae) with five (11.1%), C. inconspicua with three (6.7%), C. parapsilosis with two (4.4%) and C. guillermondii (Meyerozyma guilliermondii) with one (2.2%)… Suggest current name (previous name)\n…To a lesser extent, C. lusitaniae, C. kefyr, C. inconspicua and C. lambica have been identified causing disease in humans. Suggest To a lesser extent, C. lusitaniae, C. kefyr, C. inconspicua and C. lambica have been identified causing invasive fungal infection in humans\nTable 2 AND: anidulafungin; MF: Micafungin; CAS: caspofungin; FC: 5-fluorocytosine; PZ: Posaconazole; VOR: Voriconazole; IZ: Itraconazole; FZ: Fluconazole; AB: Amphotericin-B. Suggest MCF: Micafungin; 5FC: 5-fluorocytosine; PCZ: Posaconazole; ITZ: Itraconazole; FCZ: Fluconazole; AMB: amphotericin B\n\nDiscussion Update the references. In the discussion, the cited references are very outdated. I suggest using more up-to-date references on the species identified 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? 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": "12475", "date": "26 Sep 2024", "name": "Carolina Firacative", "role": "Author Response", "response": "Reviewer 2. I have reviewed the manuscript submitted by Sánchez Quitian ZA, Pérez Rozo GM, and Firacative C which evaluated the occurrence of pathogenic Candida species in artisanal cheeses from Boyacá, Colombia, including fluconazole-resistant isolates. The manuscript was written clearly and objectively. However, some modifications are necessary. Answer: thanks to the reviewer for the time to read and evaluate the manuscript and for each of the valuable comments and suggestions. In the revised manuscript and along with this point-by-point response, we aimed to address all issues mentioned by the reviewer. Title Occurrence of pathogenic Candida species in artisanal cheeses from Boyacá, Colombia, including fluconazole-resistant isolates. Suggest Yeast Answer: following the reviewer’s suggestion, the title was changed. Abstract …Remarkably, most isolates of C. lambica C. krusei, C. inconspicua and C. parapsilosis were resistant to fluconazole, one of the most common drugs to treat candidiasis. Suggest Remove the species C. krusei. This species is intrinsically resistant to fluconazole. Answer: thanks for the suggestion. We did not remove the name of the species; however, we modified the text to highlight that P. kudriavzevii is intrinsically resistant to FCZ. Review all yeast species nomenclature. Kidd SE., 2023 [Ref-1] or MycoBank Current name Pichia fermentans Previous name Candida lambica Pichia kudriavzevii (Candida krusei)…. Answer: thanks for the suggestion. We changed the names of all species through the text, keeping the current name according to Kidd et al. 2023. This reference is now included. The previous names are also mentioned in the introduction, table 1 and discussion. Keywords antifungal, antimicrobial resistance, artisanal cheeses, Candida, fluconazole. Suggest Yeast species or Candida, Pichia, Meyrozyma, Clavispora, Kluyveromyces Answer: following the reviewer’s suggestion, a keyword was changed. Instead of “Candida” we now include “Pathogenic yeasts” Introduction: … Our study contributes to the little information regarding the epidemiology, ecology and antifungal susceptibility profiles of Candida lambica, Candida krusei, Candida kefyr, Candida lusitaniae, Candida inconspicua, Candida parapsilosis and Candida guillermondii, two of which are part of the recently issued World Health Organization (WHO) fungal priority pathogens list (WHO 2022). Suggest Candida parapsilosis and Pichia kudrizvzeveii (Candida krusei) hight and media priority group, respectively. Answer: following the reviewer’s suggestion, we mention now the priority groups of C. parapsilosis and P. kudrizvzeveii. Methods Isolates Figure 1. Distribution of pathogenic Candida species recovered from artisanal cheeses in Boyacá, Colombia. Suggest Distribution of pathogenic Yeast species recovered from artisanal cheeses in Boyacá, Colombia. Answer: we followed the reviewer’s suggestion and changed “Candida” for “yeasts”. Also, through the text. Antifungal susceptibility testing Was the antifungal test conducted in duplicate? Resistant isolates were found. Answer: thanks to the reviewer for this question. AST was not conducted in duplicate as we followed carefully the manufacturer’s instructions and considered that the colorimetric method is comparable to the CLSI reference method for testing the susceptibility of Candida species, as reported several times. In addition, quality control was ensured by testing the CLSI-recommended quality control strains C. parapsilosis ATCC 22019 and C. krusei ATCC 6258, in each batch of the YeastOne plates. Pichia kudrizvzeveii (Candida krusei) is intrinsically resistant to fluconazole. However, in your study, one isolate was sensitive. Answer: thanks to the reviewer for noticing this. Even though P. kudrizvzeveii has been long recognized as intrinsically resistant to FCZ, we revised the definition of this term in the CLSI manual: “IR is defined as inherent or innate (not acquired) antimicrobial resistance, which is reflected in wild-type antimicrobial patterns of all OR ALMOST ALL representative of a species”. In addition, there are a few publications reporting that some isolates of P. kudrizvzeveii can still have a low MIC to this azole, so not always 100% of the isolates of the species are resistant. Badiee et al 2017 reported ranges of MIC values from 2 to >64 μg/ml, Hrabovsky et al. 2017, ranges from 2 to 256 μg/ml, in a review of Pfaller et al 2006, ranges from 4 to >64 μg/ml and Kaur et al 2020 reported resistance in only 40.5% of the isolates, among other publications. Results …Among the 45 isolates included in this study, seven species of Candida were identified. From these, C. lambica (Pichia fermentans) was the most common species, with 13 (28.9%) isolates, followed by C. krusei (Pichia kudriavzevii) with 11 (24.4%), C. kefyr (Kluyveromyces marxianus) with 10 (22.2%), C. lusitaniae (Clavispora lusitaniae) with five (11.1%), C. inconspicua with three (6.7%), C. parapsilosis with two (4.4%) and C. guillermondii (Meyerozyma guilliermondii) with one (2.2%)… Suggest current name (previous name) Answer: thanks for the suggestion. We changed the names of all species through the text, keeping the current name according to Kidd et al. 2023. This reference is now included. The previous names are also mentioned in the introduction, table 1 and discussion. …To a lesser extent, C. lusitaniae, C. kefyr, C. inconspicua and C. lambica have been identified causing disease in humans. Suggest To a lesser extent, C. lusitaniae, C. kefyr, C. inconspicua and C. lambica have been identified causing invasive fungal infection in humans Answer: the change was done accordingly. Table 2 AND: anidulafungin; MF: Micafungin; CAS: caspofungin; FC: 5-fluorocytosine; PZ: Posaconazole; VOR: Voriconazole; IZ: Itraconazole; FZ: Fluconazole; AB: Amphotericin-B. Suggest MCF: Micafungin; 5FC: 5-fluorocytosine; PCZ: Posaconazole; ITZ: Itraconazole; FCZ: Fluconazole; AMB: amphotericin B Answer: the changes were done accordingly in the text, table 2 and figure. Discussion Update the references. In the discussion, the cited references are very outdated. I suggest using more up-to-date references on the species identified in this study. Answer: thanks to the reviewer for the suggestion. However, we consider that the references are adequate. We added a new reference regarding the nomenclature of Candida." } ] } ]	1	https://f1000research.com/articles/13-789
https://f1000research.com/articles/13-1130/v1	04 Oct 24	{ "type": "Case Report", "title": "Case Report: Spontaneous cornual Pregnancy at 7 Weeks: A Gynecological challenge", "authors": [ "Chayma Cheikh Mohamed", "Asma Korbi", "Ichrak Belghaieb", "Farouk Ennaceur", "Rihab Barouni", "Wassim Khayati", "Marouen Ben Khalifa", "Houssem Haddedi", "Raja Faleh", "Asma Korbi", "Ichrak Belghaieb", "Farouk Ennaceur", "Rihab Barouni", "Wassim Khayati", "Marouen Ben Khalifa", "Houssem Haddedi", "Raja Faleh" ], "abstract": "Introduction and Importance Cornual pregnancy (CP) is a rare and dangerous type of ectopic pregnancy, occurring in 2% to 4% of cases. Due to its atypical location in the uterine horn, it poses a high risk for severe complications, such as rupture of the uterus, and life-threatening bleeding, particularly when diagnosis is delayed.\n\nCase Presentation We report the case of a 35-year-old female patient presenting with severe pelvic pain and vaginal bleeding, with 12 weeks of amenorrhea. Clinical evaluation revealed elevated β-HCG levels and transvaginal ultrasound showed a 7-week unruptured right cornual pregnancy. Surgical management involved a mini-laparotomy, which confirmed the diagnosis and a cornuostomy along with a right salpingectomy was performed. The patient’s postoperative course was uneventful, and follow-up confirmed complete recovery.\n\nClinical Discussion Cornual pregnancies, though rare, carry a significant risk of serious complications and maternal death due to delayed diagnosis. Risk factors encompass a history of miscarriage, elective abortion, sexually transmitted infections, and smoking, all contributing to abnormal implantation. Early diagnosis is challenging but crucial, with ultrasound being key for detection. Management depends on gestational age, patient stability, and future reproductive plans, with methotrexate or surgical intervention being standard options.\n\nConclusion Cornual pregnancy, despite its rarity, demands prompt and accurate diagnosis to prevent catastrophic outcomes. This case underscores the need for individualized treatment strategies and highlights the importance of early intervention. Ongoing research is vital to improving diagnostic approaches and therapeutic outcomes.", "keywords": [ "Cornual pregnancy", "ectopic pregnancy", "case report", "gynecological challenge", "uterine rupture" ], "content": "Case\n\nHerein, we describe the case of a 35-year-old Caucasian female who presented to the Department of Obstetrics and Gynecology with significant vaginal bleeding and severe pelvic pain, suggestive of a potential EP. Her medical history revealed 12 weeks of amenorrhea, no use of contraception, a gravidity status of G3 P2A0, and a uterus with a single cesarean section scar. Additionally, she had a history of appendectomy. The patient is a non-smoker, has no risk-taking behavior, and works as a school teacher. Clinical examination revealed hypotension with a blood pressure of 110/60 mmHg, tachycardia at 110 bpm, and marked hypogastric tenderness. Quantitative β-HCG levels were elevated at 17,000 IU/L, raising suspicion of an abnormal pregnancy.\n\nEndovaginal ultrasound played a critical role in the diagnostic process, demonstrating an unoccupied uterine cavity and a gestational sac positioned laterally on the right side, harboring an embryo with a crown-rump length indicative of 7 weeks of gestation, but with no detectable cardiac activity. The sac was notably eccentrically positioned, surrounded by a myometrial rim, and separated by more than 1 cm from the empty uterine cavity. Ultrasound imaging identified each ovary. Further examination revealed a 3.5 cm unruptured right CP (Figure 1).\n\nGiven the size and location of the EP, surgical management was pursued. A mini-laparotomy revealed a 5 cm unruptured CP on the right side, a critical finding that determined the course of treatment (Figure 2).\n\nA cornuostomy, along with a right salpingectomy, was performed, achieving a definitive resolution of the condition (Figure 3).\n\n\nDiscussion\n\nCornual pregnancy, a rare type of ectopic pregnancy, constitutes approximately 2% to 4% of all EP.1,2 Despite its low incidence, it carries significant clinical risks, particularly due to its potential for uterine rupture and severe maternal morbidity.4 This condition arises from implantation in the cornua, where the fallopian tube meets the uterus leading to distinct diagnostic and treatment challenges. Risk Factors such as spontaneous miscarriages, prior elective abortions, sexually transmitted infections, and smoking can disrupt the normal structure or function of the fallopian tubes and uterus, thereby increasing the likelihood of ectopic implantation.5\n\nDetecting CP early is often difficult, which heightens the risk of serious complications such as bleeding.6 Our case highlights the difficulty of early diagnosis, particularly because CP often mimics normal intrauterine pregnancies in the early stages. Ultrasound remains the primary diagnostic tool, with key indicators being an eccentrically located gestational sac surrounded by a myometrial rim and separated from the uterine cavity by more than 1 cm.7,8 These ultrasound findings were crucial in our case, guiding the timely and appropriate intervention.\n\nManaging this emergency necessitates a tailored strategy that considers several factors, including the patient’s hemodynamic stability, the gestational age of the pregnancy, future reproductive goals, and the surgeon’s level of expertise.8 Treatment options include a spectrum of approaches ranging from methotrexate injections to surgery. Methotrexate, a systemic chemotherapeutic agent, is commonly used in non-surgical management due to its ability to resolve ectopic pregnancies without invasive procedures, at a dose of 1 mg/kg.9 However, in cases like ours, where the gestational sac exceeds 40 mm or where rupture is imminent, surgical intervention is necessary to prevent catastrophic outcomes.10 In our case, a cornuostomy combined with salpingectomy was performed, achieving a definitive resolution of the condition.\n\nEven if it’s rare, the chance of recurrence in CP is still a major concern. Recurrence can lead to more ectopic pregnancies or rupture of the uterus in subsequent gestations, posing significant dangers to maternal safety. Long-term follow-up and patient counseling are essential to monitor for potential complications and to manage future pregnancies safely.11\n\nThis case emphasizes the importance of early detection and personalized management in CP. Imaging advancements and a better understanding of risk factors have improved the prognosis for patients suffering from this uncommon condition. Ongoing research is crucial to refining management strategies and improving prognosis, particularly in the areas of preserving fertility and decreasing the risk of recurrence.\n\n\nConclusion\n\nIn conclusion, CP although rare, poses significant risks due to its potential for rupture and associated maternal morbidity. This case highlights the critical importance of early detection and intervention to prevent life-threatening complications. Tailored management strategies based on patient-specific factors, including gestational age and future fertility goals, are essential. The successful resolution of this case through surgical intervention demonstrates the importance of maintaining a high level of vigilance and taking decisive action when managing similar situations. additional research and advancements in diagnostic strategies will be vital in enhancing patient outcomes and preserving fertility.\n\n\nConsent\n\nWritten informed consent was obtained from the patient for the publication of their clinical details and/or images.", "appendix": "Data availability\n\nAll data supporting the results are included within the article, and no supplementary source data are needed.\n\n\nReferences\n\nJurkovic D, Hillaby K, Woelfer B, et al.: First-trimester diagnosis and management of pregnancies implanted into the lower uterine segment Cesarean section scar. Ultrasound Obstet. Gynecol. 2003; 21(3): 220–227. PubMed Abstract \| Publisher Full Text\n\nHendriks E, Rosenberg R, Prine L: Ectopic pregnancy: diagnosis and management. Am. Fam. Physician. 2020; 101: 599–606. PubMed Abstract\n\nCai X, Fu Y, Hong K, et al.: Cornual pregnancy rupture and massive hemorrhage: A case report. Medicine (Baltimore). 1 déc 2023; 102(48): e36383. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVarun N, Nigam A, Elahi AA, et al.: Cornual Ectopic Pregnancy: Laparoscopic Management Step by Step. BMJ Case Rep. 2018; 2018: bcr2017223998. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGaetani M, Di Gennaro D, Vimercati A, et al.: Cornual Pregnancy. Gynecol. Minim. Invasive Ther. 10 août 2023; 12(3): 130–134. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharma C, Patel H: Ruptured Cornual Ectopic Pregnancy: A Rare and Challenging Obstetric Emergency. Cureus. 15(10): e47842.\n\nTimor-Tritsch IE, Monteagudo A, Matera C, et al.: Sonographic evolution of cornual pregnancies treated without surgery. Obstet. Gynecol. juin. 1992; 79(6): 1044–1049.\n\nToumi D, Medemagh M, Zouari I, et al.: Cornual pregnancy as a rare entity of ectopic pregnancy: A case report. Int. J. Surg. Case Rep. 1 mars 2024; 116: 109364. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLoukopoulos T, Zikopoulos A, Mastora E, et al.: Multidose methotrexate treatment of cornual pregnancy after in vitro fertilization: Two case reports. Case Rep. Womens Health. 14 déc 2021; 33: e00376. Publisher Full Text\n\nDhanju G, Goubran A, Zimolag L, et al.: Distinguishing between cornual, angular and interstitial ectopic pregnancy: A case report and a brief literature review. Radiol. Case Rep. 19 mai 2023; 18(7): 2531–2544. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi S, Cao M, Liu H, et al.: Management of 14 patients with cornual heterotopic pregnancy following embryo transfer: experience from the past decade. Reprod. Biol. Endocrinol. RBE. 6 oct 2021; 19: 152. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "344033", "date": "16 Dec 2024", "name": "David Langley", "expertise": [ "Reviewer Expertise Emergency Medicine", "EMS prehospital 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\n1. Please clearly list your abbreviations \"gravida 3 para... etc\". EP and CP should be clearly described within the case report and not just in the abstract.\n2. Paragraph 2 in the Case, \"Ultrasound imaging identified each ovary.\" Did they identify blood flow? Doppler flow?\n3. In the ultrasound, is there free fluid seen?\n4. After Figure 1, you make the statement \"a critical finding that determined the course of treatment.\" To be more specific, how did this affect the treatment? And if cornuostomy is the answer- what does this term mean? Salpingectomy is probably a common enough term, but try to be on the clearer side.\n5. What was the patient's outcome? How long in the hospital? Follow-up?\n6. In the discussion section, there is some relaxed language like \"Even if it's rare\" I would use more formal terms.\n7. Overall, the discussion could be strengthened with details on the overall mortality of cornual pregnancy as opposed and contrasted with other ectopic (fallopian tube, I presume?)\n8. You state early detection is the emphasis of your case? When is CP usually detected?\n9. Overall, more work is needed in the discussion section, please highlight teaching points, and more background and data on outcomes, please add the outcome for this patient this is very important.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1130
https://f1000research.com/articles/13-1123/v1	03 Oct 24	{ "type": "Case Report", "title": "Case Report: An Integrated Approach To Treating Infected Corneal Laceration With Traumatic Endophthalmitis In Paediatric Age Group", "authors": [ "Prerana A Shetty", "Jashandeep Singh", "Aditya Kapoor", "Sushank Bhalerao", "Prerana A Shetty", "Jashandeep Singh", "Aditya Kapoor" ], "abstract": "This case report presents a case of infected corneal laceration with traumatic endophthalmitis in a pediatric patient. A boy in his middle childhood sustained an ocular injury with scissors, resulting in a full-thickness corneal laceration and infection. Despite the delay in seeking treatment, the patient underwent successful surgical interventions, including corneal scraping, pars plana lensectomy, vitrectomy, and secondary intraocular lens implantation (IOL). The infection was managed with targeted antibiotics, and Staphylococcus aureus was confirmed as the causative organism. Remarkably, these efforts led to a satisfactory improvement in the patient’s vision to 20/50. This case underscores the importance of early intervention and a multidisciplinary approach in the management of pediatric ocular trauma to optimize outcomes.", "keywords": [ "Corneal tear", "infected corneal tear", "endophthalmitis", "secondary IOL", "contact lens", "BSS (BostonSight Scleral) contact lens" ], "content": "Introduction\n\nOcular trauma is an important cause of unilateral vision loss worldwide, especially in young people, and surgical repair is almost always challenging. The successful surgical repair of open globe injury and the subsequent visual rehabilitation of the patient – a topic of great significance and challenge to the practicing ophthalmologists.1,2 Vats et al reported the prevalence of ocular trauma to be 2.4% of the urban population in India. It is the second most common cause of corneal blindness in children.2 Corneal laceration and corneal perforation are common ocular traumas with potentially devastating sequelae, including corneal scarring, astigmatism, and endophthalmitis.3 There is very little literature on management of an infected corneal laceration.\n\nThe reported incidence of endophthalmitis in the absence of an intraocular foreign body following an open globe trauma range from 3.1% to 11.9%, of which the paediatric population constitutes 22% to 34.5% cases. The visual prognosis in traumatized eyes with endophthalmitis is extremely poor and worse than that of post operative endophthalmitis.4 Thus ophthalmologists should maintain a high index of suspicion for infection in open globe trauma. They should ensure a prompt management strategy to achieve an optimal anatomic and visual outcome.\n\n\nCase report\n\nIn this case, a boy in his middle childhood sustained an injury to his right eye while playing with scissors. He was taken to a local doctor who prescribed topical medications and then consulted with us two days after the injury. At presentation, his visual acuity was perception of light with an inaccurate response to the projection of rays. A detailed slit lamp examination was performed, and a gentle B-scan was conducted. The examination revealed a full-thickness infected corneal laceration with iris tissue incarceration measuring about 6 mm. Additionally, there were hypopyon and exudates in the anterior chamber. A yellowish tinge in the lens suggested an intralenticular abscess (Figure 1). On B-scan ultrasonography mild to moderate reflective echoes were observed in the posterior aspect of the vitreous cavity suggestive of traumatic endophthalmitis (Figure 2). After the initial treatment with oral antibiotics and analgesics (Amoxicillin+ clavulanic Acid 325 mg with ibuprofen + paracetamol as 15 mg/kg/ml dose), the patient underwent corneal scraping, corneal laceration repair, along with vitreous biopsy, pars plana lensectomy was done. The vitreous cavity was filled with whitish membranous exudates and vitrectomy to the extent safely possible was done and intravitreal antibiotics were administered. The microbiology reports later came out to be positive for the obtained vitreous sample and the organism was confirmed to be Staphylococcus aureus on culture. In addition, three doses of intravitreal injections (vancomycin 1 mg/0.1 ml, Ceftazidime 2.25 mg/0.1 ml and Dexamethasone 0.4 mg/0.1 ml) were administered at 48-hour intervals during initial visits. The patient was closely monitored, and intravitreal antibiotics were repeated, followed by vitreous lavage and complete lensectomy. In four months, with topical medications, surgical interventions, and timely follow-up, he recovered completely from microbial keratitis as well as endophthalmitis. Subsequently, the corneal sutures were removed, and he was scheduled for secondary IOL implantation and a three piece hydrophobic acrylic foldable IOL (Acrysof, Alcon laboratories, Inc). His final visual acuity was 20/50 with BSS (BostonSight Scleral) contact lens, which was considered satisfactory (Figure 3, and Figure 4a and b).\n\n\nDiscussion\n\nThe cornea is an optical surface and requires special treatment to preserve visual acuity during open globe injury repairs.5 Although the time lag between injury and surgery adversely affects the final vision outcome, this is not statistically significant. Issac et al. demonstrated a 1.16-fold increase in the chance of a worse visual prognosis with each day of delayed surgery.6 Our case emphasizes the potential consequences of delayed treatment, underscoring the significance of prompt medical attention for optimizing visual outcomes.\n\nSeveral cases reported by Salman et al.7 and Henry et al. involved lenticular abscess following penetrating injury. Similar to our case, both Henry et al and Salman et al. reported a positive culture for Staphylococcus species.8 In a study by Rajaraman et al., a variety of organisms causing lens abscess were found, with Staphylococcus epidermidis being predominant.9\n\nIn paediatric post traumatic endophthalmitis, the factors affecting visual prognosis have not been extensively analysed especially when there is a concurrent intralenticular abscess. Dave et al, underscored the role of an initial intervention of vitrectomy over a limited vitreous biopsy in attaining a good visual outcome in the management of lens abscess with concurrent endophthalmitis.9 A lens abscess presents distinct challenges compared to infections in other parts of the eye, as the infective organisms are trapped within the avascular, protein-rich environment of the lens. In such cases, surgical removal of the entire infected area is essential. This not only eliminates the majority of the infectious agents but also allows intraocular antibiotics to penetrate and act more effectively. It has also been suggested that the relative softness of the crystalline lens in younger individuals, due to the absence of nuclear sclerosis, facilitates the faster spread of infection across the lens and into the vitreous cavity.10\n\nThe visual outcomes in our current case parallel those documented in other reports concerning posttraumatic endophthalmitis.5 Prompt visual rehabilitation in these children, combined with effective amblyopia management, can significantly enhance their visual acuity and overall quality of life. Various optical correction options are available, including spectacles, contact lenses, and intraocular lens (IOL) implantation. In cases where children or their parents are reluctant to opt for glasses or contact lenses, secondary IOL implantation may serve as a viable alternative. In our case, we visually rehabilitated the child with a secondary IOL followed by a BSS contact lens to achieve satisfactory visual improvement.11\n\nThis case highlights the challenging nature of managing such cases, where successful management necessitates a combination of careful clinical evaluation, advanced surgical techniques, and tailored treatment plans to optimize visual recovery.\n\nEthical approval were not required.\n\n\nConsent\n\nWritten informed consent for the publication of the case report and any associated images was obtained from the patient prior to submission.", "appendix": "Data availability\n\nNo data are associated with the article.\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAcknowledgements\n\nNone.\n\n\nReferences\n\nDandona R, Dandona L: Corneal blindness in a southern Indian population: need for health promotion strategies. Br. J. Ophthalmol. 2003 Feb; 87: 133–141. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVats S, Murthy GV, Chandra M, et al.: Epidemiological study of ocular trauma in an urban slum population in Delhi, India. Indian J. Ophthalmol. 2008 Jul-Aug; 56: 313–316. PubMed Abstract \| Publisher Full Text\n\nZhang T, Jia Y, Li S, et al.: Individualized corneal patching for treatment of corneal trauma combined with tissue defects. J. Ophthalmol. 2020; 2020: 8437479.\n\nBhagat N, Nagori S, Zarbin M: Post-traumatic Infectious Endophthalmitis. Surv. Ophthalmol. 2011 May-Jun; 56: 214–251. Publisher Full Text\n\nZhou Y, DiSclafani M, Jeang L, et al.: Open Globe Injuries: Review of Evaluation, Management, and Surgical Pearls. Clin. Ophthalmol. 2022 Aug 10; 16: 2545–2559. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIssac DL, Ghanem VC, Nascimento MA: Prognostic factors in open globe injuries. Ophthalmologica. 2003; 217: 431–435. Publisher Full Text\n\nSalman A, Parmar P, Philip VR, et al.: Traumatic intralenticular abscess: a case series. Clin. Experiment. Ophthalmol. 2007; 35: 252–255. PubMed Abstract \| Publisher Full Text\n\nHenry MM, Reny A, Raspiller A: Abces traumatique du crystallin. Bull. Soc. Ophthalmol. Fr. 1969; 69: 648649.\n\nRajaraman R, Lalitha P, Raghavan A, et al.: Traumatic lenticular abscess: clinical description and outcome. Am. J. Ophthalmol. 2007; 144: 144–146. PubMed Abstract \| Publisher Full Text\n\nDave VP, Ramamurthy S, Das AV, et al.: Clinical Presentations, Microbiology, And Factors Affecting Management Outcomes In Lens Abscess With Concurrent Endophthalmitis. Retina. 2022 Jun 1; 42: 1137–1143. PubMed Abstract \| Publisher Full Text\n\nAhmed Y, Schimel AM, Pathengay A, et al.: Endophthalmitis following open-globe injuries. Eye (Lond.). 2012 Feb; 26: 212–217. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "334970", "date": "09 Nov 2024", "name": "Sara Hernández Santamaría", "expertise": [ "Reviewer Expertise Ophtalmology" ], "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 us a vision of how to treat a complex case of traumatic endophthalmitis since the request for attention by ophthalmology is late, and he is also a paediatric patient.\nIt presents a case of a boy un his middle childhood with a full thickness corneal laceration secondary to a trauma with scissors. The patient went to the ohtalmologist two days after the trauma, with infiltrated corneal laceration, an intralenticular abscess and secondary endophthalmitis. The patient required several surgeries, all of them successful, and oral antibiotic and topical treatment.\nIn my opinion, the case is described in its entirety with sufficient detail, both in the examination, and in the diagnosis and treatment. To improve, I would simply specify what kind of topical treatment was administered to the patient, if necessary reinforced antibiotic eye drops, and exactly what antibiotics were administered topically. Regarding the systemic treatment administered, it is not well specified if it was only oral antibiotic treatment or if it was also administered intravenous treatment, it would be convenient to clarify this point.\nAs for the discussion of the case, I consider that it is sufficient and very clear, facilitating the understanding and relevance of the pathology, as well as its diagnosis and treatment.\nIt is an interesting case, which I consider can be very useful for other professionals.\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": [] } ]	1	https://f1000research.com/articles/13-1123
https://f1000research.com/articles/12-966/v1	10 Aug 23	{ "type": "Research Article", "title": "Community preventive behaviour and perception on the severity of COVID-19 disease in Indonesia, 2021-2022: Structural equation modelling", "authors": [ "Tris Eryando", "Tiopan Sipahutar", "Sandeep Poddar", "Tiopan Sipahutar", "Sandeep Poddar" ], "abstract": "Background: This study investigated the determinants of community preventive behavior in complying with the Indonesian regulations to prevent COVID-19 local transmission. Methods: A cross-sectional study used to collect the data via an online cross using a form created from a google questionnaire forms. A total of 1,802 respondents were gathered at a single point in time. The authors used the Health Belief Model (HBM) approach to measure and create a model of preventive behavior for COVID-19. Results: The findings showed that self-efficacy and perceived barriers had statistically significant relationships with preventive behavior. However, the goodness of fit index showed that the proposed model was not fit for the data, which means that it was not fit to describe the empirical phenomenon under study. Conclusions: This study found that more than half of the respondents still had low perceived susceptibility and severity. Only a few respondents had significant barriers to implementing COVID-19 transmission prevention behaviors. Still, most respondents had low perceived self-efficacy, and only 60% had good behaviors related to COVID-19 prevention. We recommended increasing perceived susceptibility and severity by providing the correct information about COVID-19 in the local cultural context.", "keywords": [ "COVID-19", "perceive", "preventive behavior", "Health Belief Model", "Indonesia" ], "content": "Introduction\n\nThe world is currently besieged by the COVID-19 pandemic.1 As of February 7, 2022, there were 394,381,395 confirmed cases of COVID-19, with the World Health Organization (WHO) reporting 5,735,179 deaths.2 The COVID-19 pandemic in Indonesia from mid-2021 until the end of 2021 reached its peak (second wave) when it was dominated by the Delta variant.\n\nCOVID-19 prevention regulations largely depend on community compliance and behavior. While changing behavior is a significant challenge in health interventions. An AC Nielsen survey (2020) in six major cities with a total of 2,000 respondents, in collaboration with the United Nations International Children’s Emergency Fund (UNICEF), found that less than one-third (31.5%) of all respondents practiced all three-preventive activities (wearing masks, washing hands, and social distancing). Over one-third (36%) practiced only two of the three-preventive behaviors, less than one-fourth (23.2%) practiced only one of the three behaviors, and almost one-tenth (9.3%) did nothing at all.3 A number of studies described the associations between socio-demographic characteristics and people’s levels of perceptions about the severity of COVID-19 with their preventive behavior.3–10\n\nBased on the official government report (see https://covid19.go.id/monitoring-kepatuhan-protokol-kesehatan), some areas of Indonesia showed a compliance rate of only 60% till January 2022.11 The aim of this study was to examine changes in community behaviour to prevent local COVID-19 transmissions and changes in community perceptions about the severity level of COVID-19. The following research questions were formulated: 1) What constitutes as the community perceptions of COVID-19? 2) Is there an association between community perception and community preventive behaviour using the Health Belief Model (HBM) approach? And 3) what kind of model of preventive behaviour on COVID-19 can be predicted using the structural equation model (SEM)?\n\n\nMethods\n\nThis was a cross-sectional study using Google forms with structured survey questionnaires. The questionnaires have been tested with 30 respondents before the survey was conducted. The proportion of a large population was used to figure out the sample size for a variable, which was used to figure out the minimum sample size.12 The margin error=5%, p=50%, and Zα=95%. The minimum sample size for this study was 385 respondents. The data collection was conducted over two weeks from July 14–26, 2021, using WhatsApp, Line, and Telegram. To expand the coverage throughout Indonesia, social media influencers were asked to distribute the survey through Twitter and Instagram. The respondents who participated in this study were aged 15–62 and Indonesian citizens. On average, it took 20–25 minutes to complete the form. Respondents signed informed consent forms before completing the survey. The total final number of respondents was 1,802.\n\nThe HBM was employed as a primary reference to measure perception and preventive behavior on COVID-19. The HBM considers several main concepts that predict why people will take action to prevent, including individual characteristics, perceived susceptibility, severity, benefit, and self-efficacy.13 This study consisted of 45 observed variables and six latent variables.\n\nIndividual characteristics were represented by residence (R), age (A), gender (G), educational level (E), and occupation (O). Perceived susceptibility, severity, benefit, barriers, and self-efficacy are latent variables in this study. All questions in in the questionnaire in each latent variable were answered using a five-point Likert scale: 1 (strongly disagree), 2 (disagree), 3 (neutral), 4 (agree), and 5 (strongly agree). Observed variables X1-14, S1-5, BEN1-5, BAR1-5, and SE1-5 were used to measure perceived susceptibility, severity, benefit, barriers, and self-efficacy, in that order.\n\nCommunity preventive behavior was represented by six indicators in Figure 1 which include frequency of hosting (BHV1), frequency of visiting others (BHV2), frequency of work/study from office/school (BHV3), frequency of handshaking (BHV4), frequency travelling to a red zone (BHV5), and frequency of leaving the house when you are not feeling well (BHV6).\n\nStructural equation modelling (SEM) is a multivariate statistical analysis technique that is used to analyze structural relationships. This technique is the combination of factor analysis and multiple regression analysis, and it is used to analyze the structural relationship between measured variables and latent constructs. The authors used Lisrel version 8.8 software to construct the covariance-based SEM. SEM analysis can also be done using R. Steps of doing SEM analysis using R as follows15:\n\na. Draw model\n\nb. Input data in the form of covariance or correlation matrix\n\nc. Identify the model\n\nd. Assess parameter estimates\n\ne. Assess fit measure (chi-square, degree of freedom, residual matrix, GFI, RMSEA)\n\nf. Check the modification indices\n\ng. Rerun the model till we get the best fit of the data to the model ad theory.\n\nThe six latent variables were perceived susceptibility, severity, benefit, barriers, self-efficacy, and preventive behavior. The 45 observed variables were presented in Table 1 include construct that build by all the observed variables.\n\n\n\n1. City\n\n2. Village\n\n3. Housing area\n\n4. Apartment\n\n\n\n1. Male\n\n2. Female\n\n\n\n1. No education\n\n2. Elementary school\n\n3. Junior high school\n\n4. Senior high school\n\n5. University\n\n\n\n1. Unemployment\n\n2. Labourer/employee\n\n3. Student/college\n\n4. Housewife\n\n5. Entrepreneur\n\n6. Pensionary\n\n7. Others\n\nDescriptive statistics were presented as numbers and percentages for individual characteristics, and bar charts for perceptions and behavior. Descriptive statistical analysis was performed using IBM Statistical Package for the Social Sciences (SPSS) version 27 and presented using Microsoft Excel. The descriptive analysis simply can also be completed using Microsoft Excel. The SEM analysis was carried out using the following steps:\n\n1) Identifying the degree of freedom of the structural model.\n\n2) Assessing construct validity.\n\n3) Assessing construct reliability.\n\n4) Assessing structural model validity.16,17\n\nPerceived was categorized based on the total score. Good/high perceived were those who chose to “strongly agree” on every question. Regarding behavior, good behavior occurs if the respondent states never or rarely. Rarely was included in the category based on the assumption that people might be challenged to practice preventive behavior related to other factors that require them to leave, such as the environment or critical social activities that cannot be abandoned.\n\n\nResults\n\nThe study results are presented in several parts sequentially, starting with the respondent’s characteristics, followed by the descriptive statistics of the independent variable (community perception of the level of severity of COVID-19 disease), the descriptive statistics of the dependent variable (composite variable of community behavior), and the SEM analysis results.\n\nMost of the respondents lived in the city (46.1%) and a housing area (36.1%), and only a few lived in villages (16.6%). A large majority of the respondents were women (74.5%), and approximately 80.0% were students and workers (Table 2).\n\nIn terms of perceived susceptibility (Table 3), more than half of respondents (>50%) chose to strongly agree to practice recommended behaviors such as social distancing at least 1-2 meters in public areas; almost half of them strongly agree that they had a low risk of getting COVID-19 when avoiding using public transportation, practicing work/study from home, handshaking, and travelling to a red zone. Most respondents also strongly agree that if they are exposed to COVID-19, it will affect their health if they do not practice recommended behaviors. Likewise, concerning perceived benefit, more than 50% of respondents strongly agree that they can avoid getting COVID-19 if they practice these behaviors. In terms of perceived barriers, less than 20% felt that it would be challenging to implement the recommended behaviors. Regarding self-efficacy, this is defined as the conviction that one can successfully practice a certain behavior,13 the survey showed that less than 50% were confident that they could implement the recommended behavior.\n\nFor each type of recommended behavior as mentioned in Table 1 to prevent the transmission of COVID-19, more than 50% of respondents never and rarely hosted, visited others, worked from the office/school, shook hands, travelled to a red zone, and left the house when not feeling well (Figure 1).\n\nBased on the composite of each perceived item, it was found that only 16% of the respondents had a high percentage of good perceived susceptibility; perceived severity was 43%, perceived benefit was 54%, perceived barrier was 3%, self-efficacy was 19%, and only 60% of respondents practiced good behaviours.\n\n\nSEM results\n\nThe second step in SEM analysis is to run the identification of observed variables. A general requirement for identifying any type of model in SEM are the model’s degrees of freedom which must be a least zero (dfM ≥ 0). Hence, the solution to meet the requirement is to identify whether the model is under identified, just identified, or overidentified. Overidentified is mandatory in order to meet the requirement. An overidentified structural equation model is identified and has more observations than free parameters (dfM>0)(2). In this study, we found the degree of freedom value to be 821, hence it was concluded that the model was over-identified. Thus, the next step of the analysis can be completed.\n\nConstruct validity was performed to test whether the instrument or measurement variable could describe the latent variable correctly and precisely. For this, two tests were conducted: validity, which consisted of convergent and discriminant validity, and reliability.14 A convergent validity test examined the loading factor value of the measurement variable in each latent variable construct. If the loading factor value was greater than 0.50, the latent variable construct had good convergent validity.14 The results of the convergent validity test showed that almost all items in this study had a loading factor value of more than 0.5, except for items X11 and BHV3. These two items have a loading factor of ≤ 0.5, which indicates that they do not meet the criteria for convergent validity. Hair et al. (2019) stated that items with low loading factors that do not meet the limits of convergent validity should be excluded from the measurement of latent variables. Therefore, items X11 and BHV3 in this study were not included in the measurement of the latent variable. The convergent validity test was then carried out for a second time. All of the items had good convergent validity, which was shown by loading factor values of more than 0.5. The discriminant validity test was carried out by comparing the root value of each latent variable’s average variance extracted (AVE) with the correlation of these latent variables with other latent variables. If the root value of the variable AVE was greater than the correlation of the variable with other variables in the model, the indicator/question item had good discriminant validity.\n\nTable 4 shows the AVE root value for each latent variable and the correlation coefficient between the latent variables. The value of the AVE root is shown as the value on the diagonal of the matrix, while the values beside and below the AVE root are the correlation coefficients between two pairs of variables. The results of the evaluation of discriminant validity show that the root value of AVE in each latent variable is greater than the correlation coefficient of the latent variable with other latent variables in the structural model. Thus, it can be stated that the items/instruments in this study have good discriminant validity.\n\nThe construct reliability test was done by examining the composite reliability value. If the combined reliability value is greater than 0.7, it can be said that the variables in the study already have reliable indicators/question items.16 All latent variables were found to have a composite reliability value of more than 0.7, which means that each variable has a consistent measurement indicator and good internal consistency.\n\n\nStructural model validity\n\nTwo analyses were conducted to evaluate the structural model validity:1) dependency test and 2) assessing the goodness-of-fit of the model.\n\nThe dependence relationship test was employed by looking at the path coefficient and its p-value in the structural model. The path coefficient shows the magnitude and direction of the relationship between the two variables. According to Table 5, sex had a statistically significant relationship with perceive susceptibility; perceive susceptibility had a statistically significant relationship with perceive severity; age, sex, and education had significant relationships with perceive benefit; perceive benefit, resident, and sex had a significant relationship with perceive barrier; and perceive barrier and occupancy had a significant relationship with perceive self-efficacy. Regarding behavior, only perceived barriers and self-efficacy had statistically significant relationships with COVID-19 prevention behavior. The final structural model is as follows: behaviour = - 0.018susceptibility - 0.041severity - 0.00045benefit + 0.39barrier - 0.13*self-efficacy.\n\nThe goodness-of-fit model assessment results in Table 6. showed that none met the goodness-of-fit criteria. Therefore, the structural model in this study was not a fit for the data and was not a fit for describing the empirical phenomenon under study.\n\n\nDiscussion\n\nThe results of grouping all perceived items showed that only a few respondents (16%) had beliefs about the chances of experiencing COVID-19 (perceived susceptibility), but 43% of respondents believed how serious the COVID-19 effects were on their health. More than half of the respondents believed that the recommended behaviors to prevent COVID-19 infection could protect them from getting an infection (perceived benefit). Only 3% of respondents believed some things hindered the practice of recommended behaviors (perceive barrier), and only 19% believed that they could practice the recommended behaviors (perceive self-efficacy). This study’s results are similar to those conducted in India, Sri Lanka, Iran, and Ethiopia.8,10,18,19 The HBM theory holds that people are likely to practice preventive behaviors or actions if: 1) They believe that it will reduce their risks,13 2) They believe themselves to be susceptible to COVID-19 infection, 3) They believe that this condition would have a potentially serious impact, 4) They believe that recommended actions/behaviours would be beneficial in reducing their susceptibility to or severity of the virus infection, and 5) They believe that the anticipated benefits of doing preventive behaviours/actions outweigh the barriers.\n\nPerceived susceptibility was not a significant predictor of behavior in this study. This finding is consistent with studies that measured adherence to COVID-19 precautionary measures in China20 and Korea.21,22 A study that used a HBM framework to look at how Saudi Arabian students at Jazan University felt about the COVID-19 vaccine found that perceived susceptibility was not a good predictor of how they felt about getting the vaccine.23 However, a similar study conducted in Malaysia found that high perceived susceptibility to COVID-19 infection was also associated with the behavior of vaccination intention.24 A study that measured student behavior in the US related to non-pharmaceutical interventions (hand washing with soap and water, use of hand sanitizer, wearing a face mask in public, and practicing social distancing) found that perceived susceptibility was associated with multiple interventions more frequently.25\n\nA previous study conducted by Du Min et al. found that low perceived risk was associated with vaccine hesitancy.26 As with perceived susceptibility, perceived severity was not a significant predictor of preventive behavior in this study. Several studies regarding behavior change using BHM had similar results.22,24,25 Perceived severity, on the other hand, was a significant predictor of preventive behaviors.8,20–23,27 Perceived benefit is one predictor that is not a significant predictor of preventive behavior. This finding is inconsistent with several studies that used BHM to predict behavior change, particularly in relation to COVID-19 prevention.8,20,21,23–27\n\nThis study revealed that the perceived barrier was a significant predictor of COVID-19 preventive behaviour. This result is different from a behaviour study conducted in Sri Lanka and Iran, which found that perceived benefit and self-efficacy had a significant positive relationship to COVID-19 prevention behaviour.10,28 However, these results were similar to a study conducted in Ethiopia that measured student eating behaviour using the HBM theory in the US29 and other behavioural studies in Iran, India, and Hong Kong.8,19,30 This study also found that perceived self-efficacy was a significant predictor of COVID-19 preventive behaviour. The results show that, with lower self-efficacy, people were likely to practice COVID-19 prevention behaviour. This result is similar to several studies that examined behaviours using the BHM theory. Those studies found that perceived self-efficacy has a significant relationship to behaviour.10,18,19,21,28,31 In contrast, a study that assessed the student’s behaviour on the non-pharmaceutical intervention of COVID-19 found that perceived self-efficacy was not a significant predictor of behaviour change. In theory, an individual with good self-efficacy tends to practice recommended action/behaviour,13 which is the preventive behaviour of COVID-19. However, this study was unable to confirm these findings.\n\nThe findings in this study illustrated that most respondents (97%) had no barriers to practising the recommended behaviour. Still most respondents (81%) were not confident that they could fully implement the recommended prevention behaviours. As many as 60% of respondents practised COVID-19 prevention behaviour well. In knowledge attitude practice (KAP) studies conducted in Indonesia, this finding (percentage of good behaviour) tended to be lower than the other two findings in Indonesia, where the rate of those who performed the correct behaviour for the prevention of COVID-19 was more than 90%.32,33 Studies conducted in other countries also found that respondents who practised COVID-19 prevention behaviours were relatively high (>70%), such as in China, Nepal, Malaysia, Vietnam, and India.34–38\n\nFundamentally, perceived susceptibility and severity affect how a person decides to act.13 However, most respondents (84%) had low perceived susceptibility in this study. This means that most respondents did not believe that they were also at risk of being affected by COVID-19. This perception represented an obstacle for someone to implement recommended behaviour. It was also known that only 43% believed that if they were infected with COVID-19, they would experience harmful consequences for their bodies. Only half of the respondents believed that the recommended behaviour was able to protect them from COVID-19. This might relate to the information they obtained day-to-day. It was possible that most of them did not have a clear idea about the pathophysiology and epidemiology of COVID-19, made worse by unreliable news or hoaxes circulated on social media, which may have increased negative perceptions about COVID-19.8,39\n\nRegarding obstacles to implementing the recommended behaviour, a few respondents said it was extremely difficult to implement the behaviours (3%). This overall perception then leads to a low belief that respondents are able to implement the recommended behaviour. As a consequence, it will affect COVID-19 prevention behaviour practice. Perception is theoretically influenced by many factors, including demographics and level of knowledge.8,10,13,18,32,33 A study conducted in China found that knowledge was influenced by educational level and domicile.34 Good knowledge can form a good attitude, which then creates a good perceived.40,41 COVID-19 was a pandemic that touched almost every facet of human existence. People had to adjust their daily routines to accommodate local government rules in order to reduce the virus transmission, and these behavioural shifts may last long after the disease has passed.42 Increasing the respondents’ knowledge is essential to narrowing the gap between knowledge and practice, including myths, hoaxes circulating about COVID-19, and facts. Several important factors that may affect perceived self-efficacy are related to social norms and trust43 in the community. Unfortunately, neither of these factors (including knowledge) was investigated in this study.\n\nThe structural model of COVID-19 prevention behaviour in this study was not intended to describe the empirical phenomenon of preventive behaviour. Byrne stated that, if possible, researchers are advised to modify the model by using modification indices (MI) in SEM testing. He said that models with an MI score of more than 10 deserve attention for modification.44 Already it has proved that to confront the increase in demand for care, the need for long-term care workforce, and the costs associated with care.45 However, Hair et al. suggested that modifying the model should not change the model’s structure significantly.16\n\nThis several studies found a gap in knowledge to inform changes in policies on infection-prevention measures in the community, community infection procedures, the frequency of testing, etc.8,39,46 The unreliable information may increase the negative perception of COVID-19, leading to the community’s obedience to suggested preventive behaviors.39 Moreover, people are more worried about their families and economic conditions due to the spreading pandemic than about complying with lockdown or restriction policies. Several factors that might be related were not examined in this study, such as level of knowledge, social norms, or trust.\n\nDue to the social restrictions (the outdoor community activities are limited by the government based on the law announced every two weeks except for emergency purposes) in Indonesia, the data collection was conducted using a Google form without using a selected sampling method. Thus, the total number of respondents in this study was not representative of the total population in Indonesia and the entire territory of Indonesia. In addition, the entire population of Indonesia did not have the same opportunity to be selected as respondents due to limitations related to internet coverage and utilities. Since the prevalence and impact of COVID-19 are changing dramatically, across-sectional studies were not the best method for describing the changes. Better results might be possible using a longitudinal study.\n\n\nConclusions\n\nThis study found that more than half of the respondents still had low perceived susceptibility and severity, but more than half had high perceived benefits. Only a few respondents had significant barriers to implementing COVID-19 transmission prevention behaviors. Still, most respondents had low perceived self-efficacy, and only 60% had good behaviors related to COVID-19 prevention.\n\nThe results of this study can assist policymakers in developing health interventions related to the preventive behavior of COVID-19 transmission in the community. We recommend increasing perceived susceptibility and severity by providing the correct information about COVID-19 in the local cultural context. The results of this study can also be used as a reference for evidence-based policies so that the government can prioritize the types of interventions to improve public understanding and compliance to prevent the transmission of COVID-19.\n\nThe findings of similar studies conducted in other countries showed some consistency. By improving perceived susceptibility and severity, there would be an increase in respondents’ knowledge, increasing perceived susceptibility and severity. The results of this study can, not only be used for COVID-19 prevention policies but can also be used as a reference in making prevention policies against many types of diseases that require community behavior changes. Therefore, when making policies, there are stages that must first be met so that behavior can change, as described in the results of this study.\n\n\nEthics approval and consent to participate\n\nThe Commission approved this study for Research Ethics and Public Health Service, Faculty of Public Health, University of Indonesia Number: Ket-436/UN2.F10. D11/PPM.00.02/2021.\n\n\nConsent for publication\n\nInformed consent was obtained from all subjects involved in the study.\n\n\nAuthor contributions\n\nAll authors made substantial contributions to this research and approved the final manuscript. TE and TS contributed to every step of the study (research concept, design, data interpretation, writing, and review). SP contributed to the research review.", "appendix": "Data availability\n\nDyrad. Data for: Community perception and COVID-19 prevention, https://doi.org/10.5061/dryad.pnvx0k6rp. 47\n\nThis project contains the following underlying data:\n\n• DATA_FINAL_tio-edit2.csv (Data include all variables in the questionnaire. The data contain 1802 respondents and 89 variables. The variable names of questions 1–23 were given according to the keyword in each question, while the variable names for question number 24–35 were specified according to the question’s number and its answer option. It is recommended to read the variable code definition in sheet 2 and the area code in sheet 3.)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nFigshare. IMPLEMENTATION OF SOCIAL POLICY DISTANCING IN EFFORT PREVENTION COVID-19 IN INDONESIA. https://protect-us.mimecast.com/s/qsa7CkRwomfYPpGvjC2JN1U?domain=doi.org 14\n\nThis project contains the following supplementary material:\n\n• Kuesioner Penelitian.pdf (the google questionnaire used in this study), https://doi.org/10.6084/m9.figshare.23292686.v2. 48\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 are grateful to Prof. Dr. Dewi Susanna, dra, MS., who facilitated and supported the research process, and Universitas Indonesia for financial support. We also thankful to all respondents who were willing to involve in this study by signing the informed consent prior to answer all the questions.\n\n\nReferences\n\nBhattacharya S, Basu P, Poddar S: Changing epidemiology of SARS-CoV in the context of COVID-19 pandemic. J. Prev. Med. Hyg. 2020; 61(2): E130–E136. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: WHO Coronavirus (COVID-19) Dashboard.2022. Accessed 8 February 2022. Reference Source\n\nIndonesia TF of C-19: Distribution Map of COVID-19 Indonesia.2022. Accessed 8 February 2022. Reference Source\n\nOrganisation WH: Advice for the public: Coronavirus disease (COVID-19). World Health Organization; 2021. Accessed 8 February 2022. Reference Source\n\nMinister of Home Affairs of the Republic of Indonesia: Regulation of (the) Minister of Home Affairs of Republic Indonesia. 2021; Vol. 4: pp. 1–2.\n\nTask Force of COVID-19 Indonesia. Memahami Perilaku dan InformasiTepatuntukMencegah Penularan COVID-19. Covid19.Go. Id. 2020. Accessed February 8, 2022. Reference Source\n\nTask Force of COVID-19 Indonesia: Monitoring of Health Protocol Compliance.2021. Accessed 8 February 2022. Reference Source\n\nNguyen NPT, Hoang TD, Tran VT, et al.: Preventive behaviour of Vietnamese people in response to the COVID-19 pandemic. PLoS One. 2020; 15(9 September): 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLim JW, Gonzalez P, Wang-Letzkus MF, et al.: Understanding the cultural health belief model influencing health behaviours and health-related quality of life between Latina and Asian-American breast cancer survivors. Support Care Cancer. 2009; 17(9): 1137–1147. PubMed Abstract \| Publisher Full Text\n\nClark C, Davila A, Regis M, et al.: Predictors of COVID-19 voluntary compliance behaviours: An international investigation. Glob. Transitions. 2020; 2: 76–82. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJewell NP: Predictive Mathematical Models of the COVID-19 Pandemic Underlying Principles and Value of Projections. Am. Med. Assoc. J. 2020; 323(19): 1893–1894. Publisher Full Text\n\nJose R, Narendran M, Bindu A, et al.: Public perception and preparedness for the pandemic COVID 19: A Health Belief Model approach. Clin. Epidemiol. Glob. Heal. 2021; 9(9): 41–46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPurnama SG, Susanna D: Attitude to COVID-19 Prevention with Large-Scale Social Restrictions (PSBB) in Indonesia: Partial Least Squares Structural Equation Modeling. Front. Public Health. 2020; 8(October): 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSusanna D, Widyamurti W, Eryando T: Implementasi Of Social Policy Distancing In Effort Prevention COVID-19 In Indonesia. figshare. Journal Contribution. 2023. Publisher Full Text\n\nBasu A: Structural equation modelling with lavaan: a tutorial and an intuitive introduction.2021 [cited 2023 Jun 20]. Reference SourceReference Source\n\nMahindarathne PP: Assessing COVID-19 preventive behaviours using the health belief model: A Sri Lankan study. J. Taibah Univ. Med. Sci. 2021; 16(6): 914–919. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGlanz K, Rimer B, Viswanath K: Health Behavior and Health Education. COT, editor. Fourth Ed.John Wiley & Sons, Ltd.; 2008.\n\nRea LM, Parker RA: Designing and Conducting Survey Research. A Comprehensive Guide. Jossey-Bass A Wiley Brand; 2014.\n\nHair JF, Anderson RE, Tatham RL, et al.: Multivariate Data Analysis. Eighth Ed.Annabel Ainscow; 2019.\n\nKline RB: Principles and Practice of Structural Equation Modelling. Fourth Ed.The Guilford Press; 2016.\n\nTadesse T, Alemu T, Amogne G, et al.: Predictors of coronavirus disease 2019 (Covid-19) prevention practices using health belief model among employees in Addis Ababa, Ethiopia, 2020. Infect. Drug Resist. 2020; 13: 3751–3761. Publisher Full Text\n\nShahnazi H, Ahmadi-Livani M, Pahlavanzadeh B, et al.: Assessing preventive health behaviors from COVID-19: a cross-sectional study with health belief model in Golestan Province, Northern of Iran. Infect. Dis. Poverty. 2020; 9(1): 157–159. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTong KK, Chen JH, Yu EY, et al.: Adherence to COVID-19 Precautionary Measures: Applying the Health Belief Model and Generalised Social Beliefs to a Probability Community Sample. Appl. Psychol. Heal. Well-Being. 2020; 12(4): 1205–1223. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim S, Kim S: Analysis of the impact of health beliefs and resource factors on preventive behaviors against the Covid-19 pandemic. Int. J. Environ. Res. Public Health. 2020; 17(22): 1–21. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPark JH, Cheong HK, Son DY, et al.: Perceptions and behaviors related to hand hygiene for the prevention of H1N1 influenza transmission among Korean university students during the peak pandemic period. BMC Infect. Dis. 2010; 10: 1–8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhalafalla HE, Tumambeng MZ, Halawi MHA, et al.: COVID-19 Vaccine Hesitancy Prevalence and Predictors among the Students of Jazan University, Saudi Arabia Using the Health Belief Model: A Cross-Sectional Study. Vaccines. 2022; 10(2). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWong LP, Alias H, Wong PF, et al.: The use of the health belief model to assess predictors of intent to receive the COVID-19 vaccine and willingness to pay. Hum. Vaccin. Immunother. 2020; 16(9): 2204–2214. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHatteberg SJ, Kollath-Cattano C: Applying the health belief model to examine college students’ early-stage adoption of non-pharmaceutical interventions in response to COVID-19. J. Am. Coll. Heal. 2022; 1–6. PubMed Abstract \| Publisher Full Text\n\nDu M, Tao L, Liu J: Association between risk perception and influenza vaccine hesitancy for children among reproductive women in China during the COVID-19 pandemic: a national online survey. BMC Public Health. 2022; 22(1): 310–385. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEjeta LT, Ardalan A, Paton D, et al.: Predictors of community preparedness for flood in Dire-Dawa town, Eastern Ethiopia: Applying an adapted version of Health Belief Model. Int. J. Disaster Risk Reduct. 2016; 19(September): 341–354. Publisher Full Text\n\nKarimy M, Azarpira H, Araban M: Using health belief model constructs to examine differences in adherence to pap test recommendations among Iranian women. Asian Pac. J. Cancer Prev. 2017; 18(5): 1389–1394. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim HS, Ahn J, No JK: Applying the health belief model to college students’ health behaviour. Nutr. Res. Pract. 2012; 6(6): 551–558. Publisher Full Text\n\nWong MCS, Wong ELY, Huang J, et al.: Acceptance of the COVID-19 vaccine based on the health belief model: A population-based survey in Hong Kong.2020; 12.083(January): 1148–1156.\n\nAnsari-Moghaddam A, Seraji M, Sharafi Z, et al.: The protection motivation theory for predicting intention of COVID-19 vaccination in Iran: a structural equation modeling approach. BMC Public Health. 2021; 21(1): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuslih M, Susanti HD, Rias YA, et al.: Knowledge, attitude, and practice of Indonesian residents toward Covid-19: A cross-sectional survey. Int. J. Environ. Res. Public Health. 2021; 18(9). Publisher Full Text\n\nYanti B, Wahyudi E, Wahiduddin W, et al.: Community Knowledge, Attitudes, and Behavior Towards Social Distancing Policy as Prevention Transmission of Covid-19 in Indonesia. J. AdmKesehatIndones. 2020; 8(2): 4. Publisher Full Text\n\nGao H, Hu R, Yin L, et al.: Knowledge, attitudes and practices of the Chinese public with respect to coronavirus disease (COVID-19): An online cross-sectional survey. BMC Public Health. 2020; 20: 1–8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHussain A, Garima T, Singh BM, et al.: Knowledge, attitudes, and practices towards COVID-19 among Nepalese Residents: A quick online cross-sectional survey. Asian J. Med. Sci. 2020; 11(3): 6–11. Publisher Full Text\n\nZhong BL, Luo W, Li HM, et al.: Knowledge, attitudes, and practices towards COVID-19 among Chinese residents during the rapid rise period of the COVID-19 outbreak: A quick online cross-sectional survey. Int. J. Biol. Sci. 2020; 16(10): 1745–1752. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAzlan AA, Hamzah MR, Sern TJ, et al.: Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia. PLoS One. 2020; 15(5): 1–15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNarayana G, Pradeepkumar B, Dasaratha J: Knowledge, perception, and practices towards COVID-19 pandemic among the general public of India: A cross-sectional online survey. Curr. Med. Res. Pract. 2020; 10(2020): 153–159. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDaragmeh A, Sági J, Zéman Z: Continuous intention to use e-wallet in the context of the covid-19 pandemic: Integrating the health belief model (hbm) and technology continuous theory (tct). J. Open Innov.: Technol. Mark. Complex. 2021 May 12; 7(2): 132. Publisher Full Text\n\nHussain MW, Mirza T, Hassan MM: Impact of COVID-19 Pandemic on the Human Behavior. Int. J. Educ. Manag. Eng. 2020; 10(6): 35–61. Publisher Full Text\n\nAjilore K, Atakiti I, Onyenankeya K: College students’ knowledge, attitudes and adherence to public service announcements on Ebola in Nigeria: Suggestions for improving future Ebola prevention education programmes. Health Educ. J. 2017; 76(6): 648–660. Publisher Full Text\n\nMartinez-Lacoba R, Pardo-Garcia I, Escribano-Sotos F: Aging, dependence, and long-term care: A systematic review of employment creation. Inquiry. 2021 Dec 16; 58: 00469580211062426. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTachfouti N, Slama K, Berraho M, et al.: The impact of knowledge and attitudes on adherence to tuberculosis treatment: A case-control study in a Moroccan region. Pan Afr. Med. J. 2012; 12(1): 1–8. Publisher Full Text\n\nSusanna D, Widyamurti W, Eryando T: Data for: Community perception and COVID-19 prevention. Dataset. Dryad. 2023. Publisher Full Text\n\nSusanna D, Widyamurti W, Eryando T: IMPLEMENTATION OF SOCIAL POLICY DISTANCING IN EFFORT PREVENTION COVID-19 IN INDONESIA. Journal Contribution. figshare. 2023. Publisher Full Text" }	[ { "id": "195846", "date": "13 Sep 2023", "name": "Husnah Husnah", "expertise": [ "Reviewer Expertise Nutrition Department" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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. Abstract (minor revision)\nIn the conclusion section, significant results have been attached to preventive behavior and community perceptions of the severity of COVID-19 disease, but to support objective data, it is necessary to attach data in the form of accurate numbers in accordance with the findings in the field. In the results section, you mentioned that there is a relationship between self efficacy and perceived influence on preventive behavior. How did you come to the conclusion that these variables are related?\n\n2. Methods (major revision)\nThis is an interesting study because it is a large-scale study of the country of Indonesia. I have high hopes that this research will be successfully indexed so that it can be used as a reference by other studies in information about Community preventive behavior and perception on the severity of COVID-19 disease in Indonesia. As with other research articles that have been published in various journals, of course your research article needs to be improved to make it worth reading.\nYour research obtained data from a google form that was distributed through various social media. You managed to get thousands of responses. But I am curious how can you ensure that one respondent does not fill in the google form more than once? Is there strict control over the filling of google forms by respondents? I hope that your data does not become biased because of this.\nThen you mentioned that the respondents were spread across Indonesia. How do you ensure that the respondents are indeed spread evenly across Indonesia, which consists of 38 provinces? Perhaps you have your own reference in determining the distribution throughout Indonesia as you mentioned, please explain.\n\n3. Study and Sample (minor revision)\nThis research expands to the Indonesian public with contributions from social media influencers. How do you ensure this research is representative of all Indonesians? Respondents participating in your research are Indonesian citizens. How do you ensure that the people filling in the data are Indonesian citizens? What if a foreigner residing in Indonesia receives and fills out a questionnaire from your research, how do you know?\n\n4. Conceptual Model (major revision)\nThis research uses HBM as the main reference. What should be a common concern in using SEM must be based on a certain theory. This is because the function of SEM is to confirm the model formed on real data obtained in the field. In addition, the determination of the direction of the relationship built in the model must be theoretically corroborated. This will also affect the determination of the amount of data or research samples that are suitable for use in SEM and feasible in terms of sample adequacy in testing a theory-based model.\n\n5. Minor revision\nCorrect the English writing errors in the article. I have marked them on the linked annotated article. For example, in the questionnaire table in the methods section, and in the discussion section. The COVID-19 incidence rate has been mentioned from mid-2021 to the end of 2021. To add to the accuracy of this study, the incidence rate of COVID-19 until 2022 should also be 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?\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": "201070", "date": "22 Sep 2023", "name": "Rotimi Oguntayo", "expertise": [ "Reviewer Expertise Psychology (Crises Prevention and 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\nAbstract (Minor Revision): In the conclusion section, significant results have been attached to preventive behavior and community perceptions of the severity of COVID-19 disease, but to support objective data, it is necessary to attach data in the form of accurate numbers in accordance with the findings in the field. In the results section, you mentioned that there is a relationship between self-efficacy and perceived influence on preventive behavior. How did you come to the conclusion that these variables are related?\nMethodology (Major Revision): This is an interesting study because it is a large-scale study of the country of Indonesia. I have high hopes that this research will be successfully indexed so that it can be used as a reference by other studies in information about Community preventive behavior and perception of the severity of COVID-19 disease in Indonesia. As with other research articles published in various journals, your research article needs significant improvement to enhance its readability and credibility. You collected data through a Google Form distributed via various social media channels, resulting in thousands of responses. However, it is essential to address potential biases in data collection. How did you ensure that respondents didn't fill out the Google Form multiple times? Was there strict control over the form submissions? Additionally, you mentioned that respondents were spread across Indonesia. How did you ensure even distribution among Indonesia's 38 provinces? Please provide details or references for this distribution method. If you were unable to meet up with any of these criteria, list them as your study limitations.\nStudy and Sample (Minor Revision): This research aims to reach the Indonesian public, including contributions from social media influencers. To ensure the research's representativeness, please clarify how you ensured that the sample accurately represents all Indonesians. Your respondents are identified as Indonesian citizens, but how did you verify their citizenship? What measures were in place to prevent participation by non-Indonesian residents? Consider addressing these potential sources of bias. If you were unable to meet up with any of these criteria, list them as your study limitations.\nConceptual Model (Major Revision): This research employs the Health Belief Model (HBM) as the primary theoretical framework. It is crucial to emphasize that Structural Equation Modeling (SEM) relies on a well-established theory to validate models using real data. The direction of relationships in the model must align with theoretical support. Additionally, theoretical underpinnings are essential in determining the appropriate sample size for SEM and ensuring sample adequacy when testing a theory-based model. Please provide a more comprehensive, precise and concise theoretical foundation for your SEM analysis.\nGrammatical Errors (Minor Revision): Correct the English writing errors in the article generally. Moreover, consider updating the COVID-19 incidence rate beyond the end of 2021, extending it into 2022, to enhance the study's accuracy and encompassing quality.\nResults: The results section requires elaboration and clarification to explain how you arrived at the conclusion regarding the relationship between self-efficacy and perceived influence on preventive behavior for readers who not statistic expert to be able to read and understand while retaining the journal format.\nDiscussion: Expand on the implications of the results and how they relate to the theoretical framework. Discuss the broader significance of your findings in the context of COVID-19 prevention in Indonesia and HBM concept for clinical practice in local context. Also, consider inclusion of more recent similar COVID-19 incidence data in other country to buttress your results in this section.\nConclusion with Limitations and Implications: Summarize the key findings, discuss the study’s limitations as suggested above, and provide implications for clinical practice or public health initiatives, and future research to ascertain replicability of your work.\nIndexing of the Paper: The indexing of the paper is contingent upon addressing the major revisions outlined in the methodology and conceptual model sections. Minor revisions should also be completed in the abstract, study and sample, grammatical errors, and the inclusion of more recent COVID-19 incidence data in the discussion section. Once these revisions are made, the paper will be reevaluated for indexing.\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": [ { "c_id": "10585", "date": "28 Dec 2023", "name": "Tris Eryando", "role": "Author Response", "response": "Thank you for your valuable inputs to this paper. We already revised almost all part according to your input. Following are our response: Abstract The abstract session will be revised according to the article’s revision. The number will be put accordingly. The conclusion of relationship between self- efficacy and perceived was made based on statistical test. It will be added in the abstract. Methodology Due to the social restriction during the pandemic, the data was collected using google form. We did not do any specific treatment to limit the frequency of people submission as well as the respondents location. We also could not prevent respondent from other country to fill the link. However, when we did data cleaning, we erased data which is not located in Indonesia and having the same identity. Because of data in this study was collected through google link, the respondent indeed did not distributed evenly in all area in Indonesia and not to mention to represent and that is for sure could not represent all Indonesian population. Thus, this study is vulnerable to information and selection bias. All this information will be added in the article as our study limitation including our suggestion to minimize the bias for the further study. Study and sample As we already wrote down in limitation part, sample in this study is not representing Indonesian population. We only distributed the link as much as we can and even engage with social media influencer to speed up the distribution. We wanted to collect as much as we can during the data collection time with the minimum sample size as our benchmark. As mentioned previously, we cannot control response from other country, as well as double respondent, however when we did data cleaning, we dropped out respondent who are not located in Indonesia and having the same identity. Indeed, this situation somehow my lead to the information and selection bias. Hence, we also provided our recommendation for further study. Conceptual model This study employed HBM theory as the conceptual framework and the data was collected according to each variable mentioned in the theory. The framework was described in the article both in Figure 1 and Table 1. The point of using SEM is to test a theory by specifying a model that represent predictions of that theory among plausible constructs measured with appropriate observed variables. In this study, we tested the HBM theory using the collected data. The output of this analysis is to identify whether the analysis deals with substantive theoretical issues regardless of whether or not a model is retained. Thus, in principle, the analysis in this study did not highlight/emphasize the statistical relationship among 2 variables, instead a model as a whole. We will add the explanation in the paper, Grammatical Error, Result, Discussion, and Conclusion with Limitations and Implications >> we directly revised in the document" } ] } ]	1	https://f1000research.com/articles/12-966
https://f1000research.com/articles/13-1122/v1	03 Oct 24	{ "type": "Research Article", "title": "Predicting the incidence of recurrent positive exercise stress tests among civilian pilots: a retrospective cohort study", "authors": [ "Voltha Herry", "Indah Suci Widyahening", "Ferdi Afian", "Ika Prasetya Wijaya", "Boon-How Chew", "Dewi Sumaryani Soemarko", "Voltha Herry", "Ferdi Afian", "Ika Prasetya Wijaya", "Boon-How Chew", "Dewi Sumaryani Soemarko" ], "abstract": "Abstract\nBackground A positive exercise stress test (EST) is common among pilots, and it may indicate a greater risk of coronary artery disease (CAD). This study aimed to determine the incidence of recurrently positive EST and their predictors among civilian pilots in Indonesia.\n\nMethods This was a retrospective cohort study among civilian pilots who had the first positive EST test between January 2019 and June 2020 at the Aviation Medical Center, Jakarta. The data were retrieved from medical records. Subjects were included if there were data on subsequent ESTs at 6 and 12 months. Risk factors included total flight hours (TFH) in the last 6 months, license type, aircraft cabin pressurization system, flying limitation such as multicrew, cardiac intervention, age, smoking habit, family history of coronary artery disease, body mass index, blood pressure levels, lipid profile, and fasting blood glucose.\n\nResults Eighty-seven pilots were included; 54 of them (62.1%) had recurrent positive ESTs. All subjects were men, and the median age was 51 (range 40-64) years. Independent predictors of recurrent positive ESTs were age 60-65 years (adjusted odds ratio [ORadj]: 5.1, 95% CI: 1.12–23.16, p= 0.035), a TFH of > 275 hours (ORadj 5.1, 95% CI: 1.28–20.65, p= 0.021), and dyslipidemia (ORadj: 4.2 95% CI: 1.468–12.275, p=0.015). Having these three risk factors increased the probability of a recurrent positive EST up to 100%.\n\nConclusion The incidence of recurrently positive ESTs among civilian pilots in Indonesia was high. Airlines may want to implement a more aggressive health policy for the prevention of cardiovascular diseases among their pilots.", "keywords": [ "coronary artery disease", "risk factors", "airline pilot", "electrocardiography" ], "content": "Introduction\n\nCoronary artery disease (CAD) is a serious health problem in aviation. Acute coronary syndrome remains one of the most common causes of incapacitation among civilian pilots and can lead to incidents or fatal accidents.1 Sudden incapacitation due to arrhythmia, myocardial infarction or heart failure can be catastrophic during a flight. There are several screening modalities for detecting CAD, including electrocardiography (ECG), echocardiography, coronary calcium scoring, coronary angiography, and ECG exercise stress test (EST) or treadmill tests with or without nuclear or stress imaging. ECG EST is often used as the first-line method to screen individuals at increased risk of CAD since it is readily available and may provide useful information on cardiac functional capacity, such as blood pressure response to exercise, assessment of exercise-related arrhythmias, and aerobic fitness.2 However, EST is not recommended as a stand-alone screening tool to determine aeromedically significant CAD because it has low sensitivity and low positive predictive value.3,4\n\nCivilian pilots need medical assessment to obtain a first-class certificate that is valid for 6 months according to the Indonesian Civil Aviation Safety Regulation.5 ECG EST for civilian pilots is performed once at the age of 35 years, annually between 40 and 60 years, and then every 6 months thereafter. Positive ESTs can be asymptomatic.6 However, this finding requires further cardiovascular assessment while the pilot is grounded. Abnormal heart rhythm, either by resting or exercise ECG, must be considered unfit to fly until it is managed properly and the incapacitated pilot meets medical requirements.5 If the pilot has a second positive EST, there will be more complicated management and assessment before the pilot can be returned to duty. Clearly, positive EST is an undesirable result that should always be prevented.\n\nPositive ESTs are commonly found among civilian pilots at the Aviation Medical Center, Jakarta, and some of them recur. However, the incidence and risk factors for recurring positive EST have not been well studied. Therefore, this study aimed to determine the incidence of recurrent positive EST and its risk factors among civilian pilots in Indonesia. A positive EST warrants further diagnostic management if it recurs.7\n\n\nMethods\n\nThis was a retrospective cohort study among civilian pilots who had a positive EST between January 2019 and June 2020. Subjects were selected from the medical records at the Aviation Medical Center, Directorate General of Air Transportation, Ministry of Transportation, Republic of Indonesia, Jakarta, which is currently the only institution mandated to perform the required periodical medical check-up for all civilian airline aircrews in Indonesia. The inclusion criteria were all civilian pilots with first-time positive EST results, aged 40–65 years, and who had EST results at 6 or 12 months after the first positive EST. Pilots with incomplete medical check-up data were excluded. Written informed consent was not required since all the data were obtained secondarily from the medical records. The sample size was calculated using the formula for a prevalence study with a confidence level of 95%, an expected prevalence of 23%,8 and an error limit of 10%. The minimum sample size was 69 subjects.\n\nEthics approval was granted by the Health Research Ethics Committee, Faculty of Medicine Universitas Indonesia on 12 July 2021 (No. KET-679/UN2. F1/ETIK/PPM.00.20/2021). This study complies with the Declaration of Helsinki and was performed according to ethics committee approval. A written request to use the medical record data was sent to the Aviation Medical Center, Directorate General of Air Transportation, Ministry of Transportation, Republic of Indonesia and approval was granted on 21 July 2021 (No. S1-132/UN2.F1S.14.3/2021).\n\nThe exercise stress test was performed according to the Bruce protocol. The procedure consists of consecutive stages lasting 3 minutes each, where the patient is required to walk at an increased speed and on a steeper incline. The testing methodology can be modified according to the patient’s tolerance, with the goal of achieving an exercise duration of 6 to 12 minutes. A modified version of the Bruce protocol has been developed for individuals who are unable to engage in intense exercise. This modified protocol includes two additional stages at the beginning, both of which include lower workloads than stage 1.9 A positive result was defined by one of these criteria on the ECG result: ST segment depression >1 mm below the isoelectric line at 60 milliseconds after the J point (if horizontal or down sloping ST segment depression); ST segment depression >1.5 mm below the isoelectric line at 80 milliseconds after the J point (if upsloping ST segment depression); ST segment elevation >1 mm at 80 milliseconds after the J point; or ST segment elevation on the AVR lead. This condition was regarded as similar to horizontal ST-segment depression.10 A cardiologist assessed and determined the result based on the ECG.\n\nRisk factors tested were total flight hours (TFH) in the last six months (≤275 hours vs. >275 hours; 275 hours being the midpoint of maximum flying hours for pilots in six months according to the International Civil Aviation Organization [ICAO]), license type (Commercial Pilot License [CPL] or Air Transport Pilot License [ATPL]), aircraft cabin system (pressurized vs. unpressurized), limitation (not flying as pilot in command), cardiac intervention (either percutaneous coronary intervention [PCI] or coronary artery bypass grafting [CABG]) after the positive EST soon after being evaluated by an aviation medical examiner, age group (40-49 vs. 50-59 vs. 60-65 years), smoking habit, family history of CAD, body mass index (BMI), blood pressure, lipid profile, and fasting blood glucose. Limitation was defined as not flying as a pilot in command. BMI was categorized based on the World Health Organization (WHO) criteria as normal (18.5-24.9 kg/m2), overweight (25.0-29.9 kg/m2) or obese (above 30.0 kg/m2).11 Blood pressure was categorized according to the Joint National Committee VII criteria as hypertension (systole of ≥140 or diastole of ≥90 mmHg) or not hypertension.12 Lipid profiles were classified according to the Indonesian Society of Endocrinology Guideline into dyslipidemia (total cholesterol ≥240 mg/dl, LDL ≥160 mg/dl, or HDL ≤40 mg/dl) and normal.13 Fasting blood glucose was classified according to the Indonesian Society of Endocrinology Guideline as <126 mg/dl or ≥126 mg/dl.7\n\nThe baseline characteristics of the pilots and risk factors are presented descriptively. The associations between independent and dependent variables were analyzed using the chi-square test. Multivariate logistic regression analyses were performed for variables with a p value of <0.25 based on the univariate analysis to identify independent predictors for one recurrently positive EST at six or 12 months, expressed by the adjusted odds ratio (ORadj) and its corresponding 95% confidence intervals (CIs). The probability of a recurrently positive EST was then calculated based on the number of risk factors. Statistical analyses were performed using IBM® SPSS® Statistics version 20.\n\n\nResults\n\nA total of 87 civilian pilots had a positive EST between January 2019 and June 2020, all of whom were men with a median age of 51 (range 40-64) years. There were 33 (37.9%) pilots who received a cardiac intervention to confirm CAD. Other characteristics are shown in Table 1.\n\nRecurrently positive EST was found in 54 (62.1%) pilots. It was significantly associated with age, TFH in the last 6 months, and dyslipidemia (Table 2). Multivariate analyses revealed that age 60-65 years, a TFH of >275 hours in the last six months, and dyslipidemia were independent predictors of recurrent positive EST (Nagelkerke R2 = 0.319; Hosmer and Lemeshow test p = 0.227). The adjusted OR was 5.1 for the 60-65 years and TFH >275 hours, whereas dyslipidemia was associated with a 4.2-fold increased risk for recurrent EST (Table 3). The probability of recurrently positive EST was 100% for pilots with all three risk factors (Table 4).\n\n Chi square test.\n\n^ Fisher’s exact test.\n\n\nDiscussion\n\nOur study evaluated the EST follow-up data as the primary outcome. We found that the incidence of recurrent positive EST among civilian pilots in Indonesia was high at 62.1%. Positive EST recurred despite flying limitations or cardiac intervention (PCI or CABG), which some of the pilots underwent after the first positive EST. The independent predictors were an age of 60-65 years, a TFH of >275 hours in the last 6 months, and dyslipidemia. If the pilot had all 3 risk factors, he would definitely have a positive result on the next EST.\n\nThere are no other reports specifically addressing recurrent positive EST in the aerospace medicine literature. A study in Turkey on 26 cases (pilots and aircrew) with a history of CAD revealed that 6 (23.1%) of them had subsequent positive ESTs.6 Positive ESTs based on ST segment changes, either depression or elevation, are beneficial for risk stratification in people with intermediate-risk symptoms of CAD.14 However, pilots are usually asymptomatic, and according to the American Heart Association guidelines, asymptomatic individuals have very low (<5%) or low (5-10%) pretest probabilities of CAD.15 Therefore, positive EST warrants further diagnostic management, especially if it recurs. During the period of assessment, which was conducted immediately as the EST showed a positive result, a pilot was considered unfit to fly. Grounded pilots create additional burdens to airlines, such as increased medical costs and loss of working hours for at least 6 months. Returning pilots with known CAD to flight duties requires a comprehensive evaluation and control of modifiable risk factors.2 Knowing the risk factors and predictors of recurring positive EST will be valuable as potential health nudges for prevention.\n\nOur study showed that older age was a risk factor for recurrent positive EST. Aging is a well-known nonmodifiable risk factor for CAD.16 Pilots aged >60 years are also classified as having a high risk of CAD.17 The mechanisms of aging and cellular physiological alterations leading to increased cardiovascular risk have been reviewed elsewhere.18\n\nWe found that a total flight time >275 hours in the last six months significantly increased the risk of recurrent positive EST. Another study revealed that a total flight time ≥5000 hours is among the independent predictors of a high risk of atherosclerotic cardiovascular disease.19 Some researchers have suggested that flight time is associated with cosmic radiation and intermittent hypoxia, which affect lipid metabolism and trigger coronary stenosis. Cosmic radiation exposure triggers oxidative stress and continuously accelerates changes in lipoprotein structure and lipid metabolism. The body responds by increasing the release of lipid molecules into the bloodstream as a protective mechanism against damage to the cell membrane induced by lipid peroxidation, which disturbs lipid metabolism.20,21 Repetitive intermittent hypoxia inhibits the absorption of cholesterol through hypoxia-inducible factor 1 (HIF-1). Hypoxia affects adipose tissue by activating inflammation and releasing inflammatory mediators into the bloodstream. This will cause systemic inflammation and disruption of nitrite oxide production, causing epithelial and endothelial dysfunction.22,23\n\nDyslipidemia also emerged as an independent predictor of recurrent positive EST in this study. It is associated with fat accumulation in the arterial wall, accelerating the atherosclerosis process by narrowing the lumen and blocking the blood supply.24 Airline pilots consumed more dyslipidemia medication than did the general population; the prevalence of statin treatment among pilots also increased with age.25 Pharmacologic intervention for hyperlipidemia among pilots should be initiated based on the Indonesian Society of Endocrinology recommendation for individuals in Indonesia when the LDL-cholesterol level is more than 130 mg/dL. This approach is more aggressive than many other guidelines, as pilots are classified as having intermediate cardiovascular risk.26\n\nOur findings imply that pilots with positive EST should control their modifiable cardiovascular risk factors more stringently, particularly their lipid profile. Older age and increased flying time also increase the risk of recurrent EST, but these factors cannot be controlled and are associated with increased flying responsibility and expertise. At best, pilots aged more than 60 years should check their lipid profile more often and reduce their flying time to less than 275 hours within 6 months. Nutritional assessment and intervention may be needed. However, risk mitigation in aerospace medicine should be considered in the context of an abnormal working environment, i.e., a dry and pressurized cabin, hypoxia and hypobaric, spatial disorientation, and heightened stress.27,28 No risk scoring system has been developed for civilian pilots. Lifestyle modifications and pharmacological interventions at lower risk thresholds may be useful for traditional assessments of pilots who are considered to be at low risk.20\n\nThe limitation of our study was the retrospective cohort design with secondary data from the medical records. Therefore, several potential risk factors, such as physical activity, dietary patterns, and current medication, could not be evaluated. However, basic information on modifiable and occupational risk factors for CAD was available for further analyses.\n\n\nConclusion\n\nThe incidence of recurrently positive EST among civilian pilots in Indonesia was high. The independent risk factors were an age of 60-65 years, more than 275 cumulative flight hours in the last six months, and dyslipidemia. Pilots were advised to control their risk factors, particularly their lipid profile, to prevent recurrent positive EST. Among pilots, airlines may want to have more aggressive health policies for the prevention of cardiovascular diseases, such as enhanced cardiovascular screening for those with risk factors. A medical specialist who obtained competencies in maintaining the health of pilots and all aviation personnel at an airline, such as an aviation medicine specialist, would be expected to have a better understanding of aviation cardiology.\n\nEthics approval was granted by the Health Research Ethics Committee, Faculty of Medicine Universitas Indonesia on 12 July 2021 (No. KET-679/UN2. F1/ETIK/PPM.00.20/2021). This study complies with the Declaration of Helsinki and was performed according to ethics committee approval. A written request to use the medical record data was sent to the Aviation Medical Center, Directorate General of Air Transportation, Ministry of Transportation, Republic of Indonesia and approval was granted on 21 July 2021 (No. S1-132/UN2.F1S.14.3/2021).", "appendix": "Data availability\n\nThe data belong to the Directorate General of Air Transportation, Ministry of Transportation, Republic of Indonesia and access was restricted for security reason. Data access will be granted once users have consented to the data sharing agreement and provided written plans and justification for what is proposed with the data. Data access may be obtained by submitting a request to the corresponding author (Indah Suci Widyahening) and will be reviewed by the Aviation Medical Center, Directorate General of Air Transportation, Ministry of Transportation of the Republic of Indonesia 5 and subjected to the Regulation of the Ministry of Health of the Republic of Indonesia no. 85/2020, on Data Sharing.\n\nOpen Science Framework: Predicting the incidence of recurrent positive exercise stress tests among civilian pilots: a retrospective cohort study. https://doi.org/10.17605/OSF.IO/4B9FQ.\n\nFile included: STROBE checklist.\n\n\nAcknowledgements\n\nThe authors would like to express their gratitude to the Aviation Medical Center, Directorate General of Air Transportation, Ministry of Transportation, Republic of Indonesia, Jakarta, for their support in this study and Dr. Sunu Budhi Raharjo from the National Cardiovascular Center Harapan Kita, Jakarta for his valuable inputs in the development of this manuscript.\n\n\nReferences\n\nLord D, Conlon HA: Cardiovascular risk factors in airline pilots. Workplace Health Saf. 2018; 66: 471–474. PubMed Abstract \| Publisher Full Text\n\nGray G, Davenport ED, Bron D, et al.: The challenge of asymptomatic coronary artery disease in aircrew; detecting plaque before the accident. Heart. 2019; 105: s17–s24. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDetrano R, Gianrossi R, Froelicher V: The diagnostic accuracy of the exercise electrocardiogram: a meta-analysis of 22 years of research. Prog. Cardiovasc. Dis. 1989; 32: 173–206. PubMed Abstract \| Publisher Full Text\n\nWilson RF, Marcus ML, Christensen BV, et al.: Accuracy of exercise electrocardiography in detecting physiologically significant coronary arterial lesions. Circulation. 1991; 83: 412–421. PubMed Abstract \| Publisher Full Text\n\nMinistry of Transportation, Republic of Indonesia: Regulation Number PM 69 Year 2017 on Civil Aviation Safety Regulation Part 67 on Medical Standard and Certification. Reference Source\n\nLauer M, Froelicher ES, Williams M, et al.: Exercise testing in asymptomatic adults. Circulation. 2005; 112: 771–776. Publisher Full Text\n\nMinistry of Transportation, Republic of Indonesia: Regulation Number KP 238 Year 2018 on Staff Instruction Part 67-02 on Manual of Aviation Medical Assessment.\n\nErdal M, Aparci M, Isilak Z, et al.: Clinical Features of Aviators with Coronary Artery Disease Diagnosed by Multislice CT Angiography. Anatol. J. Cardiol. 2014; 14: 150–154. PubMed Abstract \| Publisher Full Text\n\nVilcant V, Zeltser R: Treadmill Stress Testing. [Updated 2023 Jun 20]. StatPearls. Treasure Island (FL): StatPearls Publishing; 2024 Jan. Reference Source\n\nIndonesian Heart Association: Guidelines of Treadmill Test: Procedure and Interpretation. Jakarta: Indonesian Heart Association; 2016. Reference Source\n\nWorld Health Organization: Body mass index (BMI).2022. Reference Source\n\nChobanian AV, Bakris GL, Black HR, et al.: Seventh Report of The Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure. American Heart Association; 2003. Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure (ahajournals.org)\n\nIndonesian Society of Endocrinology: Guidelines of Dyslipidemia Management in Indonesia. Jakarta: Indonesian Endocrinologist Association; 2021. 23-11-21-Website-Panduan-Dislipidemia-2021-Ebook.pdfReference Source\n\nBourque JM, Beller GA: Value of exercise ECG for risk stratification in suspected or known CAD in the era of advanced imaging technologies. JACC Cardiovasc. Imaging. 2015; 8: 1309–1321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGibbons RJ, Balady GJ, Bricker JT, et al.: American College of Cardiology/American Heart Association Task Force on Practice Guidelines. Committee to Update the 1997 Exercise Testing Guidelines. ACC/AHA 2002 guideline update for exercise testing: summary article. A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines (Committee to Update the 1997 Exercise Testing Guidelines). J. Am. Coll. Cardiol. 2002; 40: 1531–1540. PubMed Abstract \| Publisher Full Text\n\nHajar R: Risk factors for coronary artery disease: Historical perspectives. Heart Views. 2017; 18(3): 109–114. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHouston S, Mitchell S, Evans S: Application of a Cardiovascular Disease Risk Prediction Model Among Commercial Pilots. Aviat. Space Environ. Med. 2010; 81: 768–773. PubMed Abstract \| Publisher Full Text\n\nPaneni F, Diaz Canestro C, Libby P, et al.: The aging cardiovascular system: Understanding it at the cellular and clinical levels. J. Am. Coll. Cardiol. 2017; 69: 1952–1967. Publisher Full Text\n\nBuila NBBJ-M, Kabanda GK, Bayauli PM, et al.: Atherosclerotic cardiovascular disease short-term risk estimate among civilian licensed aircrew. World. J. Cardiovasc. Dis. 2019; 09: 92–108. Publisher Full Text\n\nChairina N, Werdhani R, Gathmyr D: Association of Total Flight Hours with Lipid Blood Profiles among Civilian Pilots in Indonesia. J. Phys. Conf. Ser. 2018; 1073: 042012–042017. Publisher Full Text\n\nGaspardone A, Polisca P, Crea F, et al.: Effect of Hypoxia on Coronary Blood Flow and Myocardial Oxygen Extraction in Patients with Coronary Artery Disease. J. Am. Coll. Cardiol. 2002; 25: 322.\n\nGao L, Chen Q, Zhou X, et al.: The role of Hypoxia-inducible Factor 1 in Atherosclerosis. J. Clin. Pathol. 2012; 65: 872–876. PubMed Abstract \| Publisher Full Text\n\nAndrei AM, Berbecaru-Iovan A, Ioan FR, et al.: Interplay between Hypoxia, Inflammation and Adipocyte Remodeling in the Metabolic Syndrome. Hypoxia and Human Diseases. 2017; 16: 303–328. Publisher Full Text\n\nGarg R, Anggarwal S, Kumar R, et al.: Association of atherosclerosis with dyslipidemia and comorbid conditions: A Descriptive Study. J. Nat. Sci. Biol. Med. 2015; 6: 163–168. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSykes AJ, Larsen PD, Griffiths RF, et al.: A study of airline pilot morbidity. Aviat. Space Environ. Med. 2012; 83: 1001–1006. PubMed Abstract \| Publisher Full Text\n\nWirawan IMA, Griffiths RF, Larsen PD: Cardiovascular risk factor modification in asymptomatic adults and implications for pilots. J. UOEH. 2020; 42: 187–201. PubMed Abstract \| Publisher Full Text\n\nSutton NR, Banerjee S, Cooper MM, et al.: Coronary artery disease evaluation and management considerations for high risk occupations: commercial vehicle drivers and pilots. Circ. Cardiovasc. Interv. 2021; 14: e009950. PubMed Abstract \| Publisher Full Text\n\nNicol ED, Rienks R, Gray G, et al.: An introduction to aviation cardiology. Heart. 2019; 105: s3–s8. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "331311", "date": "15 Oct 2024", "name": "Andrea Sonaglioni", "expertise": [ "Reviewer Expertise Cardiology", "echocardiographiy", "exercise stress echocardiography", "heart failure", "mitral valve prolapse", "pectus excavatum", "atrial fibrillation", "heart failure", "aortic stenosis", "pulmonary hypertension", "coronary artery 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\nIn this interesting paper, the Authors found that an age of 60-65 yrs, a THF of >275 hours in the last 6 months and dyslipidemia were independently correlated with recurrently positive EST among civilian pilots In Indonesia. The Authors stated that 37.9% of pilots with positive EST underwent a cardiac intervention to confirm CAD. How many pilots had obstructive CAD on subsequent coronary angiography? Could the Authors add in the Results section the percentage of false positive EST results? It is known that EST has a low specificity for detecting CAD, due to a great number of false positive EST results. At the end of the Discussion section, the Authors could add a paragraph concerning the potential causes of false positive EST results. I suggest the Authors to discuss a number of exercise-induced ST-segment changes simulating myocardial ischemia, such as those described in individuals with exaggerated atrial repolarization waves (Ta wave), in hyperventilating individuals, in individuals with mitral valve prolapse and finally in individuals with concave-shaped chest wall and/or pectus excavatum. The Authors could cite and discuss the following references: Sapin P, et al., 1995 (Ref 1) Gardin J, et al.,1980 (Ref 2) Tebbe U, et al., 1985 (Ref 3) Sonaglioni A, et al., 2020 (Ref 4)\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/13-1122
https://f1000research.com/articles/13-1117/v1	03 Oct 24	{ "type": "Research Article", "title": "Influence of titanium nanoparticles on cytotoxicity and inflammatory cytokines expression in gingival fibroblasts - An in vitro study", "authors": [ "Sai Sreeja S", "Rahul Bhandary", "Amitha Ramesh", "Biju Thomas", "Veena Shetty", "Geethu Venugopalan", "Uday Simha Putta", "Bhaskarya Bhaskar Bora", "Jayaprakasha Shetty", "Mohana Kumar Basavarajappa", "Sai Sreeja S", "Amitha Ramesh", "Biju Thomas", "Veena Shetty", "Uday Simha Putta", "Bhaskarya Bhaskar Bora", "Jayaprakasha Shetty", "Mohana Kumar Basavarajappa" ], "abstract": "Background Despite the success of titanium (Ti) implants in dental rehabilitation, emerging evidence implicates the release of titanium oxide nanoparticles (TiO2NPs) from the implant surface as a potential contributor to the initiation of the pathogenic process leading to peri-implantitis and ultimately failure of the implants. However, a comprehensive investigation to elucidate the dose-dependent effects of TiO2NPs on cytotoxicity and inflammatory responses is lacking. The present study was undertaken to evaluate the effect of different concentrations of TiO2NPs on the cytotoxicity and inflammatory cytokine expression in Human Gingival Fibroblasts (HGFs).\n\nMethods HGFs were isolated from gingival tissue samples obtained from periodontally and systemically healthy subjects. Ti standard solution for ICP was diluted to create concentrations of (0.001 ppm, 0.01 ppm, 0.1 ppm, 1 ppm, 10 ppm, and 100 ppm) for cell culture media containing titanium. HGFs were then cultured in these varying concentrations for specific time periods (days 1, 3, 5, and 7) to assess cell viability. A cytotoxicity assay was performed to determine the levels and expression of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and anti-inflammatory cytokines (IL-10, IL-12, TGF-β) using qRT-PCR and ELISA techniques.\n\nResults Our findings demonstrate a concentration and duration-dependent decrease in HGF viability upon exposure to titanium nanoparticles. Notably, a 50% reduction in cell viability was observed at the highest concentration (100 ppm). qRT-PCR analysis revealed a significant upregulation of pro-inflammatory cytokines, particularly IL-1β and IL-6, in HGFs exposed to titanium. Interestingly, the expression of anti-inflammatory cytokines (IL-10, IL-12, and TGF-β) remained comparable or even equivalent compared to controls across different titanium concentrations.\n\nConclusions The study revealed a concentration and duration-dependent influence on HGF viability and cytokine profile, suggesting potential cytotoxicity and modulation of the inflammatory response mediated by TiO2NPs. Further research is necessary to elucidate the underlying mechanisms and their implications for dental implant biocompatibility.", "keywords": [ "Dental implant", "Fibroblasts", "Metal Nanoparticles", "Peri-implantitis", "Titanium" ], "content": "Introduction\n\nDental implants have become a cornerstone of modern dentistry, offering a reliable and long-term solution for tooth replacement. However, concerns regarding the failure rates of even osseointegrated dental implants continue to be a focus of research.1\n\nThe peri-implant tissue encompasses a well-defined zone encircling the implant body, typically extending approximately 1 millimeter in width.2,3 This critical interface, known as the peri-implant space, facilitates crucial interactions between the implant and the surrounding soft tissue (peri-implant mucosa) and hard tissue (alveolar bone).4,5 However, a delicate balance exists within this space. Various local and systemic factors, including bacterial biofilms, implant biomaterial and surface characteristics, and prosthetic factors, can all disrupt the implant-tissue interface by inducing an inflammatory reaction. This disruption leads to peri-implantitis, a well-established complication associated with dental implants and a leading cause of bone loss and implant failure.6–8\n\nTitanium (Ti) is the most widely used material for dental implants due to its excellent mechanical properties and bio-inertness.9 However, recent advancements in understanding the biological and mechanical complexities of implant failure have shed light on a detrimental link between titanium release and the development of peri-implantitis. This association includes potential contributions from hypersensitivity reactions to implant materials, tribocorrosion processes at the implant-tissue interface, and the release of nanoparticles, due to fretting (type of residual stress generated by tangential micromotion at areas of contact with normal tension) and/or micromovements during mastication as well as due to triggering of surface oxidation caused by acidic environments triggered by biofilm and/or biofilm induced inflammatory process7,10–13\n\nThe presence of titanium particles and their degradation products has been increasingly documented within the peri-implant environment and surrounding tissues of patients with dental implants. These particles, identified in bone, peri-implant soft tissues, draining lymph nodes, and even lungs and spleen, are widely attributed to originate from the implant itself.14–16 Of particular concern are the unique physicochemical properties of titanium nanoparticles (Ti NPs), especially their small size and ability to interact with biological systems. These characteristics raise the possibility of Ti NPs breaching the blood-brain barrier (BBB) and potentially accessing the central nervous system (CNS).17,18\n\nWhile titanium dioxide nanoparticles (TiO2 NPs) have been implicated in various adverse health outcomes, the primary focus of research has been on pulmonary toxicity.19 Emerging evidence suggests TiO2 NPs also exert significant immunotoxicity, manifesting as lymphocyte over-proliferation, macrophage infiltration, and elevated pro-inflammatory cytokines like IL-1β, IL-6, and TNF-α.20 Mechanistically, pro-inflammatory responses, reactive oxygen species (ROS) generation, and dysregulated autophagy are postulated to contribute to TiO2 NP-induced immunotoxicity.20 However, the precise mechanisms underlying these effects remain elusive.19\n\nThe periodontium, a connective tissue organ with an epithelial covering, plays a critical role in implant success.21 Fibroblasts, the predominant cell type in the periodontium, influence the health of both the implant and surrounding tissues.21 Studies suggest a link between titanium particles and peri-implantitis, an inflammatory condition around dental implants.22 While titanium particles have been found in both inflamed and non-inflamed tissues,17,23 their precise role in inflammation remains unclear. in vitro studies have demonstrated the influence of TiO2 NPs on cell viability and gene expression in various cell types.24–27\n\nHowever, the concentration-dependent effects of TiO2 NPs on human gingival fibroblasts, key players in wound healing and tissue homeostasis, are yet to be explored. This research aims to address this gap by investigating the cytotoxicity and cytokine expression of human gingival fibroblasts exposed to varying concentrations of TiO2 NPs\n\n\nMethods\n\nThe study was conducted with ethical approval from the institutional review board and all procedures were performed following the ethical standards of the Declaration of Helsinki (as revised in 2013). Written informed consent was obtained and gingival tissue samples were collected from a total of three (n=3) systemically and periodontally healthy participants who reported to the Department of Periodontology. All participants were between 18 and 30 years old and presented with probing depths ≤ 3 mm, no clinical attachment loss, and less than 10% bleeding sites.\n\nGingival tissue explants (n=3) were collected and stored in a sterile saline solution. Following transport, tissues were rinsed extensively with phosphate-buffered saline (PBS) (Gibco-Invitrogen, Grand Island, NY, USA, Cat No. 21300-025) and sectioned into small pieces (approximately 1 × 1 mm). The tissue explants were then placed in culture dishes containing Dulbecco’s Modified Eagle Medium (DMEM) (Gibco-Invitrogen, Grand Island, NY, USA, Cat No. 11995065, 500 ml bottle) supplemented with 10% fetal bovine serum (FBS),(Gibco-Invitrogen, Grand Island, NY, USA, Cat No. 10270106), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco-Invitrogen, Grand Island, NY, USA, Cat No. 15140122). Cultures were maintained in a humidified incubator at 37°C with 5% CO2. Once adherent and confluent, gingival fibroblasts were detached using 0.25% trypsin-EDTA (Gibco-Invitrogen, Grand Island, NY, USA, Cat No. 25200072) solution and sub cultured at a 1:4 ratio in fresh medium. The culture medium was replaced every 3-4 days to maintain optimal growth conditions.\n\nCommercially available titanium oxide nanoparticles (TiO2 NPs) with a particle size less than 100 nm (Sigma-Aldrich, St. Louis, MO, USA, Cat No. 700347, 25 gram) were used for this study. A standard solution of TiO2 NPs was prepared in the cell culture medium at a concentration of 1000 ppm (Ti concentration = 1000 ppm in 20% HCl solution). The concentration of titanium in the stock solution was verified using inductively coupled plasma optical emission spectrometry (ICP-OES). This stock solution was serially diluted to obtain working concentrations for the experiments, such as 0.001 ppm, 0.01 ppm, 0.1 ppm, 1 ppm, and 10 ppm. The pH of the culture medium was adjusted to maintain physiological conditions (~7.2) after the addition of TiO2 NPs. Based on a cytotoxicity assay, concentrations of 0.01 ppm, 0.1 ppm, and 10 ppm were selected for further investigation of their effects on inflammatory cytokine expression in gingival fibroblasts.\n\nThe cytotoxicity of TiO2 NPs towards HGFs was evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay (HiMedia, Mumbai, India Cat No. RM1131) Briefly, HGFs were seeded in 96-well plates and allowed to adhere overnight. Cells were then exposed to varying concentrations of TiO2 NPs (e.g., 0.001 ppm, 0.01 ppm, 0.1 ppm, 1 ppm, and 10 ppm) for 1, 3, 5, and 7 days. Following incubation with MTT, the formazan crystals formed within viable cells were solubilized, and the absorbance was measured at a wavelength of 570 nm using a microplate reader (Thermo Scientific Multiskan™ FC Microplate Reader). The quantity and quality of the isolated RNA were assessed using a spectrophotometer (e.g., Nanodrop ND-1000) by measuring the absorbance at 260 nm and 280 nm. Subsequently, cDNA synthesis was performed using a reverse transcription kit (e.g., RNA PCR Core Kit) according to the manufacturer’s instructions. Briefly, PrimeScript RTase was used to convert RNA to cDNA at 42°C.\n\nThe synthesized cDNA was employed as a template for qRT-PCR to quantify the mRNA expression levels of target genes encoding interleukin (IL)-1β, interferon (IFN)-γ, tumor necrosis factor (TNF)-α, IL-6, IL-4, transforming growth factor (TGF)-β, and IL-10. Specific primers for these target genes were designed using appropriate software to ensure optimal amplification efficiency and specificity. The primer sequences are presented in the Extended data.41\n\nThe qRT-PCR reactions were performed using a commercially available SYBR Green master mix kit (e.g., SYBR Green FastMix Kit) following the manufacturer’s protocol. A StepOnePlus Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA) was used for thermal cycling and fluorescence detection. During qRT-PCR, SYBR Green dye fluoresces when bound to double-stranded DNA. As the PCR reaction progresses and amplifies the target DNA, the increasing amount of double-stranded DNA leads to a proportional increase in fluorescence signal. The StepOnePlus instrument monitors this fluorescence in real-time, allowing for the quantification of target gene expression throughout the PCR process.\n\nTo minimize non-specific amplification during reaction setup or pre-cycling steps, Takara Ex Taq HS polymerase (Takara Bio Inc., Kusatsu, Japan) was included in the reaction mixture. This hot-start polymerase variant remains inactive at room temperature, preventing the formation of primer-dimers or mispriming events until the reaction reaches the optimal activation temperature.\n\nFollowing qRT-PCR, the amplified products exposed to various concentraions of TiO2 NPs, were loaded on a 1.5% agarose gel stained with 0.5 μg/mL ethidium bromide in Tris-acetate-EDTA (TAE) buffer (HiMedia, Mumbai, India, Cat No. ML016). Electrophoresis was performed until the loading dye migrated approximately two-thirds of the gel length. The gel was visualized using a UV documentation system (Thermo Fisher Scientific) to verify the presence and size of PCR products for the target genes (IL-1β, IFN-γ, TNF-α, IL-6, IL-4, TGF-β, and IL-10).\n\nThe levels of secreted cytokines (IL-1β, TNF-α, IL-6, IL-4, TGF-β, and IL-10) were quantified in the culture supernatants of HGFs following exposure to TiO2 NPs for 24 and 72 hours using a commercially available ELISA kit (Thermo Fisher Scientific). The experiment was performed in triplicate for each sample. The absorbance of the samples and standards was measured at 450 nm using a Spectrophotometer.\n\nData are presented as mean ± standard deviation (SD) from at least three independent experiments. Statistical analysis was performed using GraphPad Prism software (GraphPad Software, La Jolla, CA, USA). One-way or two-way analysis of variance (ANOVA) was used to assess differences between groups, followed by Tukey’s post-hoc test for multiple comparisons. A p-value less than 0.05 was considered statistically significant.\n\n\nResults\n\nHuman gingival fibroblasts (HGFs) were used for evaluating the cytotoxicity and the expression of selected cytokines upon the exposure of different concentrations of titanium NPs (TiO2) at different durations. The representative image of HGFs showing the fibroblastic morphology is presented in Figure 1 (Extended data).\n\nThe values are presented as percentage mean ± standard deviation (SD). MTT assay was performed on day 1, 3, 5 and 7 of culture. The assay was conducted in triplicates. Different superscripts (a, b, c, d, and e) indicate a statistically significant difference at P<0.05. HGFs cultured in basal media were considered as a control.\n\nThe viability of the HGF cells were assessed as follows, On day 1, the viability of HGFs exposed to TiO2 at concentrations ranged from 0.001 ppm to 100 ppm varied from 49.5% to 78.9%. Except at 0.01 ppm, all other concentrations of TiO2-exposed HGFs showed significant (p<0.05) differences, with reduced viability compared to the control. It was also noted that 50% of the cells showed cytotoxic effects of TiO2 at higher concentrations of exposure, such as 10 ppm and 100 ppm of TiO2. However, no significant (p>0.05) differences in the viability values were observed in HGFs treated with TiO2 with concentrations ranging from 0.01 ppm to 1 ppm (Figure 1).\n\nOn day 3, the viability values of HGFs treated with TiO2 with 0.001 ppm to 100 ppm varied from 39.8% to 75.4%. A higher cytotoxicity effect of TiO2 with more than 50% of cell death was observed at concentrations of 1, 10 and 100 ppm.\n\nOn day 5, the exposure of HGFs to TiO2 at concentrations 1, 10 and 100 ppm resulted in the viability of 32.13%, 29.71% and 32.98% respectively. The highest viability of 66.1% and 68.2% were recorded in HGFs exposed to 0.01 ppm and 0.001 ppm of TiO2, respectively. However, the values were significantly lower when compared to the control (p<0.05).\n\nOn day 7, the viability of HGFs treated with TiO2 at concentrations ranging from 0.1 ppm to 100 ppm resulted in higher cytotoxicity with values varying from 46.47% to 22.84%. Further, the highest viability values of 59.92% at 0.001 ppm and 59.01% at 0.01 ppm were observed in HGFs when compared to the control (92.2%).\n\nThe proliferation rates of HGFs were analysed in terms of absorbance values measured at different time points following their exposure to TiO2 at varying concentrations. A higher absorbance value of 0.4347 was recorded in HGFs treated with 0.001 ppm of TiO2 and lowest absorbance value of 0.3225 was recorded in HGFs exposed to 100 ppm of TiO2. On day 3, the highest absorbance value of 0.4203 was recorded in HGFs treated with 0.001 ppm of TiO2 and the lowest absorbance value of 0.3044 was recorded in HGFs exposed to 100 ppm of TiO2. On day 5 the highest absorbance value of 0.3877 was recorded in HGFs treated with 0.001 ppm and the lowest absorbance value of 0.2655 was recorded in HGFs exposed to 10 ppm of TiO2.\n\nOn day 7, the highest absorbance value of 0.3654 was recorded in HGFs treated with 0.001 ppm and the lowest absorbance value of 0.2456 was recorded in HGFs exposed to 100 ppm of TiO2 (Figure 2).\n\nMTT assay was performed on day 1, 3, 5 and 7 of culture, and the optical density (OD) values are presented. The assay was conducted in triplicates. Different superscripts (a, b, c, d, e, and g) represent a statistically significant difference with P<0.05. HGFs cultured in basal media was considered as a control.\n\nExpression of inflammatory cytokines by qRT-PCR\n\nThe effect of TiO2 on the mRNA expressions of selected proinflammatory and anti-inflammatory markers in HGFs exposed to selected concentrations, such as 0.01 ppm, 0.1 ppm, and 10 ppm was analyzed at 24 hrs and 72 hrs by qRT-PCR. The mRNA expressions of target cytokines were normalized to 18s rRNA which was used as a reference or housekeeping gene.\n\nExpression of IL-1 beta analyzed at 24 hrs of exposure revealed that the expression of IL-1 beta was significantly (P<0.05) higher at 0.01 ppm. However, at 72 hrs, the expression levels were not significant (p>0.05) in TiO2-treated HGFs in all tested concentrations in comparison to control (Figure 3). Expression of TNF-alpha analyzed at 24 hrs was significantly (P<0.05) higher in control cells than in TiO2-exposed HGFs. However, at 72 hrs, the levels of TNF-alpha were not significant (p>0.05) in TiO2-treated HGFs in comparison to control (Figure 4). Expression of IL-6 analyzed at 24 hrs and 72 hrs following the exposure of HGFs to 0.01 ppm, 0.1 ppm, and 10 ppm of TiO2. The results indicated that the expression of IL-6 at both 24 hrs and 72 hrs of exposure was not statistically significant (p>0.05). However, the expression levels of IL-6 were higher in TiO2-treated HGFs than in control (Figure 5).\n\nHGFs were stimulated with or without 0.01 ppm, 0.1 ppm and 10 ppm of TiO2. Gene levels of IL-1 beta at 24 hrs and 72 hrs were analyzed. The relative expression levels were normalized to the reference gene, 18s rRNA. The values are expressed as mean ± standard deviation (SD). Superscripts a and b indicate statistically significant differences at P<0.05.\n\nHGFs were stimulated with or without 0.01 ppm, 0.1 ppm, and 10 ppm of TiO2. Gene levels of TNF-alpha at 24 hrs and 72 hrs were analyzed. The relative expression levels were normalized to the reference gene, 18s rRNA. The values are expressed as mean ± standard deviation (SD). Superscripts a and b indicate statistically significant differences at P<0.05.\n\nHGFs were stimulated with or without 0.01 ppm, 0.1 ppm and 10 ppm of TiO2. Gene levels of IL-6 at 24 hrs and 72 hrs were analyzed. The relative expression levels were normalized to the reference gene, 18s rRNA. The values are expressed as mean ± standard deviation (SD).\n\nExpression of IL-10 analyzed at 24 hrs was significantly (P<0.05) higher in HGFs cultured with TiO2. Especially, TiO2 at 0.01 ppm resulted in higher expression of IL-10, and higher levels of 1 ppm and 10 ppm did not show any significant (P>0.05) difference in expression levels with control. At 72 hrs, a similar expression pattern of IL-10 was observed (Figure 6). Expression of TGF- beta analyzed at 24 hrs was not significant (p>0.05) in TiO2 treated HGFs when compared with control. However, at 72 hrs, the expression of TGF- beta was significantly (P<0.05) higher in controls with 0.01 ppm of TiO2 than in 0.1 ppm and 10 ppm (Figure 7). Expression of IL-12 analyzed at 24 hrs did not show any significant difference among TiO2 treated HGFs and Controls. However, at 72 hrs, the expression of IL-12 was significantly (P<0.05) higher in HGFs exposed to TiO2 than in control cells (Figure 8).\n\nHGFs were stimulated with or without 0.01 ppm, 0.1 ppm and 10 ppm of TiO2. Gene levels of IL-10 beta at 24 hrs and 72 hrs were analyzed. The relative expression levels were normalized to the reference gene, 18s rRNA. The values are expressed as mean ± standard deviation (SD). Superscripts a and b indicate statistically significant differences at P<0.05.\n\nHGFs were stimulated with or without 0.01, 0.1 and 10 ppm of TiO2. Gene levels of TGF-beta at 24 hrs and 72 hrs were analyzed. The relative expression levels were normalized to the reference gene, 18s rRNA. The values are expressed as mean ± standard deviation (SD). Superscripts a and b indicate statistically significant differences at P<0.05.\n\nHGFs were stimulated with or without 0.01 ppm, 0.1 ppm and 10 ppm of TiO2. Gene levels of IL-12 at 24 hrs and 72 hrs were analyzed. The relative expression levels were normalized to the reference gene, 18s rRNA. The values are expressed as mean ± standard deviation (SD). Superscripts a and b indicate statistically significant differences at P<0.05.\n\nThe levels of IL-1 beta analyzed at 24 hrs and 72 hrs was not significant (P>0.05) in TiO2 treated HGFs in comparison to control. The level of TNF- alpha analyzed at 24 hrs and 72 hrs was not significant (P>0.05) in TiO2 treated HGFs in comparison to control cells. The level of IL-6 analyzed at 24 hrs significantly (P<0.05) higher expression at 10 ppm of TiO2. At 72 hrs, the level of IL-6 was not statistically significant (P>0.05) in TiO2 treated HGFs at 0.01 ppm and 0.1 ppm in comparison to control cells (Figure 9).\n\nEffect of TiO2 nanoparticles on the cytokine expression of pro-inflammatory cytokines (IL-1 β, TNF- α, and IL-6 respectively), in human gingival fibroblasts (HGFs) exposed to different concentrations and durations. HGFs were stimulated with or without 0.01, 0.1 and 10 ppm of TiO2. Cytokine levels of IL-1 β, TNF- α, and IL-6 at 24 hrs and 72 hrs were analyzed by ELISA. The values are presented as pg/ml, and expressed as mean ± standard deviation (SD). Different superscripts (a, b) indicate a statistically significant difference at P<0.05.\n\nThe level of IL-10 analyzed at 24 hrs revealed that the expression of IL-10 at 24 hrs and 72 hrs in all tested concentrations was not statistically significant (P>0.05) in TiO2 treated HGFs in comparison to control cells. The level of TGF-beta analyzed at 24 hrs showed statistically significant difference (P<0.05) among TiO2 treated HGFs in comparison to control cells. However, at 72 hrs, no statistically significant (P>0.05) differences were found between the control cells and TiO2 treated HGFs (Figure 10).\n\nHGFs were stimulated with or without 0.01, 0.1, and 10 ppm of TiO2. Cytokine levels of IL-12 at 24 hours and 72 hours were analyzed by ELISA. The values are presented as pg/ml and expressed as mean ± standard deviation (SD). Different superscripts (a, b, c) indicate a statistically significant difference at P<0.05.\n\nThe level of IL-12 analyzed at 24 hrs was statistically significant (P<0.05) in TiO2 treated HGFs in comparison to control cells. However, at 72 hrs, no statistically significant (P>0.05) differences in IL-12 levels were found between the control and TiO2 treated HGFs (Figure 10).\n\n\nDiscussion\n\nImplants are widely employed as the restorative modality for replacing missing natural teeth. In the early 1970s, implant therapy was primarily considered as the treatment option for completely edentulous patients. However, in recent years, patients with partial edentulism have also become candidates for dental implants. There are various types of implants with several newer biomaterials used as zirconia, roxolid, surface-modified titanium, etc.\n\nAlloy-incorporated titanium mainly Ti-6Al-4V is considered as the most commonly used metal for the manufacture of dental implants because of the superior biocompatibility and physical properties such as low elastic modulus.26,27 Titanium implants in bone have been shown to continually emit Ti particles typically starting from a few hours to several months after the implant placement, that could exert a negative influence to the surrounding tissues.28 In general, Ti particles are insoluble in nature therefore their elimination from the body is challenging and they typically get scattered and accumulate in the hard and soft tissue surrounding the implant. Elevated concentrations of Ti particles become excessive, oral intraepithelial homeostasis is lost resulting in a exacerbate inflammation of the adjacent tissues, and causes dynamic imbalance between osteoblasts and osteoclasts. In addition, the Ti particles that gets released from the implant surface are not only confined to the tissue surrounding the implant, but they also travel with the circulation and accumulate gradually in the peripheral organs, generating systemic and allergic reactions.28 TiO2 NPs may diffuse into the peri-implant area triggering an inflammatory response and resorption of the alveolar bone, which mediates the development of peri-implantitis.29\n\nPeri-implantitis, a significant complication affecting up to 20% of patients and 30% of implants,30 is characterized by inflammation in the tissues surrounding dental implants. The World Workshop on Periodontology defines healthy peri-implant tissues as those exhibiting no bleeding on probing and minimal bone loss.31 In contrast, peri-implant mucositis presents with bleeding on probing but minimal bone loss. Peri-implantitis, however, is a more severe condition characterized by bleeding or suppuration upon probing, increased probing depth, and significant bone loss.31\n\nHGFs and periodontal cells serve as representatives of periodontium and therefore are widely used for in vitro research in periodontology.32 HGFs are considered as the major cellular components responsible for the repair of damages tissue and for creating a seal around the implants from the oral microflora.33 In the present study, TiO2 NPs particles of varied concentrations were used to study their reaction of human gingival fibroblasts for various durations. Evaluation of the cytotoxic effects, cytokine and gene expression was carried out in the present study. In the present study, TiO2 NPs particles of varied concentrations were used to study their interaction with human gingival fibroblasts for various duration, to elucidate the concentration-dependent cytotoxicity and modulation of the inflammatory response elicited by TiO2 NPs in human gingival fibroblasts (HGFs).\n\nIn the present study, viability of the HGFs were evaluated by an MTT assay in an interval of day 1, 3, 5 and 7 with varying concentrations of TiO2 ranging from 0.001 ppm to 100 ppm. The results demonstrated that the cytotoxicity of the HGFs have been affected on exposure to TiO2 nanoparticles when compared to the control group. This detrimental impact on HGFs also depends on the different concentrations of TiO2 nanoparticles as well their exposure to different time intervals. The finding of deterministic effects of Ti on the HGF cell lines can be matched with the finding of Choi MG et al. who reported similar negative impact of TiO2 nanoparticles on various cell lines including fibroblasts and osteoblasts activity.34 He et al. also reported the toxic effects of Ti particles on the survival of PDL cells, which is similar to the present study.35\n\nA significant decrease in the viability of HGF was noted with higher the concentration of TiO2 NPs and a longer exposure time led to a greater reduction in the cellular viability. It was also found that the proliferation of HGF at the end of 7 days, was the least in 100 ppm concentration of TiO2. This finding was in accordance with the study conducted by Jin et al. who had reported a direct proportional effect of the concentration and duration of TiO2 exposure on cytotoxicity.36 The cytotoxic effects of TiO2 NPs could be due to their ability to induce production of reactive oxides resulting in an elevated oxidative stress of the cells that could lead to damage of nucleic acids and lipids, interfering with signaling transduction pathways and modulating transcription factors (such as nuclear factor-B and activator protein-1). Subsequently, these mechanisms activate the antioxidant defense system and potentially cause cell death due to oxidative DNA damage.36\n\nIn the present study, A higher absorbance value of 0.4347 was recorded in HGFs treated with 0.001 ppm of TiO2 and the lowest absorbance value of 0.3225 was recorded in HGFs exposed to 100 ppm of TiO2, representing the proliferation of HGFs. Reduction in the proliferation capacity was noted with increase in the concentration of TiO2. These findings were supported by in vitro studies that have demonstrated that titanium particles at very minimal concentrations can stimulate fibroblast growth. Whereas higher concentrations inhibit the proliferation.37 The increased concentration TiO2 can suppress the proliferation of fibroblasts by mediating various growth factors at the cellular level, however, the mechanisms are poorly understood.\n\nLiterature evidences have reported that Ti-based particles could induce the proinflammatory response similar to an allergic reaction. Recent researchers have found that TiO2 NPs can elicit an inflammatory response, without the assistance of binding proteins to toll like receptor -4 (TLR-4), indicating the strong potential of TiO2 NPs to cause inflammation.21,38 In the present study, the expression of TNF- alpha was found to be reduced in HGFs exposed to TiO2 than the control group. But, Taira et al. had reported an increase in TNF-α on exposure to TiO2, which is in contrast to our findings.39\n\nThe expression of anti-inflammatory cytokines such as IL-10, TGF-β, IL-12 were found to be significantly higher in HGFs exposed to varied concentrations of TiO2, which demonstrates the activation of anti-inflammatory mechanism in response to the cellular changes caused due to TiO2 particles. Callejas JA et al. had reported similar high gene expression of IL-10 and TGF-β in response to Ti particles.40 IL-12 is a crucial cytokine associated with early innate immune response. It is also the primary mediator in maintaining the cell-mediated immune response, contributing to chronic inflammatory illness and studies have reported a higher expression of IL-12 genes to correlate with severe peri implantitis. Therefore, increased expression of these anti-inflammatory genes can lead to development of peri implantitis by activation of osteoclastogenesis. TNF-α is also considered as an important mediator associated with bone loss in peri-implantitis, correlating with the chronic and advanced stage of the disease. In the present study, our observation of reduced expression of TNF-α could be due to the short-term exposure to TiO2 particles (i.e only for 72 hours), rather than chronic exposure. TNF-α may also enhance osteoclast development indirectly by up-regulating the synthesis of RANKL by stromal cells and by enhancing the responsiveness of osteoclast precursors to RANKL. This may be another mechanism by which TNF-α promotes osteoclast formation.36,39\n\nIn the present study, a significant difference was noted in the expression of IL-6 upon initial exposure to TiO2 nanoparticles. The current findings are concurrent with that of Okuda et al.19 and Taira et al. in their study using DNA microarray technology reported similar overexpression of IL6 gene.39 The upregulation of expression of IL-6 could be attributed to the overexpression of heat shock protein 70 (HSP70) gene as a biologic response to TiO2 exposure due to the activity of cytotoxic mediators. It is also reported that the nanoparticles possessing magnetic properties can induce necrotic and cell death of the fibroblasts. The IL-6 gene is also upregulated by inflammation due to the release of TiO2 nanoparticles into the periodontal tissues.19 IL-1β expression is regarded as a marker representing the activation of inflammasome and cell viability. However, in this study the expression of IL-1β and IL-6 was more or less similar to that of controls by the end of 72 hours.\n\nThe results of ELISA indicated that the release of proinflammatory cytokines such as IL-1β, TNF-α, IL-6 to be unaltered in TiO2 exposed groups regardless of the concentrations on comparison with control HGFs. Also, the release of anti-inflammatory cytokines such as IL-10, TGF-β, IL-12 were almost similar in all tested concentrations of TiO2. This study reports a weaker pro and anti-inflammatory cytokine release from Human gingival fibroblast cells on exposure to TiO2. Similarly, Callejas JA et al. also reported reduced pro inflammatory cytokine release, which is relatable to our finding.40\n\nThe cytotoxic and altered gene expression of pro and anti-inflammatory mediators associated with increased concentrations of TiO2 can be related to the development of Peri-implantitis. Most studies have reported titanium particles of size 1–10 micrometer to be released from the implant surface, which are capable of diffusing into the tissues and systemic organs of the body. Recent studies have demonstrated that proinflammatory cytokines especially TNF-α, IL-1 and IL- 6 are generated during phagocytosis by local macrophages and the creation of an erosive pannus, which increases bone resorption by osteoclasts. Differentiation of macrophages into bone-resorbing osteoclast cells and subsequent bone resorption occurs extensively in the presence of TiO2 particle debris.34\n\nFrom the results obtained from this study, it is evident that the cytotoxic and immunologic response associated with TiO2 is directly related to the concentration and duration of exposure. However, the present study is bound for certain inherent limitations due to the nature of the study design. Also, the present study lacks evaluation of the cytotoxic and immunologic effects based on particle size of TiO2. Further researches, comparing the effects of TiO2 released from surface modified titanium implants should be undertaken to facilitate a multi-dimensional understanding of the adverse effects of TiO2 released from dental implants\n\n\nEthics and consent\n\nThis study was conducted with ethical approval from the Institutional Ethical Committee of the AB Shetty Memorial Institute of Dental Sciences, Nitte (Deemed to be University) (Certification number: ABSM/EC/112/2021), granted on 9th January, 2021. All procedures complied with the ethical standards of the Declaration of Helsinki, 2013.\n\n\nConsent to participate\n\nWritten informed consent was obtained and gingival tissue samples were collected from a total of three (n=3) systemically and periodontally healthy participants who reported to the Department of Periodontology, following approval from the Institutional Ethics Committee (ABSM/EC/112/2021).", "appendix": "Data availability\n\nThe data supporting the findings of this study are available in Open Science Framework with the following identifier:\n\nOSF: Influence of titanium nanoparticles on cytotoxicity and inflammatory cytokines expression in gingival fibroblasts - An in-vitro study https://doi.org/10.17605/OSF.IO/9QJG2.\n\nThis project contains the following underlying data:\n\n1. Data File 1: TI_V123 – Cell viability data set\n\n2. Data File 2: TI_Ab123 – Cell proliferation\n\n3. Data File 3: TI_PC123- PCR Data set\n\n4. Data File 4: TI_EL123 -ELISA Data set\n\n5. Data File 5: CRIS- CRIS Checklist for In-vitro studies\n\n6. Data File 6: Extended Data\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nSai SR: Influence of titanium nanoparticles on cytotoxicity and inflammatory cytokines expression in gingival fibroblasts - An in vitro study [Dataset]. OSF; 2024. https://doi.org/10.17605/OSF.IO/9QJG2 41\n\nThe data supporting the findings of this study are available in Open Science Framework with the following identifier:\n\nOSF: Influence of titanium nanoparticles on cytotoxicity and inflammatory cytokines expression in gingival fibroblasts - An in vitro study. https://doi.org/10.17605/OSF.IO/9QJG2 41\n\nThis project contains the following extended data:\n\n1. Extended Data: Contains information on Abbreviations used, Primer sequences, cDNA synthesis, Protocol for PCR, ELISA and additional images\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nSai SR: Influence of titanium nanoparticles on cytotoxicity and inflammatory cytokines expression in gingival fibroblasts - An in vitro study [Dataset]. OSF; 2024. https://doi.org/10.17605/OSF.IO/9QJG2 41\n\nThe authors affirm that the study has been conducted and reported in accordance with the CRIS (Consolidated Reporting for In-vitro Studies) guidelines, and a detailed description of the study’s background, objectives, and significance have been provided. The manuscript includes comprehensive information on the cell lines used, culture conditions, experimental design, and methods of data analysis. We have presented our results clearly with appropriate figures and tables, and have included detailed statistical analyses. The discussion contextualizes our findings, acknowledges the study’s limitations, and proposes future research directions. All relevant references are cited, and we have disclosed any potential conflicts of interest.\n\nSupplementary materials supporting our study are provided, and we have ensured that data availability is clearly communicated. Although our research involves only in-vitro methods, we have adhered to ethical guidelines concerning the use of cell lines.\n\nhttps://doi.org/10.17605/OSF.IO/9QJG2\n\n\nAcknowledgements\n\nWe gratefully acknowledge the Department of Periodontology for providing the resources and facilities necessary to conduct this research.\n\n\nReferences\n\nAraujo MG, Lindhe J: Peri-implant health. J. Periodontol. 2018; 89: 89. Publisher Full Text\n\nBerryman Z, Bridger L, Hussaini HM, et al.: Titanium particles: An emerging risk factor for peri-implant bone loss. Saudi Dent. J. 2020; 32: 283–292. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCai K, Hou Y, Hu Y, et al.: Correlation of the cytotoxicity of TiO2 nanoparticles with different particle sizes on a sub-200-nm scale. Small. 2011; 7: 3026–3031. PubMed Abstract \| Publisher Full Text\n\nCallejas JA, Gil J, Brizuela A, et al.: Effect of the size of titanium particles released from dental implants on immunological response. Int. J. Mol. Sci. 2022; 23: 7333. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoi MG, Koh HS, Kluess D, et al.: Effects of titanium particle size on osteoblast functions in vitro and in vivo. Proc. Natl. Acad. Sci. USA. 2005; 102: 4578–4583. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCzajka M, Sawicki K, Sikorska K, et al.: Toxicity of titanium dioxide nanoparticles in central nervous system. Toxicol. In Vitro. 2015; 29: 1042–1052. Publisher Full Text\n\nDuarte PM, De Mendonça AC, Máximo MB, et al.: Clinical oral implants research.2009; 20: 514–520.\n\nFretwurst T, Nelson K, Tarnow DP, et al.: Is metal particle release associated with Peri-implant bone destruction? An emerging concept. J. Dent. Res. 2018; 97: 259–265. PubMed Abstract \| Publisher Full Text\n\nGaretto LP, Chen J, Parr JA, et al.: Remodeling dynamics of bone supporting rigidly fixed titanium implants: a histomorphometric comparison in four species including humans. Implant. Dent. 1995; 4: 297. Publisher Full Text\n\nHashim D, Cionca N: A comprehensive review of Peri-implantitis risk factors. Curr. Oral Health Rep. 2020; 7: 262–273. Publisher Full Text\n\nHe X, Hartlieb E, Rothmund L, et al.: Intracellular uptake and toxicity of three different Titanium particles. Dent. Mater. 2015; 31: 734–744. PubMed Abstract \| Publisher Full Text\n\nJin C-Y, Zhu B-S, Wang X-F, et al.: Cytotoxicity of titanium dioxide nanoparticles in mouse fibroblast cells. Chem. Res. Toxicol. 2008; 21: 1871–1877. Publisher Full Text\n\nJorge JRP, Barão VA, Delben JA, et al.: Titanium in dentistry: Historical development, state of the art and future perspectives. J. Indian Prosthodont. Soc. 2013; 13: 71–77. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim J-J, Lee J-H, Kim JC, et al.: Biological responses to the transitional area of dental implants: Material- and structure-dependent responses of Peri-implant tissue to abutments. Materials (Basel). 2019; 13: 72. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLappas CM: The immunomodulatory effects of titanium dioxide and silver nanoparticles. Food Chem. Toxicol. 2015; 85: 78–83. PubMed Abstract \| Publisher Full Text\n\nLekic PC, Pender N, McCulloch CAG: Is fibroblast heterogeneity relevant to the health, diseases, and treatments of periodontal tissues? Crit. Rev. Oral Biol. Med. 1997; 8: 253–268. PubMed Abstract \| Publisher Full Text\n\nMano SS, Kanehira K, Taniguchi A: Comparison of Cellular Uptake and Inflammatory Response via Toll-Like Receptor 4 to Lipopolysaccharide and Titanium Dioxide Nanoparticles. Int. J. Mol. Sci. 2013; 14: 13154–13170. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarcantonio C, Nicoli LG, Marcantonio Junior E, et al.: Prevalence and possible risk factors of Peri-implantitis: A concept review. J. Contemp. Dent. Pract. 2015; 16: 750–757. PubMed Abstract \| Publisher Full Text\n\nMatusiewicz H: Potential release of in vivo trace metals from metallic medical implants in the human body: From ions to nanoparticles-A systematic analytical review. Acta Biomater.\n\nMessous R, Henriques B, Bousbaa H, et al.: Cytotoxic effects of submicron- and nano-scale titanium debris released from dental implants: an integrative review. Clin. Oral Investig. 2021; 25: 1627–1640. PubMed Abstract \| Publisher Full Text\n\nMombelli A, Hashim D, Cionca N: What is the impact of titanium particles and biocorrosion on implant survival and complications? A critical review. Clin. Oral Implants Res. 2018; 29: 37–53. PubMed Abstract \| Publisher Full Text\n\nNoronha Oliveira M, Schunemann WVH, Mathew MT, et al.: Can degradation products released from dental implants affect peri-implant tissues? J. Periodontal Res. 2018; 53: 1–11. PubMed Abstract \| Publisher Full Text\n\nOkuda-Shimazaki J, Takaku S, Kanehira K, et al.: Effects of titanium dioxide nanoparticle aggregate size on gene expression. Int. J. Mol. Sci. 2010; 11: 2383–2392. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOliveira N, Schunemann M, Mathew WV, et al.: Periodontal Res. 2018; 53: 1–11.\n\nOlmedo DG, Nalli G, Verdú S, et al.: Exfoliative cytology and titanium dental implants: A pilot study. J. Periodontol. 2013; 84: 78–83. PubMed Abstract \| Publisher Full Text\n\nPathak AK, Goel K, Shakya V, et al.: Periodontal parameters around implants and natural teeth. Natl. J. Maxillofac. Surg. 2016; 7: 52–55. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPettersson M, Almlin S, Romanos GE, et al.: Inflammation.2022; 45: 2027–2037.\n\nPettersson M, Kelk P, Belibasakis GN, et al.: Titanium ions form particles that activate and execute interleukin-1β release from lipopolysaccharide-primed macrophages. J. Periodontal Res. 2017; 52: 21–32. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRehn B, Seiler F, Rehn S, et al.: Toxicol. Appl. Pharmacol. 2003; 189: 84–95. PubMed Abstract \| Publisher Full Text\n\nRomagnani S, Parronchi P, D’elios M, et al.: Immune mechanisms in the pathogenesis of inflammatory gastrointestinal disorders. Ital. J. Gastroenterol. 1996; 28 Suppl 2: 11–17. PubMed Abstract\n\nRomanos G, Fischer G, Delgado-Ruiz R: Titanium wear of dental implants from placement, under loading and maintenance protocols. Int. J. Mol. Sci. 2021; 22: 1067. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRomanos GE, Delgado-Ruiz R, Sculean A: Concepts for prevention of complications in implant therapy. Periodontol. 2000; 81(81): 7–17. Publisher Full Text\n\nSaini M: Implant biomaterials: A comprehensive review. World J. Clin. Cases. 2015; 3: 52–57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSanz M, Chapple IL: Working Group 4 of the VIII European Workshop on Periodontology. Clinical research on peri-implant diseases: consensus report of Working Group 4. J. Clin. Periodontol. 2012; 39 Suppl 12: 202–206. PubMed Abstract \| Publisher Full Text\n\nSomerman MJ, Archer SY, Imm GR, et al.: A comparative study of human periodontal ligament cells and gingival fibroblasts in vitro. J. Dent. Res. 1988; 67: 66–70. Publisher Full Text\n\nSong B, Liu J, Feng X, et al.: A review on potential neurotoxicity of titanium dioxide nanoparticles. Nanoscale Res. Lett. 2015; 10: 1042. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSuárez-López del Amo F, Garaicoa-Pazmiño C, Fretwurst T, et al.: Dental implants-associated release of titanium particles: A systematic review. Clin. Oral Implants Res. 2018; 29: 1085–1100. PubMed Abstract \| Publisher Full Text\n\nTaira M, Kagiya T, Harada H, et al.: Microscopic observations and inflammatory cytokine productions of human macrophage phagocytising submicron titanium particles. J. Mater. Sci. Mater. Med. 2010; 21: 267–275. PubMed Abstract \| Publisher Full Text\n\nTaira M, Nezu T, Sasaki M, et al.: Gene expression analyses of human macrophage phagocytizing sub-μ titanium particles by allergy DNA chip (GenopalTM). Biomed. Mater. Eng. 2009; 19: 63–70. PubMed Abstract \| Publisher Full Text\n\nVijayashree RJ, Sivapathasundharam B: The diverse role of oral fibroblasts in normal and disease. J. Oral Maxillofac. Pathol. 2022; 26: 6–13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSai SR: Influence of titanium nanoparticles on cytotoxicity and inflammatory cytokines expression in gingival fibroblasts - An in vitro study. [Dataset]. OSF. 2024. Publisher Full Text" }	[ { "id": "334144", "date": "11 Nov 2024", "name": "Waad Kheder", "expertise": [ "Reviewer Expertise Dental Implants", "Molecular Medicine and Translational Research", "Prosthodontic Dentistry", "Bone Regeneration" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 Thank you for submitting the article entitled \" Influence of Titanium Nanoparticles on Cytotoxicity and Inflammatory Cytokines Expression in Gingival Fibroblasts - An In Vitro Study\" This study examined the concentration-dependent effects of titanium dioxide nanoparticles (TiO₂NPs) on the expression of pro-inflammatory (IL-1β, IL-6, TNF-α) and anti-inflammatory (IL-10, IL-12, TGF-β) cytokines as well as the viability of human gingival fibroblasts (HGFs). The findings demonstrated that longer exposure times and greater concentrations of TiO₂NPs alter cytokine expression and decrease HGF viability. This topic holds significant relevance due to the increasing use of titanium implants in dental practices and the potential for nanoparticle release to influence surrounding tissues adversely. Understanding these effects is crucial for implant biocompatibility and long-term success.\nStrengths of the Study\nThe study clearly identifies gaps in knowledge regarding the dose-dependent effects of TiO2NPs on HGFs, aiming to clarify potential risks to peri-implant tissue health. The study addressed an important issue in dental implantology by exploring how titanium nanoparticles may contribute to peri-implantitis, a prevalent complication of dental implants. The study used a well-structured technique that incorporated multiple TiO₂NPs concentrations and time intervals to evaluate cytotoxicity and cytokine expression. The authors used a range of concentrations and varied exposure times to assess the dose and time-dependent cytotoxic effects of TiO2NPs. Techniques such as MTT assay for cell viability, qRT-PCR and ELISA for detailed insights into cytokine expression levels, enhancing the study's reliability. The study’s findings that TiO2NP exposure can decrease cell viability and increase pro-inflammatory cytokine expression support concerns regarding peri-implantitis. This evidence could guide future dental material choices and safety evaluations.\n\nLimitations of the Study\nSample size: The study included gingival tissue samples from three healthy individuals. Increasing the sample size would result in a stronger dataset and improved generalizability of the findings. Inflammatory Markers: While major cytokines such as IL-1β, IL-6, TNF-α, and IL-10 were examined, including other markers could provide a more complete picture of the inflammatory response. Short-Term Exposure Data: The study's time limit (up to 7 days) may not accurately reflect the chronic exposure found in patients with implants. Extending exposure times may better imitate real-world situations.\nGeneral Comments The manuscript followed the journal requirements regarding clarity, rigor, and transparency. However, a more specific description of mechanistic insights and potential clinical consequences for the use of titanium implants could increase the study's significance. Minor faults with grammar and flow exist, but they do not detract from the overall readability.\nExamples: · In sentences like “HGFs were isolated from gingival tissue samples obtained from periodontally and systemically healthy subjects,” consider simplifying the phrase structure for readability: “HGFs were isolated from healthy gingival tissue samples.” · Replace complex constructions like “varied concentrations of TiO2NPs were used to study their interaction with human gingival fibroblasts for various durations” with “various concentrations of TiO2NPs were tested on human gingival fibroblasts for different durations.”\nIntroduction The background was informative and presents the clinical relevance of the study. However, the introduction could benefit from a more detailed description of previous studies specifically addressing TiO₂NPs effects on gingival fibroblasts, if available, to establish the study's novelty.\nMethods The methodology was rigorous and sufficiently detailed. However, including the exact sizes of TiO₂NPs would enhance reproducibility. Clarifying why these specific concentrations (0.01 ppm, 0.1 ppm, 10 ppm) were selected for further cytokine expression analysis would be beneficial, as it might indicate threshold levels of cytotoxicity.\nResults The results were presented clearly, with the dose-dependent trends in cytotoxicity and cytokine expression well-illustrated through appropriate figures, however several areas could be clarified:\nData related to IL-1β, and IL-6 expression appear inconsistent over different time points, which is acknowledged but not explained. Additional analysis or discussion could address these variations. Including more visual data, such as representative images of cell morphology changes at different TiO₂NPs concentrations, could further illustrate cytotoxic effects.\nDiscussion The discussion successfully placed the findings in the context of existing literature. However: Consider expanding on the mechanisms by which TiO₂NPs modulate cytokine expression. While oxidative stress was mentioned, referencing additional pathways could deepen the understanding of potential pathways to peri-implantitis.\nConclusion Overall, this study provided valuable information regarding the potential cytotoxic and inflammatory effects of TiO2NPs on gingival fibroblasts, highlighting a possible risk factor for peri-implantitis. Expanding on this work with larger, diverse samples and extended exposure studies could further enhance our understanding and ultimately improve the safety and success of titanium dental implants. With the suggested minor revisions, this paper will be a strong addition to the literature on nanotoxicology in dental materials.\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/13-1117
https://f1000research.com/articles/13-306/v1	22 Apr 24	{ "type": "Case Report", "title": "Case Report: Post-operative mitral valve replacement complicating with a large cardiac mass and role of TEE in decision making", "authors": [ "Narasimha Pai D", "Chaithra Nayak", "Padmanabh Kamath", "Syed Waleem Pasha", "Deepa Noronha", "Narasimha Pai D", "Padmanabh Kamath", "Syed Waleem Pasha", "Deepa Noronha" ], "abstract": "Background Postoperative complications are an integral part of valve surgery. Common complications include hematomas, bleeding, valve dehiscence, paravalvular leak, and acute PV thrombosis. With the available data from published articles, the rate of all valve-related complications is 0.7 to 3.5% per patient annually. [1] The pathology involved is multifactorial, often blood vessel injury leading to bleeding and hematoma. Although postoperative complications are evident, incidental diagnosis of a cardiac mass in an asymptomatic and hemodynamically stable patient postoperatively is crucial, requiring non-invasive imaging for immediate surgical action.\n\nCase presentation A woman in her 50s presented with chief complaints of worsening dyspnoea with suddenonset and chest pain. Clinical findings showed apex shifted downward and outward, wide split S2, and a mid systolic murmur radiating to the mid axillary line. Twelve-lead ECG showed LA enlargement, that aligned with X-ray findings. 2D Echocardiography revealed MVP with severe MR and a dilated LV. The patient underwent successful mitral valve replacement as per ACC/AHA class I recommendation. However, postoperative TTE showed a remarkably large mass measuring 5.6 cm4.6 cm in the RA. Reexploration was performed, followed by mass excision. Plenty of organized clots were seen compressing the RA. TEE showed no evidence of mass. Following stabilization,the patient was discharged considering optimal INR values and prosthetic valve function assessed by echocardiography. The patient’s symptoms improved during the first follow-up.\n\nConclusion Although postoperative cardiac complications are common, appropriate diagnosis with TTE and TEE has benefited surgeons. TEE-guided reexploration aids surgeons in decision-making and strategic approaches. Failure to diagnose such complications in asymptomatic patients can ultimately complicate the procedure. Henceforth, sonographers must be skilled in the detection and identification of unusual complications to guide redo interventions. Such an approach minimizes mortality, redo procedures, and avoids CPB hence reducing long-term prognosis and outcomes with valve replacement.", "keywords": [ "Prosthetic mitral valve", "Echocardiography", "Reexploration", "Cardiac mass", "Complication" ], "content": "Introduction\n\nImmediate postoperative complications are part and parcel of surgical valve replacement. Commonly witnessed complications include hematoma, bleeding, valve dehiscence, paravalvular leak, and acute prosthetic valve thrombosis. With the data available from published articles, the rate of all valve-related complications was 0.7 to 3.5% per patient annually.1 The pathology involved is multifactorial, often involving blood vessel injury leading to bleeding and hematoma formation. Although postoperative complications are quite evident, we report an unusual case of incidental diagnosis of a cardiac mass in an asymptomatic and hemodynamically stable patient postoperatively, requiring non-invasive imaging in immediate surgical action.\n\n\nCase report\n\nA woman in her 50s presented with chief complaints of breathlessness for one year and associated palpitations for the past three months. On evaluation, breathlessness was sudden in onset and progressively worsened from NYHA class II to III. The patient had a history of PND and a known case of rheumatic heart disease (duration unclear) that was managed conservatively. There was no prior history of orthopnea. However, she did report experiencing exertional palpitations characterized by sudden onset and relief upon resting. No family history of cardiac illnesses was documented. On examination, her blood pressure and pulse rate were 130/78 mmHg and 90/min, respectively. Physical examination showed the apex to be outwards and shifted to the lower 6th ICS 1 cm lateral to the mid-clavicular line, hyperdynamic in character, and well localized, suggestive of an ‘LV’ type apex. On auscultation, a non-ejection click was heard at the apex with soft S1 and a wide split S2. LVS3 and LVS4 were absent. A mid-systolic murmur of grade 3/6 was heard at the apex immediately after the click, with radiation to the mid axillary line.\n\nA standard 12-lead ECG was performed which showed sinus arrhythmia with a notched P wave in the inferior leads and a prominent biphasic P wave in lead V1, suggestive of biatrial enlargement (Figure 1). Chest radiography revealed cardiomegaly with a double-density shadow and LV enlargement. These findings suggested a left heart aetiology (Figure 2).\n\n2D transthoracic echocardiography was performed one day before the planned procedure. The findings showed mitral valve prolapse (bileaflet) with eccentric MR jet (EROA 0.43 cm2, regurgitant volume = 91 ml), dilated LA, and borderline dilated LV with preserved LV function. The RV function was preserved with mild TR. Absence of pericardial effusion/thrombus was documented during the preoperative echocardiography. 2D echocardiography confirmed severe mitral regurgitation requiring surgery as per the current ACC/AHA class I recommendation and was referred to a cardiothoracic surgeon for further management, wherein she was advised to undergo mitral valve replacement. To rule out coronary artery disease, a diagnostic coronary angiography was performed which revealed normal epicardial arteries (Figure 3).\n\nPreoperative investigations included routine blood tests, thyroid function tests, serology, cardiac enzymes, urine analysis, and serum electrolytes. The procedure was planned following all the above-mentioned investigated parameters being within their reference limits. All the investigated parameters were within the reference limits, and the procedure was planned accordingly. The procedure was executed with aseptic precautions and general anesthesia. A median sternotomy was performed, where the pericardium was opened and cradled. The patient was adequately heparinized and constantly monitored for the coagulation parameters. Routine aortic and bicaval cannulation of the SVC, IVC, LA was carried out and antegrade cardioplegic cannula was carried out besides initiating CPB. Aorta was cross-clamped and root cardioplegia was administered to arrest the heart. The left atrium was opened, followed by excision and replacement of mitral valve with a 31 M TTK Chitra Heart Valve using a 2/0 pledgetted suture. The valve was checked for its functionality using transoesophageal echocardiography. The left atrium was closed in two layers with 3/0 prolene. Routine deaeration and cross-clamping were performed, and the bypass was smoothly weened off. Protamine was administered and routine decannulation was performed followed by placement of RV pacing wire along with mediastinal drain tubes. On achieving hemostasis, the sternum was closed with steel wires, and the chest was closed in layers.\n\nThe patient was transferred to the intensive care unit for postoperative care. The vital signs were stable, and the patient received inotropic support. Postoperative echocardiography could not be performed because of an insufficient acoustic window soon after the patient was received. However, TTE was performed within 24 hours to assess prosthetic valve function. Valve functioning appeared optimal, with a trivial transvalvular leak. The forward flow gradients were acceptable (5/3 mmHg) with adequate biventricular function. Postoperative echo remarkably showed a large mass measuring 5.6 cm4.6 cm extensively occupying the RA cavity when examined from the apical 4-chamber (Video 1) and subcostal 4-chamber views (Video 2). The subcostal IVC long axis showed an IVC within normal limits and adequate collapsibility (Video 3). No flow obstruction was noted across the tricuspid valve or SVC (Figure 4) (Video 4).\n\nAlthough the patient was adequately anticoagulated post procedure, transoesophageal echocardiography confirmed the presence and extension of a mass (Video 5) which intruded the RA cavity. An organized echogenic mass, homogenous in appearance, was observed along the lateral wall of the RA with regular borders (Figure 5) (Video 6).\n\nMitral valve replacement was performed using the traditional approach of a vertical left atriotomy. Susceptibility to thrombus formation can be anticipated due to the presence of a prosthetic valve or sluggish flow in the setting of CHF or cardiomyopathy, which was not observed. The likelihood of thrombus formation within the right atrium was considered the to be least likely based on the echocardiographic diagnosis, since the patient had no provoking factors, as listed above. Intraoperative echocardiography was performed to assess cardiac function before proceeding with surgery, which revealed the absence of clots within the right atrium and major venous channels. Although the atria were dilated, no spontaneous contrast was observed within the chambers, which could be a precursor to thrombus formation.\n\nNormal anatomical variants include prominent thymus glands situated in the superior and anterior mediastinum. It intervenes between the sternum in the front and the pericardium located between the right atria. The thymus progressively increases in size during puberty and undergoes involution at a later age. From the surgeon’s point of view, the thymus was unnoticeable during the examination and was likely to be mistaken for a mass on echocardiography. No history of radiation and chemotherapy or hypercoagulable state/DVT/PE was documented.\n\nPostoperative radiography revealed the absence of mediastinal widening with a well-functioning prosthesis and acceptable transvalvular gradients. TEE exhibited good prosthetic function in the absence of a thrombus. The above-listed conditions were not observed and thus omitted before concluding the possible causes of complications. Various studies have identified common immediate postoperative complications, including active bleeding, PVT, wound infection, valve dehiscence causing paravalvular leak, and mediastinal haemorrhage that required reoperation. Other complications include apical extra pleural hematomas, which were identified on chest radiographs as mediastinal widening with increased mediastinal tube drainage.2 Therefore, we believe that a possible complication favouring intracardiac or extracardiac mass requires reexploration under the guidance of TEE.\n\nOn TEE, prosthetic valve function was good (Video 7), with trivial transvalvular leakage and a non-thrombosed valve with a large mass occupying the RA cavity (Figure 6). This led surgeons to decide whether to re-explore the heart or chest only. TEE was performed on a table to assist the surgeon in deciding on a strategic approach for mass excision.\n\nThe diagnosis required immediate management and surgical excision under TEE imaging, with or without exploration of the right atrium. Reexploration was planned under TEE guidance and CPB as a standby if the location was intracardiac. The procedure was performed under general anaesthesia. The sternal wires were then opened and retracted. Multiple organized clots were noted in excess, over the right atrium compressing it externally, consequently placing them intrapericardially (extracardiac) (Figure 6). The clots were excised and had no signs of active bleeding. Post reexploration, TEE did not disclose any intracardiac mass (Video 8), and the RA was decompressed; hence, the patient did not undergo cardiopulmonary bypass (Figure 7) (Video 9). Prosthetic valve function was good after excision of the clot (Video 10). Postoperative ECG showed 1st-degree AV block and frequent VPCs (Figure 8).\n\nChest radiography was performed after re-exploration that showed intact sternal rings, with well seated mitral prosthesis (Figure 9). The patient was stable and transferred to the intensive care unit. Repeat blood investigations were performed, and the output was monitored. The serum creatine and electrolyte levels were within the reference limits. She was advised to undergo physiotherapy rehabilitation as supportive care and was discharged a week later.\n\nThe patient was stable on discharge and was asked to monitor the INR and revisit the physician after noticing any signs of bleeding or worsening symptoms. Postoperative echocardiography showed a well-functioning prosthesis and resolution of the clot on the RA side. The patient was symptomatically better (NYHA class I) during the first follow-up at 15 days post-discharge. Chest radiography showed prosthesis in situ with no signs of pericardial or pleural effusion. Currently, she is under regular follow-up and is being screened for prosthetic valve function and symptoms.\n\n\nDiscussion\n\nPostoperative valve-related complications commonly include site and mediastinal bleeding, prosthetic valve dysfunction, prosthetic valve endocarditis, and thromboembolic events.3 Complications are elements of valvular surgery that require intense follow-up; hence, echocardiography plays a vital role in the detection of early complications. However, British guidelines recommend echocardiographic imaging soon after implantation to detect early valve deterioration and plan accordingly on the timing for redo intervention.4 From the point of care, repeat echocardiography is indicated at a frequency that depends on the underlying pathology in order to assess LV performance and pericardial effusion postoperatively.\n\nEchocardiography is indicated if there is a suspicion based on the new onset of symptoms that commonly include breathlessness, fever, or clinical findings with a new onset of murmur.4 Patients undergoing valve replacement require careful postoperative follow-up. Unlike the abovementioned complications, this case had an unusual presentation of extracardiac/intrapericardial hematoma that extrinsically compressed the right atrium with no evidence of pericardial tamponade, an immediate postoperative complication.\n\nA similar case reported intrapericardial hematoma presenting with isolated right atrial tamponade, wherein the diagnosis was confirmed by computed tomography (CT) followed by transthoracic echocardiography.5\n\nStudies state that, a prior history of cerebrovascular events is a risk factor for thromboembolic episodes or bleeding complications.6–8 Moreover, studies have reported that significant mediastinal bleeding requiring exploration is not related to preoperative coagulation factors, anticoagulant use, or total cardiopulmonary bypass time.9 The current patient experienced bleeding within 24 h after the surgery, which was evident by the collection of blood in the mediastinal drains. This is a routine bleeding observed in most cardiac surgery patients, as heparin was used during the procedure. Postoperative complications are likely to be missed if they are located outside of the imaging plane.10\n\nThe current study showed that, hematoma surrounding the right atrium as a result of bleeding due to blood vessel injury was difficult to distinguish as intrapericardial/extracardiac hematoma from the djacent tissues on TTE. Although TEE imaging is considered standard imaging during cardiac procedures, its utility has yielded greater assistance for surgeons in tracing hematoma and its extent, limiting procedural time, considering suitable decisions, and looking for any residue post exploration. The necessity of TEE is imperative for further management in this case. Although studies state TEE as point of care peri-and post-operative, it aids surgeons in excising hematoma on table, thereby limiting the CPB time and minimizing bleeding as a result of anticoagulation.\n\nHence, a thorough echocardiographic examination through multiple windows postoperatively is essential, as mediastinal bleeding involves multifactorial mechanisms. This case report provides insights into the importance of TEE and its utility both operatively and postoperatively, aiding surgeons in resolving this dilemma and considering appropriate management. we thereby conclude that TEE-guided reexploration has enormously directed surgeons in making notable decisions.\n\n“Her initial diagnosis of the disease was made at a tertiary care hospital. We explained the disease severity and prognosis, if not treated. Her symptoms worsened, limiting her daily activities. Initially, we were concerned about the major surgery, but post counseling, we decided to move ahead. We were explained about the procedural complications by the surgeon. Postsurgical nursing care was helpful in her early recovery. The initial days after discharge were difficult, but with constant family support, she was able to adjust to the environment and perform routine activities independently. We are very thankful to the hospitality and care provided by the health care staffs throughout her stay”.\n\nDetails provided by patient’s son.\n\nEthical approval was not required as it is case report. Written informed consent was acquired from the patient’s representative, with approval for waiver granted by the ethics committee. The patient’s guardian has granted consent for publication of the case details while ensuring participant anonymity. The patient has also agreed to the submission of the case report to the journal.", "appendix": "Data availability\n\nNo data were associated with this article.\n\nFigshare: Case Report: Post-Operative Mitral Valve Replacement Complicating with a Large Cardiac Mass and Role of TEE in Decision Making”, figshare data, 10.6084/m9.figshare.25547809.v1. 11\n\nThis project contains the following underlying data:\n\nDate file 1: Case images\n\nDate file 2: Media files and Care checklist\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe acknowledge Dr. Harish Raghavan and Mrs. Indira for actively providing patient care during follow-up. We also acknowledge our clinical staff for tracing the relevant data collected from medical records. We are thankful to the nursing care staff for collecting the hematological data.\n\n\nReferences\n\nMisawa Y: Valve-related complications after mechanical heart valve implantation. Surg. Today. 2015 Oct; 45(10): 1205–1209. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarter AR, Sostman HD, Curtis AM, et al.: Thoracic alterations after cardiac surgery. Am. J. Roentgenol. 1983 Mar 1; 140(3): 475–481. Publisher Full Text\n\nKhan IA, Patwardhan A: Early complications in patients undergoing mitral valve replacement surgery: An observational study. J. Datta Meghe Inst. Med. Sci. Univ. 2020 Jul 1; 15(3): 454. Publisher Full Text\n\nChambers JB, Garbi M, Briffa N, et al.: Indications for echocardiography of replacement heart valves: a joint statement from the British Heart Valve Society and British Society of Echocardiography. Echo Res. Pract. 2019 Mar 1; 6(1): G9–G15. PubMed Abstract \| Publisher Full Text\n\nHuang HD, Garcia M, Alam M, et al.: Postoperative intrapericardial hematoma presenting as isolated right atrial tamponade. J. Cardiol. Cases. 2014 Feb 1; 9(2): 48–49. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMisawa Y, Fuse K, Saito T, et al.: Fourteen-year experience of the Omnicarbon prosthetic heart valve. ASAIO J. 2001; 47: 677–682. PubMed Abstract \| Publisher Full Text\n\nLabaf A, Grzymala-Lubanski B, Stagmo M, et al.: Thromboembolism, major bleeding and mortality in patients with mechanical heart valve-a population- based cohort study. Thromb. Res. 2014; 134: 354–359. PubMed Abstract \| Publisher Full Text\n\nBourguignon T, Bergöend E, Mirza A, et al.: Risk factors for valve-related complications after mechanical heart valve replacement in 505 patients with long-term follow up. J. Heart Valve Dis. 2011; 20: 673–680. PubMed Abstract\n\nMichelson EL, Torosian M, Morganroth J, et al.: Early recognition of surgi-cally correctable causes of excessive mediastinal bleeding after coronary arterybypass graft surgery. Am. J. Surg. 1980; 139: 313–317. PubMed Abstract \| Publisher Full Text\n\nKerber RE, Payvandi MN: Echocardiography in acute hemopericardium: pro-duction of false negative echocardiograms by pericardial clots. Circulation. 1977; 55–56(Suppl. 111): 11–24.\n\nNarasimha P, Chaithra N, Padmanabh K, et al.: Case report. figshare. Dataset. 2024. Publisher Full Text" }	[ { "id": "291827", "date": "19 Jun 2024", "name": "Adem Aktan", "expertise": [ "Reviewer Expertise This case report comprehensively address a rare complication and provide significant clinical insights. However", "publication following the suggested improvements in the manuscript is appropriate." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report meticulously address a rare complication following cardiac valve replacement, offering significant clinical insights. However, several refinements can be suggested for the manuscript:\n1. The introduction should commence with an emphasis on the definition and implications of an intrapericardial hematoma, rather than starting with a general overview of postoperative complications. 2. In the case report, clinical findings and diagnostic imaging results should be presented in a more coherent sequence. There should be a clear linkage established between clinical observations and radiological evaluations. 3. The section on Transoesophageal Echocardiography (TEE) could more prominently underscore how TEE guided decision-making and its critical role in patient management. 4. Additional details are warranted regarding postoperative management strategies and follow-up protocols. 5. In the discussion section, recommendations can be provided on how similar case reports can be integrated into the literature and suggestions can be made for managing such rare complications. 6. The conclusion should succinctly highlight the clinical significance of the case report and its implications for future clinical practice and management of similar cases. 7. References 1, 9, and 10 should be updated with more recent sources.\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": [ { "c_id": "12456", "date": "01 Oct 2024", "name": "chaithra Nayak", "role": "Author Response", "response": "Mrs. Chaithra Nayak, Department of Cardiology, KMC, Mangalore Dear reviewers, We thank you for your valuable time and comments Please find the responses for the comments received attached with a response sheet Dear Dr. Adem Aktan Thank you for your thoughtful and insightful review of our paper. 1. The introduction should commence with an emphasis on the definition and implications of an intrapericardial hematoma, rather than starting with a general overview of postoperative complications. Response comments: This was truly a valuable comment. We have incorporated the necessary information related to the definition of the complication witnessed in the case report and have carried out the essential revisions as stated above (Page no. 4, paragraph 1). 2. In the case report, clinical findings and diagnostic imaging results should be presented in a more coherent sequence. There should be a clear linkage established between clinical observations and radiological evaluations Response comments: We sincerely appreciate your comments and observations. We have made the necessary revisions to better communicate the clinical findings (Page no. 5, paragraph 1,2). 3. The section on Transesophageal Echocardiography (TEE) could more prominently underscore how TEE guided decision-making and its critical role in patient management. Response comments: Thank you for your valuable comments and suggestions. After thoroughly reviewing the manuscript and checking for the reviewer's comments, we strongly feel a disparity in projecting TEE as a superior imaging tool. TEE, however, played a vital role in imaging the complication in this current study. However, due to its limitations, did not yield greater benefits in determining the location. Therefore, its utility in decision-making is less highlighted here (Page no.9, paragraph 4). 4. Additional details regarding postoperative management strategies and follow-up protocols are warranted. Response comments: Thank you for the suggestions. The above-stated points are critically reviewed by us. The management strategies are aligned and post-operative follow-up data are adequately covered under the section Outcome and follow-up (Page no.10, paragraph 1,2,3). 5. In the discussion section, recommendations can be provided on how similar case reports can be integrated into the literature and suggestions can be made for managing such rare complications Response comments: We appreciate your time in thoroughly revising this paper. Findings related to the management of postoperative complications for similar case studies are included and their novel treatment approaches for such similarly reported cases (Page no.8, paragraph 2; Page no.9, paragraph 1,2). 6. The conclusion should succinctly highlight the clinical significance of the case report and its implications for future clinical practice and management of similar cases. Response comments: We value your feedback points upon reviewing the paper. We have thoughtfully added the points highlighting the clinical importance and the need for imaging which is crucial to monitor such complications. The above-mentioned comments with necessary corrections have been implemented in this paper (Page no. 11,12,13). 7. References 1, 9, and 10 should be updated with more recent sources. Response comment: We are thankful for the in-depth revision. The necessary corrections have been carried out (Page no 15,16)." } ] }, { "id": "291828", "date": "01 Jul 2024", "name": "Raif Kılıç", "expertise": [ "Reviewer Expertise Heart valve diseases", "heart failure", "arrhythmia", "interventional cardiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this case report, the authors presented a case example describing a postoperative cardiac mass and the role of TEE in the diagnosis of this mass. I congratulate the operators as it was a very well managed complication. However, I will have some revision suggestions in the article;\n-To what do you attribute the formation of the post-op mass? Inadequate anticoagulation?, coagulopathy?... It is recommended to add this to the article. - In the TEE performed after the procedure, could it be determined whether the mass was outside the atrium or not? If not, then how can it be superior to TTE? Could imaging with TTE, which is easier to perform, instead of TEE, be sufficient? - Cerebrovascular events were mentioned in the discussion section, but they are not related to the topic. Removal or correction is recommended.\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? Partly", "responses": [ { "c_id": "12457", "date": "01 Oct 2024", "name": "chaithra Nayak", "role": "Author Response", "response": "Dear reviewer, We thank you for your valuable time and comments Please find the responses to the comments received Dear Dr. Raif Kılıç Thank you for your thoughtful and insightful review of our paper. The following are the responses to the comments received 1.To what do you attribute the formation of the post-op mass? Inadequate anticoagulation? coagulopathy?... It is recommended to add this to the article. Response Comment: Thank you for your valuable comments In the current case, we attribute hematoma formation to suture line bleeding. As per the recommended protocol, the patient was adequately anticoagulated during the perioperative period. We believe that such complications witnessed irrespective of the underlying etiology must be addressed for necessary management. 2. In the TEE performed after the procedure, could it be determined whether the mass was outside the atrium or not? If not, then how can it be superior to TTE? Could imaging with TTE, which is easier to perform, instead of TEE, be sufficient? Response comment: We appreciate your time and valuable comments in this context After carefully reviewing the comments, we would like to highlight the challenge we encountered in assessing the utility of TEE in imaging. One significant limitation of both TTE and TEE is their ability to characterize tissue and accurately determine the location of a mass. In this particular case, TEE did not play a significant role in distinguishing whether the mass was intra- or extracardiac, highlighting a limitation of the imaging modality (Page no.9 paragraph 4, Page no.10, para 1). 3. Cerebrovascular events were mentioned in the discussion section but are unrelated to the topic. Removal or correction is recommended. Response comment: We are grateful for your time and deep insights into this paper. The necessary modifications have been carried out and upgraded with the recent references." } ] } ]	1	https://f1000research.com/articles/13-306
https://f1000research.com/articles/11-1135/v1	04 Oct 22	{ "type": "Brief Report", "title": "Reduction of chickens use to perform in vitro pre-screening of novel anticoccidials by miniaturisation and increased throughput of the current Eimeria tenella compound-screening model", "authors": [ "Sara Arias-Maroto", "Kelsilandia Aguiar-Martins", "Javier Regidor-Cerrillo", "Luis Ortega-Mora", "Virginia Marugan-Hernandez", "Sara Arias-Maroto", "Kelsilandia Aguiar-Martins", "Javier Regidor-Cerrillo", "Luis Ortega-Mora" ], "abstract": "We have developed an in vitro model for the evaluation of potential anticoccidial properties of novel compounds aimed to control chicken coccidiosis, a costly disease for the poultry industry. This disease is caused by protozoan parasites of the genus Eimeria (Apicomplexa), and it is mainly controlled by chemoprophylaxis with ionophores and chemical anticoccidials; however, there is an overall agreement about the limitation of these traditional drugs and the need to improve current methods of control. Anticoccidial activities of novel compounds is currently evaluated by expensive experiments that involve large numbers of chickens. The use of our in vitro model for the pre-screening of essential oils led to a reduction of 67% of the chickens used in the in vivo trials for validation. Eimeria parasites can only complete their life cycle in their animal host, therefore chickens are required for their propagation as they cannot be propagated in vitro. In this study, we describe how further optimisation of this in vitro model by miniaturisation can have an additional impact in reduction of the number of chickens used for the generation of parasite stocks for provision of the in vitro model. We have estimated that the use of one chicken could support the evaluation of 10 compounds with a 96-well plate format versus only two compounds with a 24-well plate format, which means an 80% reduction in chicken use. In this study we have proved that the miniaturisation into a 96-well plate format perfectly mimics the invasion and replication observed before in the 24-well plate format. In addition, the 96-well plate format has allowed the simultaneous pre-screening of higher numbers of anticoccidial drugs at different concentrations following streamlined protocols in a more cost-effective way, factors that are beneficial for a wider uptake of the model by other researchers investigating anticoccidial compounds.", "keywords": [ "in vitro model", "miniaturisation", "animal reduction", "high throughput", "anticoccidial compounds", "chicken coccidiosis", "Eimeria species" ], "content": "\n\n\n\nScientific benefit:\n\n\n\n• Increased throughput for evaluation of new compounds aimed to control chicken coccidiosis by miniaturising the previously developed in vitro compound-screening model\n\n3Rs benefit:\n\n\n\n• Evaluation of novel anticoccidial compounds will require fewer chickens for the generation of parasite stocks\n\nPractical benefits:\n\n\n\n• Reduced variability: simultaneous evaluation of a larger number of anticoccidial compounds\n\n• Cost effectiveness: less materials and reagents are necessary per evaluated compounds\n\n• Streamlined protocols: 96-well plate format is used through the whole process (cell culture, DNA isolation and qPCR analysis)\n\nCurrent application:\n\n\n\n• High-throughput screening of potential anticoccidial compounds under investigation by commercial companies and/or public research organisations\n\nPotential applications:\n\n\n\n• Adaptation of equivalent in vitro models for other Eimeria species causing disease in poultry or livestock\n\n\nIntroduction\n\nThe use of in vitro models in biosciences and biomedical research has supported many scientific advances and has emerged as a suitable alternative to reduce time and cost associated with in vivo models by replacing and/or reducing the use of experimental animals in many areas. The implementation of in vitro models for anticoccidial drugs pre-screening as an alternative to in vivo tests is leading to the replacement and reduction of an important number of chickens used in research in coccidiosis control (Thabet et al., 2017). Chicken coccidiosis is an enteric disease caused by different species of the genus Eimeria (Apicomplexa) (Burrell et al., 2020), characterized by malabsorption, diarrhoea and haemorrhage with an important impact on chicken meat and egg production worldwide that cause >£10 billion per annum losses (Blake et al., 2020). Coccidiosis has also impacted on the ‘Five Freedoms’ of animal welfare, more in particular affecting the ‘freedom from discomfort’ and ‘freedom from pain, injury’ (Webster, 2001). Resistance against current anticoccidial drugs, as well as near-prohibition of ionophores antibiotics in some parts of the world and public concerns about the use of drugs in animals for human consumption, has led to an increased research in new substitute compounds, evidenced by the high number of new publications in the area in recent years (>25 in vivo studies within the past two years involving >7,000 chickens).\n\nWe previously developed an in vitro model to evaluate anticoccidial compounds effects in Eimeria tenella (Marugan-Hernandez et al., 2020) and a first direct application for the evaluation of two essential oils (Sidiropoulou et al., 2020) led to a reduction of the number of chickens used for in vivo testing. Results obtained in vitro showed that each of the essential oils exhibited anti-parasitic effects at different concentrations. This supported the selection of a single experimental group (90 animals + control group) of a combined treatment at a single dose, excluding the evaluation of the compounds separately since the in vitro model had already proved their dose-independent individual effects; therefore, it was not considered necessary to re-evaluated this in vivo. The in vivo experiment was reduced from six to two experimental groups (test and control), resulting on a reduction of 90×4=360 chickens in a single study (67%). This in vitro model has been standardised, applied and published using a 24-well plate format (Marugan-Hernandez et al., 2020); in this study, we aimed to adapt the model to a 96-well plate format. This miniaturisation will reduce the numbers of parasites needed for compound testing, and therefore the number of chickens used to generate parasites stocks, additionally allowing the evaluation of a higher number of compounds simultaneously. Eimeria spp. cannot complete their life cycle in vitro; therefore, the natural host (chicken) is necessary to produce stocks for further experimental procedures. The use of one chicken can generate enough initial parasite material (oocysts) for the pre-screening of two compounds in the 24-well plate format. The use of the 96-well plate format will allow the pre-screening of 10 compounds per animal, this has the potential to reduce local animal use for the study of anticoccidial compounds by 80%.\n\n\nMethods\n\nThis study was carried out in strict accordance with the Animals (Scientific Procedures) Act 1986 (United Kingdom Parliament Act). All animal studies and protocols were approved by the Royal Veterinary College Animal Welfare and Ethical Review Board (AWERB) and performed under the United Kingdom Government Home Office under specific project licence (PDAAD5C9D).\n\nEimeria tenella Wisconsin (Wis) strain (McDougald & Jeffers, 1976) was propagated chickens. Table 1 summarises the detailed information of the experiment and used animals following ARRIVE guidelines.\n\n\n\n• Single group of chickens for standard amplification of E. tenella Wis parasites\n\n\n\n• Ten chickens were caged in two groups of 5 animals\n\n• Stocking density of 5 kg/m2 (Defra maximum legal stocking density is 39 kg/m2)\n\n\n\n• All animals included\n\n\n\n• All animals were used, randomisation does not apply\n\n\n\n• All animals were used, blinding does not apply\n\n\n\n• Optimal output of E. tenella Wis oocysts (~40 million/chicken) at the given dose (4,000/chicken)\n\n\n\n• n/a\n\n\n\n• Breed: White Leghorn – specific pathogen free (from APHA)\n\n• Sex: mixed sex\n\n• Age: 3-week-old (arrival)/5-week-old (end)\n\n\n\n• Placed in cages at arrival (no further change will be done)\n\n• Acclimation for 1 week\n\n• Oral gavage with 4,000 oocysts suspended in 1 ml of distilled water at 4-week-old\n\n• Expected severity: Mild\n\n• Schedule 1 at 5-weeks-old\n\n\n\n• Sufficient oocysts were obtained for provision of the in vitro experiments (~400 million)\n\nPastor-Fernandez et al. (2019) provides detailed protocols for oocysts isolation and excystation as well as for sporozoite purification. Sporulated oocysts were stored in water at 4oC for up to six months, the moment from which they start to lose viability for in vitro tests. Freshly purified sporozoites were used to infect cell monolayers immediately.\n\nStandard protocols for cell culture maintenance were the same described for the standardisation of the in vitro model for compound-screening (Marugan-Hernandez et al., 2020). Briefly, Madin-Darby bovine kidney (MDBK) cells (NBL-1; ECACC-Sigma-Aldrich) were used as host cell cultures and maintained in a 37oC humidified incubator with 5% CO2 atmosphere. Cells were cultured in Advanced Dulbecco’s modified Eagle’s Medium (AdDMEM; Gibco) supplemented with 2% heat-inactivated foetal bovine serum (FBS; Sigma) and 100 U/mL penicillin/streptomycin (Fisher, Leicestershire, UK). Confluent cell monolayers (100%) were passaged twice a week to a new confluence of 70-80% by washing them in Ca2+- and Mg2+-free PBS and released with 3mL 0.25% Trypsin/EDTA (Gibco), incubated for three minutes, followed by neutralisation with 5 mL volume of complete medium. The cell suspension was centrifuged at 1,500 g for 10 minutes at room temperature after which the pellet was suspended in 5 mL of fresh medium. Cells were counted and seeded on T75 flasks (Thermo Fisher Scientific) at a density of 10×106 cells with AdDMEM at 15 ml of final volume or seeded on flat bottom 96-well microtiter plates (Thermo Fisher Scientific Nunc) at a cell density of 0.05×106 cells in each well in 100 μl of AdDMEM culture media for subsequent infection with sporozoites (see Optimisation of infection ratios section).\n\nOptimisation of infection ratios\n\nCells were seeded on flat bottom 96-well microtiter plates (Thermo Fisher Scientific Nunc) at a cell density of 0.1×106 or 0.05×106 cells in each well in 100 μl of AdDMEM culture media (lower density than 0.3×106 per well in 500 μl used in 24-well plates) for subsequent infection after two hours with sporozoites at different sporozoites:cells ratios (1:1, 2:1, 4:1; Table 2). Three wells were used per conditions (A, B, C) and incubated at 41oC, 5% CO2. After 4 hours, infected monolayers were removed with 3 mL 0.25% Trypsin/EDTA (Gibco) and cells counted in a Fuchs-Rosenthal counting chamber. Empty cells were recorded as non-infected, cells with the presence of at least one sporozoites were recorded as infected. Two counts were done per well (Table 2).\n\na) Cells were infected with multiple sporozoites which will compromise cell monolayer stability.\n\nAnalytical standard preparations of the classical anticoccidial drugs amprolium hydrochloride (AMP), robenidine hydrochloride (ROB) and salinomycin monosodium hydrate (SAL) were purchased from Sigma (Sigma-Aldrich). Drugs were prepared at 10 mg/mL stock in dimethyl sulfoxide (DMSO; Merck) and dilutions for final working concentrations of 50 μg/ml, 20 μg/mL, 5 μg/mL, and 1 μg/mL were freshly prepared from the stock in AdDMEM just before incubation with sporozoites.\n\nMDBK cells were seeded in four different 96-well plates (one per each harvested time point) at a density of 0.05×106 cells per well and incubated for four hours at 37oC, 5% CO2. Right after, sporozoites (0.2×106 per well) of E. tenella Wis strain were pre-incubated for 1 h at 41oC, 5% CO2 with each anticoccidial compound concentration; untreated sporozoites were used as controls for invasion and replication. After pre-incubation, sporozoites were centrifuged at 1,500 g for 10 minutes at room temperature and washed with PBS to rinse them free of drugs, then resuspended in 300 μl of AdDMEM (equivalent to 100 μl per well). Sporozoites were then added to MDBK monolayers seeded in 96-well plates (after the 4 hours incubation period) and incubated at 41oC, 5% CO2. All the wells were washed twice in AdDMEM to remover extracellular sporozoites. The first time point was harvested at two hours post infection (hpi) by washing twice with PBS, then adding RTL buffer (Qiagen) and storing the plate at -20oC until used for genomic DNA isolation. The other infected monolayers were collected and stored in the same way at 24, 44 and 52 hpi. Three wells were used per condition (for untreated and treated sporozoites and for each drug concentration at each time point). Two whole separated experiments carried out in different weeks were performed.\n\nGenomic DNA (gDNA) was isolated from the samples stored in RTL buffer (Qiagen) using the AllPrep DNA/RNA 96 Kit (Qiagen) following manufacturer’s instructions using the vacuum manifold for processing 96-well plates (Qiagen).\n\nCFX96 Touch R Real-Time PCR Detection System (Bio-Rad) was used to perform the quantitative PCR following the procedures described previously, using DNA-binding dye SsoFastTM EvaGreen Supermix (Bio-Rad) (Marugan-Hernandez et al., 2016). For parasite quantification, the number of haploid genomes (equivalent to single sporozoites or merozoites) per well (three wells/sample, technical replicates) was determined for each condition using gDNA specific primers for E. tenella 5S rDNA (Fw_5S: TCATCACCCAAAGGGATT, Rv_5S: TTCATACTGCGTCTAATGCAC) (Clark et al., 2008) and a standard curve of sporozoite gDNA extracted by the same methods (gDNA equivalent to 107 followed by serial dilution until 102). Once the run was completed, a baseline was calculated by Bio-Rad CFX Manager software (Bio-Rad) and applied to each sample to compare the quantification cycles (Cq values) obtained from different wells.\n\nThe number of sporozoites for each data point analysed by qPCR was automatically determined for each well by a regression analysis using Bio-Rad CFX Manager software (Bio-Rad). Three replicates were included per sample to allow single points showing a standard deviation of more than 0.5 to be excluded from the analysis without affecting the quantification, if all three curves were out of this range, qPCR was repeated for this sample.\n\nIn vitro inhibition percentage for each anticoccidial drug and concentration was calculated following the equation implemented by Thabet et al. (2017):\n\nComparison of replication rates after drug treatment were done by calculating slopes of the regression line (m) between 24 and 44 hpi, which were calculated following the universal formula:\n\n\nResults\n\nFor the miniaturisation of the model to a 96-well plate format, we screened out the optimal combination of MDBK cells and E. tenella sporozoites. Good monolayer confluences were achieved with 0.05×106 cells/well. An optimal rate of invasion and development without causing multiple sporozoite infection per cell was obtained with a 4:1 sporozoites:cell ratio (0.2×106 sporozoites/well). Parasite invasion and development was evaluated in a time course experiment followed by qPCR (Figure 1). Increasing amounts of parasite DNA were detected from 24 hpi onwards as described for the 24-well format, indicative of nuclear replication. The linear rate of replication was equivalent to the one described in a 24-well plate format (Figure 1), validating in this way the suitability of a 96-well plate format to track and evaluate sporozoites invasion and replication. Higher variability was found for the latest time point (52 hpi) which is explained by the rupture of schizonts which will release merozoites as has been observed before (Marugan-Hernandez et al., 2020); these merozoites are washed from the monolayers and therefore not contributing to the parasite numbers when analysed by qPCR. Fewer parasite number were detected for the 96-well plate format along the time course, which correlated with the lower initial numbers of sporozoites used for monolayers infection (0.2 million/well versus 1 million/well).\n\nThe continuous line represents the number of zoites quantified by qPCR in samples collected at 2, 24, 44 and 52 hpi as the average of the two different replicated experiments performed in separated weeks in a 96-well plate format. Discontinuous line represents data extracted from Marugan-Hernandez et al. (2020) equivalent to the number of zoites quantified by qPCR at the same time points as the average of the three different replicated experiments performed in separated weeks in a 24-well plate format. Error bars represent the standard deviation between repeated experiments for each plate format. Both types of plate format show an equivalent linear fashion growth after 24 hpi.\n\nPre-treatment of sporozoites with different concentrations of AMP, ROB and SAL, three drugs with reported anticoccidial activity, showed different degrees of inhibition of invasion and replication (Table 3). The pre-treatment with AMP at any concentration caused a moderate inhibition of invasion at 2 and 24 hpi (10-45%; average of 22%); however, those sporozoites which were successful at invasion then developed at the same rate as the untreated controls (slope of the regression curve was parallel to that exhibited by the untreated control). Pre-treatment with ROB had little effects on invasion (inhibition of 0-20%, average 5.6%); nevertheless, sporozoites did not replicate well once intracellularly (slope decreased compared with untreated controls, with sporozoite numbers decreasing for the highest concentration, 50 μg/mL). Pre-treatment with SAL exhibited effects in both invasion and development. Invasion was inhibited at higher levels than for AMP (10-60%; average 27%) and intracellular replication was severely impaired for the higher concentrations (50 and 20 μg/mL). In general, for every drug, higher inhibition of invasion and replication was observed for the higher concentration, although some variations were observed. These results evidence the suitability of the miniaturised model to detect inhibition of invasion and/or replication.\n\nEach value represents the average of the percentage of inhibition±standard deviation or slope of two different experiments including each three wells per condition, calculated using the equations displayed in Data analysis section.\n\n* Slope average value for untreated sporozoites: 309,189.\n\n\nDiscussion\n\nIn this study, the in vitro model developed to evaluate compounds with potential anticoccidial effects on sporozoites of E. tenella has been successfully miniaturised from a 24-well plate format to a 96-well format. Conditions were refined to create an optimal confluence of the monolayer supporting invasion rates of >70% in the new format. These conditions have proved to support schizonts and merozoite development as described before in the original model (Marugan-Hernandez et al., 2020). The tracking of the sporozoites invasion and development by qPCR in time course experiments have shown the same linear growth fashion than described before and the evaluation of traditional anticoccidial drugs to validate the model has also proved the suitability of this model to detect different levels of inhibition of invasion and/or development.\n\nEimeria parasites are self-limited monoxenous (single-host) parasites, and despite many efforts, there are no efficient in vitro systems supporting continuous replication or the completion of the life cycle; in consequence, research on this species depends on the use of animals. Examination of the literature shows that testing of novel anticoccidial compounds, mainly natural products, is in expansion. In 54 refereed publications between 2017 and 2021 a total of 19,786 chickens (~4,000 per annum) were used to evaluate novel compounds for anticoccidial effects. In addition to these chickens already mentioned, there are chickens used in unpublished studies from pharmaceutical/nutrition companies or those only providing negative results, numbers of which are harder to discover. Looking specifically at some 2021 publications, if pre-screening with in vitro models had been used by Fu et al. (2021), concentrations could have been adjusted to reduce animals from 630 to 480 (23.8%). Similarly, the use of in vitro models could have excluded one testing group for both Lima et al. (2021) and Herrero-Encinas et al. (2021), reducing animals from 900 to 720 (20%) and 400 to 320 (20%), respectively. If we extrapolate these data (an average of 20% reduction) to the total published studies in 2021, the use of our in vitro models could have avoided the experimental use of 792 chickens (out of 3,958) globally, or 3,958 (out of 19,786) in the last 5 years. Nevertheless, we still need some chickens to generate enough parasite materials to perform the in vitro pre-screenings. Therefore, the described modification to the in vitro model will have a direct impact on the reduction of animal use.\n\nTesting one compound at four different concentrations (excluding untreated controls) requires 12 million of sporozoites in the 24-well plate format whereas only 2.4 million are necessary in the 96-well plate one. Efficiency of sporozoite excystation and purification from oocysts is set at 1:1 in our experimental settings. A single chicken can produce an average of 30 million oocysts without causing clinical symptoms. Therefore, with the use of one chicken, we could test at least ten compounds (plus untreated compounds) with the 96-well format, whereas only two compounds (plus controls) could be tested in the 24-well plate format. This supposes a direct 80% reduction in animal use for the evaluation of anticoccidial compounds locally. However, since we have collaborations with several research institutions and companies at different locations worldwide, this miniaturised model will also have a significant global impact on the number of chickens undergoing a mild severity procedure for the generation of E. tenella oocysts.\n\nAnother advantage of this miniaturisation is the high-throughput capacity to test many compounds simultaneously, while reducing materials, reagents and time to perform them. Up to seven compounds could be tested on a single plate per time point (including controls) using <10 mL of culture media, versus only two compounds per plate using volumes of >20 mL per plate in the 24-well plate format. Time is also significantly reduced by a streamlined protocol using 96-well plates and multichannel pipettes throughout the whole experiment, from cell culture to DNA isolation and qPCR analysis. These added benefits will also impact positively in the wider uptake of the model by other researchers since costs and time to achieved results will be significantly reduced.\n\n\nData availability\n\nDRYAD: Reduction of chickens use to perform in vitro pre-screening of novel anticoccidials by miniaturisation and increased throughput of the current Eimeria tenella compound-screening model, https://doi.org/10.5061/dryad.mw6m90605 (Marugan-Hernandez & Arias, 2022).\n\nThis project contains the following files:\n\n- Experiment_1.xlsx\n\n- Experiment_2.xlsx\n\n- 1st_EXPERIMENT_-_2hpi_DMSO_-_ROB_20.pcrd\n\n- 1st_EXPERIMENT_-_2hpi_ROB_5_-_24hpi_AMP_20.pcrd\n\n- 1st_EXPERIMENT_-_24hpi_AMP_5_-_SAL_20.pcrd\n\n- 1st_EXPERIMENT_-_24hpi_SAL_5_-_44hpi_ROB_20.pcrd\n\n- 1st_EXPERIMENT_-_44hpi_ROB_5_-_52hpi_AMP_20.pcrd\n\n- 1st_EXPERIMENT_-_52hpi_AMP_5_-_SAL_20.pcrd\n\n- 1st_EXPERIMENT_-_52hpi_SAL_5-1___Controls.pcrd\n\n- EXP_2._2hpi_DMSO-ROB_20.pcrd\n\n- EXP_2._2hpi_ROB_5_-_24hpi_DMEM.pcrd\n\n- EXP_2._24hpi_AMP_50_-_ROB_1.pcrd\n\n- EXP_2._24hpi_SAL_50_-_44hpi_AMP_20.pcrd\n\n- EXP_2._44hpi_AMP_5_-_SAL_20.pcrd\n\n- EXP_2._44hpi_SAL_5_-_52hpi_AMP_1.pcrd\n\n- EXP_2._52hpi_ROB_50_-_SAL_1.pcrd\n\n- README.txt\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgments\n\nThe authors wish to thank Aimee Holland for her excellent technical assistance.\n\n\nReferences\n\nBlake DP, Knox J, Dehaeck B, et al.: Re-calculating the cost of coccidiosis in chickens. Vet. Res. 2020; 51: 115. PubMed Abstract \| Publisher Full Text\n\nBurrell A, Tomley FM, Vaughan S, et al.: Life cycle stages, specific organelles and invasion mechanisms of Eimeria species. Parasitology. 2020; 147: 263–278. PubMed Abstract \| Publisher Full Text\n\nClark JD, Billington K, Bumstead JM, et al.: A toolbox facilitating stable transfection of Eimeria species. Mol. Biochem. Parasitol. 2008; 162: 77–86. PubMed Abstract \| Publisher Full Text\n\nFu Y, Zhou J, Zhang L, et al.: Pharmacokinetics and anticoccidial activity of ethanamizuril in broiler chickens. Vet. Parasitol. 2021; 289: 109318. PubMed Abstract \| Publisher Full Text\n\nHerrero-Encinas J, Menoyo D, Blanch M, et al.: Response of broiler chickens fed diets supplemented with a bioactive olive pomace extract from Olea europaea to an experimental coccidial vaccine challenge. Poult. Sci. 2021; 100: 575–584. PubMed Abstract \| Publisher Full Text\n\nLima GA, Barbosa BFS, Araujo R, et al.: Agaricus subrufescens and Pleurotus ostreatus mushrooms as alternative additives to antibiotics in diets for broilers challenged with Eimeria spp. Br. Poult. Sci. 2021; 62: 251–260. Publisher Full Text\n\nMarugan-Hernandez V, Arias S: Reduction of chickens use to perform in vitro pre-screening of novel anticoccidials by miniaturisation and increased throughput of the current Eimeria tenella compound-screening model, Dryad, [Dataset].2022. Publisher Full Text\n\nMarugan-Hernandez V, Cockle C, Macdonald S, et al.: Viral proteins expressed in the protozoan parasite Eimeria tenella are detected by the chicken immune system. Parasit. Vectors. 2016; 9: 463. Publisher Full Text\n\nMarugan-Hernandez V, Jeremiah G, Aguiar-Martins K, et al.: The Growth of Eimeria tenella: Characterization and Application of Quantitative Methods to Assess Sporozoite Invasion and Endogenous Development in Cell Culture. Front. Cell. Infect. Microbiol. 2020; 10: 579833. PubMed Abstract \| Publisher Full Text\n\nMcDougald LR, Jeffers TK: Comparative in vitro development of precocious and normal strains of Eimeria tenella (Coccidia). J. Protozool. 1976; 23: 530–534. PubMed Abstract \| Publisher Full Text\n\nPastor-Fernandez I, Pegg E, Macdonald SE, et al.: Laboratory Growth and Genetic Manipulation of Eimeria tenella. Curr. Protoc. Microbiol. 2019; 53: e81. PubMed Abstract \| Publisher Full Text\n\nSidiropoulou E, Skoufos I, Marugan-Hernandez V, et al.: In vitro Anticoccidial Study of Oregano and Garlic Essential Oils and Effects on Growth Performance, Fecal Oocyst Output, and Intestinal Microbiota in vivo. Front. Vet. Sci. 2020; 7: 420. PubMed Abstract \| Publisher Full Text\n\nThabet A, Zhang R, Alnassan AA, et al.: Anticoccidial efficacy testing: in vitro Eimeria tenella assays as replacement for animal experiments. Vet. Parasitol. 2017; 233: 86–96. PubMed Abstract \| Publisher Full Text\n\nWebster AJ: Farm animal welfare: the five freedoms and the free market. Vet. J. 2001; 161: 229–237. PubMed Abstract \| Publisher Full Text" }	[ { "id": "210464", "date": "02 Nov 2023", "name": "Benjamin Adjei-Mensah", "expertise": [ "Reviewer Expertise Nutrition", "Gut physiology", "Poultry 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\nBrief report title: Reduction of chickens use to perform in vitro pre-screening of novel anticoccidials by miniaturisation and increased throughput of the current Eimeria tenella compound screening\nThis brief report aimed to adhere to the 3R, focusing much on the reduction aspect by reducing the number of chickens involved in the study. The goal was to use a high number of well plates (96) to pre-screen 10 compounds using a single chicken against a previous study of 24 well plates, which pre-screened two compounds per chicken.\nThe article is clear and cites relevant literature to back the claims of the findings of this study. Appropriate experimental design has been followed and therefore makes the work relevant in the academic space. The statistical approach and its interpretation are appropriate for readability and comprehension. Based on the data provided and the findings, this work can be reproduced. Additionally, the conclusions drawn are supported by the findings of the study.\nHowever, I found these minor issues that need to be attended to:\nThe article still requires English Language editing (proofreading).\n\nThe authors should be clear on the number of replications. Were all the 10 birds induced with the oocysts? If so, was it the only one that was used during the in vitro studies?\n\nCheck that there is space between all the reported values and their SI units.\n\nI expected some comparisons to be made in the discussion of the findings of the synthetic compounds against that which was reported using the essential oils since the former already have public health issues as indicated in the introduction.\n\nThe authors should be clear on the number of replications. Were all the 10 birds induced with the oocysts? If so, was it the only one that was used during the in vitro studies?\n\nCheck that there is space between all the reported values and their SI units.\n\nI expected some comparisons to be made in the discussion of the findings of the synthetic compounds against that which was reported using the essential oils since the former already have public health issues as indicated in the introduction.\n\nAre the 3Rs implications of the work described accurately? Yes\n\nAre a suitable application and appropriate end-users identified? Yes\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": "12516", "date": "01 Oct 2024", "name": "Virginia Marugan-Hernandez", "role": "Author Response", "response": "We would like to thank Benjamin Adjei-Mensah for his time and effort reviewing our manuscript. We provide below responses for the different queries and issues raised. Reviewer comment: The article still requires English Language editing (proofreading). Author response: The article has gone further proofreading, changes have been highlighted throughout the manuscript using ‘Track Changes’ tool. Reviewer comment: The authors should be clear on the number of replications. Were all the 10 birds induced with the oocysts? If so, was it the only one that was used during the in vitro studies? Author response: We would like to clarify that the chickens are used to generate oocysts that would be later used to release the sporozoite stage to proceed with the in vitro infections. There are no ‘replicates’ in these type of experiments, as there is uniformity between the different batches of productions as we use a reference strain (not field isolates). For oocyst amplification, groups of 10 animals are typically used, and to minimize the overall numbers, the research group operates a pooled resource so that each batch is utilized efficiently, with minimal wastage (this means that when a batch has been produced, this will be used by different researchers for different experiments, and when is needed, a new round of amplification will be done). Chickens will be orally infected with 4,000 oocyst/animal, with an expected yield of ~300 - 500 x 106 sporulated oocysts per 10 chickens. All this details are contained in Table 1. In order to clarify this, some text has been added in ‘Parasites and chickens’ section: ‘Eimeria tenella Wisconsin (Wis) strain ( McDougald & Jeffers, 1976) was propagated in ten four-week-old White Leghorn chickens reared under specific pathogen-free conditions. Each chicken was inoculated with 4,000 oocysts to obtain sufficient oocysts for all the in vitro experimental procedures. Table 1 summarises the detailed information of the experiment and used animals following ARRIVE guidelines.’ Based on this yields, we did the estimation that the use of one chicken (which would produce ~30 x 106 oocysts) would allow the evaluation of 10 compounds with a 96-well plate format versus; whereas this will only allow to evaluate two compounds with a 24-well plate format, as the number of sporozoites (and therefor oocysts) needed per well is much higher. More details for this has been also added on the ‘Discussion’ section: ‘Testing one compound at four different concentrations (excluding untreated controls) requires 12 million of sporozoites in the 24-well plate format (4 concentrations x 3 wells x 1 million/well) whereas only 2.4 million are necessary in the 96-well plate one (4 concentrations x 3 wells x 0.2 million/well); this means the miniaturised model requires 5 times less parasite material. Efficiency of sporozoite excystation and purification from oocysts is set at 1:1 in our experimental settings. A single chicken can produce an average of 30 million oocysts without causing clinical symptoms. Therefore, with the use of one chicken, we could test at least ten compounds (2.4 million/compound x 10 = 24 million oocysts, plus untreated compounds) with the 96-well format, whereas only two compounds (12 million/compound x 2 = 24 million oocysts, plus controls) could be tested in the 24-well plate format. This supposes a direct 80% reduction in animal use (testing 10 compounds would require 5 chickens in the 24-well plate format versus only 1 in the 96-well plate format, which means 4 less chickens out of 5), for the evaluation of anticoccidial compounds locally.’ Regarding the in vitro experiments. The number of replicates are specified in ‘Invasion and replication inhibition assays’ section: ‘Two different biological replicated were performed in different weeks.’ Reviewer comment: Check that there is space between all the reported values and their SI units. Author response: This has been done (highlighted by the ‘Track Changes’ tool). Reviewer comment: I expected some comparisons to be made in the discussion of the findings of the synthetic compounds against that which was reported using the essential oils since the former already have public health issues as indicated in the introduction. Author response: Previous studies using the 24-well plate format to evaluate essential oils from oregano, garlic, thyme and sage (Sidiropoulou et al., 2020-2022) only focused in invasion. In this studies, high dosed of essential oils (100 μg/ml) show similar effects to Robenidine at 5 μg/ml However, as we did no evaluate any essential oil in our current study, we did not include any of these findings on the discussion. As we have recently published the evaluation of essential oils in the 96-well plate format, a small paragraph has been included in this regard in the ‘Discussion’ section: ‘This 96-well plate model has already supported the evaluation of essential oils and their main active compounds ( Felici et al., 2023), where the formers have shown similar effects on invasion and replication than ROB and SAL. This is important as research in natural compounds it is essential to replace current anticoccidials for which several resistances have been developed in field strains threatening their efficacy. These latest results evidence the suitability of the miniaturised model to detect inhibition of invasion and/or replication of natural compounds in addition to classical anticoccidal drugs.’" } ] }, { "id": "173894", "date": "13 Nov 2023", "name": "Joseph D. Turner", "expertise": [ "Reviewer Expertise Parasitology", "drug discovery & development", "infection biology", "immunobiology. Referee suggested by the NC3Rs for their scientific expertise and experience in assessing 3Rs impact." ], "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 work of Arias-Maroto et al., details miniaturisation of an Eimeria tenella sporozoite invasion and replication assay in immortalised bovine kidney epithelial cells. The in vitro assay, if successful in emulating the larger plate system, would further cut down the number of experimentally infected chickens required to generate parasites for these drug assays.\n3Rs statement When stating the 80% reduction metric of use of chickens for generation of parasites due to miniaturisation, it would be informative if the authors could estimate numbers of chickens used for this purpose per annum in their lab, in the UK or globally that may be reduced via adoption of a miniaturised assay, as they have done in the discussion.\nMethods\nRationale for selection of seeding densities in 96-well plates needs more explanation - was it based on scaling of volume, well area or well volume compared with 24 well plate, for instance?\n\nReaders may wish to understand why it is necessary to culture at 41 degrees centigrade for infection of MDBK with sporozoites as this is unusual for mammalian cell culture.\n\nA flow chart of the invasion and replication inhibition assays would help clarify timings of when sporozoites and drugs were added / removed, as without careful reading this is hard to follow.\nResults and conclusions\nI agree the data supports the conclusion that infection and growth rate of Eimeria is similar between optimised 24 and 96 well plate cultures, but a suitable statistical comparison would be needed to confirm this.\nFurther, there is a lack of statistics to test whether any of the drug compounds significantly inhibited invasion and/or growth - using PCR quantifications at either time point or the overall growth rate.\n\nFurther, there is no discussion whether these drugs and concentrations tested induce similar or different levels of inhibition in the miniaturised 96-well system compared with the prior standardised 24 well plate system.\nWithout statistical tests of the 3 replicates per condition to demonstrate meaningful levels of drug efficacy, and how reproducible between different experiments, and how consistent cf the 24-well original screen, it is not currently possible to conclude the 96-well plate system 'has been successfully miniaturised'.\n\nSuggest revisions before considering the work fully valid:\nPlease test that Eimeria infectivity / growth is not significantly different in 96- v 24-well plate systems.\n\nPlease could the authors provide statistical tests to determine which drugs significantly reduce invasion and/or replication in their miniaturised assay.\n\nCould the authors compare drug efficacy achieved in 24 vs 96 well assays with any or all drug compounds screened?\n\nAre the 3Rs implications of the work described accurately? Partly\n\nAre a suitable application and appropriate end-users identified? Yes\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? No\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": "12517", "date": "01 Oct 2024", "name": "Virginia Marugan-Hernandez", "role": "Author Response", "response": "We would like to thank Joseph D. Turner for his time and effort reviewing our manuscript. We provide below responses for the different queries and issues raised. Rationale for selection of seeding densities in 96-well plates needs more explanation - was it based on scaling of volume, well area or well volume compared with 24 well plate, for instance? The two densities were derived of the previously optimised number for the 24-well plate format that was conferring a 100% confluence without an excess of cells (Marugan-Hernandez et al., 2020). This has been now detailed in ‘Optimisation of infection ratios’ section: ‘Based on the amount of 0.3×10 6 per well in 500 μl, previously optimised for the 24-well plates format to confer a confluence of 100% without excess of cells (where the surface of each well is four time larger than in the 96-well plate format; 0.3×10 6 / 4 = 0.075×10 6), we tested 0.1×10 6 and 0.05×10 6 cells per well for the 96-well plate format (just above and below to the equivalent figure).’ Readers may wish to understand why it is necessary to culture at 41 degrees centigrade for infection of MDBK with sporozoites as this is unusual for mammalian cell culture. The temperature in the chicken intestine is 41oC and this is the optimal temperature for Eimeria tenella development, if the temperature is lower, the parasite will not replicate. This has been clarified in ‘Optimisation of infection ratios’ section: ‘This temperature is necessary for parasite development, as chicken Eimeria parasites develop in the intestine of chickens, whose internal temperature is 41 oC, higher than mammalian hosts. MDBK cells can support this increased temperature for up to six/seven days, longer than the required time for in vitro parasite replication.’ A flow chart of the invasion and replication inhibition assays would help clarify timings of when sporozoites and drugs were added / removed, as without careful reading this is hard to follow. A flow chart has been included (Figure 1) aimed to clarify the experimental design of the invasion and replication assays. ‘Figure 1. Flow chart of sporozoite invasion and replication inhibition assays. 1. MDBK cells were seeded into 96-well plates to form a confluent monolayer (0.05x106 cells/well); 2. Sporozoites were purified from oocysts using DE-52 columns (Pastor-Fernandez et al., 2019); 3. Sporozoites were pre-incubated with anticoccidial drugs at four different concentrations (or without drugs for controls) for 1 hour at 4oC; 4. Sporozoites were centrifuged, resuspended in AdDMEM and added to MDBK monolayers to allow invasion. 5. Infected cell monolayers were lysed and collected; 6. Genomic DNA was extracted from collected infected cell monolayers; 7. Real time qPCR was used to evaluate the number of parasite genomes for each sample.’ I agree the data supports the conclusion that infection and growth rate of Eimeria is similar between optimised 24 and 96 well plate cultures, but a suitable statistical comparison would be needed to confirm this. A statistical comparison using the non-parametric Spearman's rank test has been included. This has shown a high degree of correlation with r=1. All this has been detailed in ‘Data analysis’ and ‘Sporozoites of E. tenella invaded and replicated at equivalent rates when transferred to a 96-well plate format’ sections: ‘Correlation (r) between sporozoite quantification between the 24 and 96-well plate format cultures was determined using the nonparametric Spearman's rank test using GraphPad Prism version 6.00 (GraphPad Software, La Jolla, California, USA).’ ‘The linear rate of replication showed a very strong correlation between the 96 and the 24-well plate format models (r=1; 95% confidence interval; Figure 2)’ Further, there is a lack of statistics to test whether any of the drug compounds significantly inhibited invasion and/or growth - using PCR quantifications at either time point or the overall growth rate. Statistical analysis have been included to evaluate differences in the ‘number of zoites’ between the different groups. This has now been detailed in ‘Data analysis’ and ‘Eimeria tenella 96-well plate format in vitro model is suitable to evaluate inhibition of invasion and development after treatment with traditional anticoccidials’ sections. A new figures (Figure 3) has been added. ‘Comparison of groups evaluating differences in ‘number of zoites’ after anticoccidial drug treatment vs. controls was performed using non-parametric Kruskal-Wallis test. The analysis was followed by Dunnett’s multiple comparisons as a post-hoc test. Statistically significant differences were established using a p<0.05. All analyses were performed using GraphPad Prism version 6.00.’ ‘Pre-treatment of sporozoites with different concentrations of AMP, ROB and SAL, three drugs with reported anticoccidial activity, showed a relative dose dependant effect ( Figure 3). There were no significant differences in the number of sporozoites able to invade host cells after the pre-treated groups vs. the controls at either 2 and 24 hpi ( Figure 3, A and B). However, treatment with the highest dose of AMP (50 μg/ml) show a significant reduction in replication at both 44 and 52 hpi. Similarly, treatment with ROB (50 μg/ml) exhibited a significant reduction in parasite numbers at 52 hpi ( Figure 3, C and D).’ ‘Figure 3. Effects of anticoccidial drugs in intracellular numbers of parasites. A and B. Graphs shows the number of parasites by qPCR after invasion at 2 and 24 hpi, respectively (before nuclear division has started, see Figure 2); C and D. Graphs shows the number of parasites by qPCR after nuclear replication at 44 and 52 hpi, respectively. X-axis numbers represent the specific drug dilution used in μg/ml. Asterisks indicate significant differences with the DMEM/DMSO controls (Dunnett’s multiple comparison test p<0.05).’ Further, there is no discussion whether these drugs and concentrations tested induce similar or different levels of inhibition in the miniaturised 96-well system compared with the prior standardised 24 well plate system. We have included the comparison of anticoccidial drugs pre-treatment between the 24 and 96-well plate format in the ‘Discussion’ section: ‘When the same anticoccidial drugs (AMP, ROB and SAL) were evaluated in the 24-well plate format, only concentrations of 5 μg/ml were tested ( Marugan-Hernandez et al., 2020). Comparing this same concentration in the 96-well plate format, AMP and SAL showed equivalent effects in parasite numbers in invasion and replication for both models. AMP did not show any significant change regarding the controls at any point, whereas SAL did not show differences in invasion, but replication was significantly reduced at 44 hpi (Two-way ANOVA, followed by Dunnett’s post-hoc test). ROB at 5 μg/ml did not correlate with previous results from the 24-well plate model where strong effects were found in both invasion and replication. In the 96-well plate format, ROB did not show any effect in invasion or replication at 5 μg/ml. Interestingly, this concentration has shown inhibitory effects in subsequent studies ( Felici et al., 2023) performed in the 96-well plate format, that were equivalent to the 24-well plate format described before. We attributed the lack of significant effects from ROB at 5 μg/ml in the current study to a loss of effect due to continue use of the drug (where stock has gone several freeze-thaw rounds), which we have observed after using it as inhibition control in further studies.’ Without statistical tests of the 3 replicates per condition to demonstrate meaningful levels of drug efficacy, and how reproducible between different experiments, and how consistent cf the 24-well original screen, it is not currently possible to conclude the 96-well plate system 'has been successfully miniaturised'. Please test that Eimeria infectivity / growth is not significantly different in 96- v 24-well plate systems. Please could the authors provide statistical tests to determine which drugs significantly reduce invasion and/or replication in their miniaturised assay. Could the authors compare drug efficacy achieved in 24 vs 96 well assays with any or all drug compounds screened? All these points have been now included in the new version of the manuscript. Detailed responses can be seen above." } ] } ]	1	https://f1000research.com/articles/11-1135
https://f1000research.com/articles/11-1524/v1	15 Dec 22	{ "type": "Brief Report", "title": "Smartphone use and social media addiction in undergraduate students", "authors": [ "Nichapa Parasin", "Monthinee Watthanasuwakul", "Palagon Udomkichpagon", "Teerachai Amnuaylojaroen", "Monthinee Watthanasuwakul", "Palagon Udomkichpagon" ], "abstract": "Background: Children’s use of social media has increased significantly over the past decade. As a result, they are susceptible to smartphone addiction. In particular, parents' and children's well-being and behaviors are negatively affected by smartphone addiction. Such addiction likely affects both physical performance and lifestyle. Adolescents utilize their smartphones while performing other tasks. The secondary task might divert attention away from the primary task. Reaction time is the combination of brain processing and muscular movement. Texting or communicating on a smartphone while performing another task may affect reaction time. Thus, the purpose of this study was to explore the influence of smartphone use on reaction time in undergraduate students who were addicted to smartphones. Methods: The Smartphone Addiction Scale-Short Version (SAS-SV) was used to assign 64 undergraduate students to the smartphone addiction group (n = 32) and the control group (n = 32). The reaction time (RT) of an organism is used to determine how rapidly it responds to stimuli. All participants were examined on the RT test under three conditions: no smartphone use (control), texting, and chatting on a smartphone. Participants were questioned by smartphone through text message or chat with the support of a researcher during the texting and conversation conditions. While responding to the questions, the participant was administered an RT test. Results: The results showed that smartphone addiction tends to have a reduced influence on reaction time when compared to the control group. Also, texting or conversing on a smartphone while doing other work had a substantial impact on reaction time in the undergraduates. Conclusions: Combining smartphone use with other activities tends to reduce undergraduate students' reaction time.", "keywords": [ "Smart phone addiction", "Social media addiction", "Children", "Smart phone used" ], "content": "Introduction\n\nThe Internet is tremendously useful in a variety of applications, including productive electronic commerce, instant knowledge sharing, cultural exchange, and enjoyment.1–3 Smartphones are devices that combine Internet and phone functionality. They provide qualitatively distinguishing features in addition to the benefits of the Internet. Children use smartphones to watch videos, express themselves, communicate with friends, and search for information. The portability and convenience of a smartphone allow it to be utilized anywhere and at any time. However, although smartphones provide several benefits in our lives, we must be aware of their negative implications, the most concerning of which is smartphone addiction, which relates to the unrestrained use of smartphones. Individuals with smartphone addiction endure emotional, mental, and physical challenges.2,3\n\nEven though smartphone addiction does not remain listed in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition4 or the upcoming International Classification of Diseases, Eleventh Revision, evidence suggests that there is an increasing perception of the issue.5 Smartphone addiction is a new type of addictive behavior that has developed from the rapid proliferation of smartphones across the internet, resulting in a severe behavioral addiction.6 According to the National Information Society Agency in Korea, smartphone addiction surpasses internet addiction.7 Lin et al.8 identified four characteristics of smartphone addiction, including compulsion, functional impairment, tolerance, and withdrawal. Smartphone addiction has been found to correlate with a variety of negative effects on physical health, including brain tumors, cancer, a weakened immune system, neck and wrist pain, and sleep disorders.9,10 Prolonged smartphone use at nighttime might cause insomnia, stress, and sadness.11 Screen time and Internet use have been shown to have an impact on sleep,12,13 and SNS addicts have been shown to have poorer sleep quality than non-SNS addicts.14\n\nAdolescents, in particular, are at a significant risk of becoming addicted to smartphones. They are inextricably linked to their smartphones, which they consider to be a second personality.15 In addition, the adolescents spent the most time of their daily routine with smartphone applications, such as, mobile messengers, web browsing, gaming, and social media.16 Several smartphone owners insist that they could not really operate without their devices.17 Adolescents go through a variety of physical and psychological changes during their growth. Despite the fact that teenagers depend on their parents for survival and identity, they are also working to separate themselves from them in order to grow as individuals and carve out a place for themselves. Adolescents become more dependent on smartphones during these transitional periods. Compared to adults, they are significantly more sensitive to and embrace new technologies. Adolescents express themselves online as “digital natives,” aiming to stay current with fashion trends, using a variety of apps, and seeking emotional connections and support.18 They specialize in multitasking and require fast feedback and input.18\n\nFurthermore, social comparison, concern for one's reputation, and identity formation are all long-standing characteristics of adolescence,19 as is the need for social approval and acceptance, which is impacted by the judgment of one's peers.20,21 However, current smartphones enhance the negative potential of addictive behavior, especially through the amplification of anxiety as adolescents navigate the power dynamics that support their online connectivity.22 In another aspect, power dynamics influence who youth seek acceptance from online, how they use smartphones, and how they understand online content. Furthermore, internet comparisons between oneself and others may become more common and increase relative deprivation, reducing self-esteem and negatively damaging mental health. When these characteristics, such as novelty seeking in teenagers, are combined with their immature control abilities, they are predisposed to developing smartphone and social media addiction.23 In this study, we examined the features of smartphone addiction in adolescents aged 18 to 22 years. In addition, we sought to examine if there would be a difference in reaction times between those who didn't use smartphones and those who did in a smartphone-addicted undergraduate student. Furthermore, we compared the smartphone use patterns of a risk group for smartphone addiction and a normal user group, as well as the risk variables for smartphone addiction.\n\n\nMethods\n\nThis is a cross-sectional study (blind assessor and statistician) that included 64 graduate students who used a smartphone for social media every day for at least a year before participation. The data was collected in a laboratory room at the Department of Physical Therapy, School of Allied Health Science, University of Phayao, between February and August 2019.\n\nThe participants were recruited via poster advertising in the local area. The primary outcome of the study was sample size that was calculated as follow (eq (1))\n\nAn initial sample size was 29 in each group which allowing for a dropout rate of 10% (n=3). Finally, at least 64 participants (32 per group) were recruited in this study. The participant recruited for this study was undergraduate students aged between 18 and 22 years, and had used smartphones for social media every day for at least a year before participation. Also, the question survey was developed in this study to exclude participants who had myopia, poor vision, impaired vision, or color blindness, as well as auditory or any perception deficiencies, upper body muscle weakness, sensory loss associated with any type of neurological illness, major surgery, or limb injuries.\n\nThe purposes and processes of the study was explained to the participants before the experiment began, and all participants were promised that their data would be kept anonymous and confidential. Informed consent was signed from all subjects before they participated in the study. The study was conducted in accordance with the Declaration of Helsinki, and the Human Ethic Committee of the University of Phayao approved the project (No.2/095/61, effective from 5 November 2018 to 5 November 2019).\n\nThe reaction time (RT) of an organism is an assessment of how rapidly it responds to a stimulus. The RT is the amount of time that passes between when the stimulus is sent and when the subject shows the relevant voluntary reaction. Three forms of RT were characterized by DukeElder S.25; Luce26; Welford.27 (1) Simple RT: In this scenario, there is only one stimulus and one reaction. (2) Recognition RT: Any stimulus should be responded to, whereas others should not. (3) Choice RT: There are several stimuli and reactions in this situation. The nervous system recognizes the stimulus in human RT. The message is subsequently relayed to the brain by the neurons. The message is sent from the brain to the spinal cord, and eventually to the hands and fingers. Average RTs have been reported to be approximately about 190 and 160 m/s for light and sound stimuli, respectively.27 Fast RTs can be beneficial in some activities, such as athletics and sports, but slow RTs might have catastrophic consequences when driving.\n\nThe Multichoice Reaction Timer (Grand Sport brand, 383059/No.BHX 0012), produced in Bangkok (Thailand), was used to measure the reaction time to visual stimuli as well as the response time (Figure 1). It consists of a simple interface for the researcher with controls for generating stimuli, a monitor displaying the light of communicated stimuli in three colors (red, blue, and yellow), a set of three hand-operated buttons, and a screen of the obtained score with a second's precision. The two stations of the apparatus were placed along a line 2 meters apart, such that the controller could perceive the optical pulses but the controller's interface was out of the subject's range of vision. A hand-operated toggle and a visual stimulus were used to measure response time to a single stimulus. Each subject was told to sit in front of the light box with their hands on the table. The participants were instructed to press the button as soon as they saw a light on the box (red, blue, or yellow), which measured the response time in seconds while three light stimuli were used randomly in the ten trials and repeated three times for each condition recorded in the exam. The average response time from the test were used for the analysis of the risk for smartphone addiction. s.\n\nAfter signing the informed consent form, the participants were screened by the researcher based on the inclusion and exclusion criteria. Then, all participants were separated into two groups based on their scores on the Smartphone Addiction Scale Thai Short Version (SAS-SV-TH).28 The participants were scheduled for general data collection (age, weight, height, and duration and frequency of smartphone use) and an RT test with the researcher. The study was carried out on the same day at the University of Phayao's Department of Physical Therapy, School of Allied Health Science. To prevent the effects of exhaustion produced by everyday responsibilities, the trials were conducted in the morning in a well-lit, silent room with only the investigators present. It is a self-report evaluation of 10 items with Likert's type ratings of 1–6 (1 = strongly disagree and 6 = strongly agree) meant to identify a prospective high-risk category for smartphone addiction. The scale's dependability was demonstrated by a Cronbach's alpha of 0.911.29 Subjects with an SAS-SV-TH score of more than 31 points (in male) or 33 points (in female) were allocated to the smartphone addiction group.29\n\nThe RT test was administered to all participants in three conditions: no smartphone use (control), texting, and chatting on a smartphone. During the control condition, participants did not have access to their devices and had no interaction with other people or devices in a distraction-free area with only study professionals present for supervision. During the texting and conversation conditions, participants were questioned via smartphone (through text message or chat) with the assistance of a researcher. The subject was given an RT test while answering the questions as listed in Table 1.\n\nSTATA version 17 was used for all statistical analyses. The data is presented as the mean standard deviation (SD) (eq (1)).\n\nxi is each value of population\n\nμ is the population mean\n\nn is the size of population\n\nThe one-sample Kolmogorov–Smirnov test (eq (2)) was performed to check the normality of the distribution of each continuous variable.\n\nF0X = Observed cumulative frequency distribution of a random sample of n observations.\n\nFrX = The theoretical frequency distribution.\n\nBecause of the general distribution of data used, sample t-tests were employed to compare the RT between the addiction group and the control group in three conditions. In a within-group analysis, the mean values of RT between the control, texting, and talking conditions were compared by the pair sample t-test. Statistical significance was determined using p-values < 0.05.\n\n\nResults\n\nFigure 1 depicts a flow diagram of the recruitment process. The eligibility of 102 subjects was determined. Overall, 38 participants were excluded because they did not match the inclusion criteria (n = 18) or declined to participate (n = 20). The demographic information of all participants is listed in Table 2. A total of 64 undergraduate students (13 males, mean age 20.61±1.16 years) were selected from the University of Phayao, Phayao Province in Thailand.30 They were separated into two groups according to the SAS-SV score. There weren't any statistically significant distinctions in gender, age, weight, or height between the two groups. The SAS-SV-TH score difference was only statistically significant at a p-value of 0.000.\n\n* A significant baseline difference.\n\nIn an among-group analysis (Table 3), the addiction group tended to have a slightly higher RT than the control group. Still, there was no difference in the average changes in RT between the addiction group and the control group. While comparing among the three conditions of smartphone use (Figure 2), a within-group analysis, the RT of the conversation and texting conditions in both groups was significantly improved compared with their control condition. In the smartphone group, the RT in the texting condition (1.742 ± 0.599 s) was significantly greater (p-value < 0.001) than in the talking condition (1.309 ± 0.322 s.) and also in the control condition (1.044 ± 0.221 s.). Similarly, in the control group, there was a significant (p-value < 0.001) difference in RT between talking (1.225 ± 0.272 s) and in the control condition (0.995 ± 0.284 s.). Moreover, there was the greatest increase in RT between the control condition and the texting condition (p-value < 0.001).\n\n\nDiscussion\n\nIn any of the three conditions, there wasn't any substantial difference in visual reaction time (VRT) here between the smartphone addict group and the control group. The results were not inconsistent with our hypothesis that smartphone-addicted people may show a lower VRT. However, there are possible mechanisms that provide for the different hypotheses. Perhaps the most likely mechanism is the idea that those individuals who are smartphone addicts have a higher rate of smartphone use. Social networking was the most popular smartphone application among the smartphone addicts. The average usage time of texting or talking was almost 30 minutes per session, with several sessions per day. On the other hand, individuals in the control group took only 5–15 minutes per time for entertainment applications. In the test conditions, the smartphone addicts group had similar smartphone usage. Eye-hand coordination when texting in social networking apps and when performing repetitive tasks such as performance practice and brain training has been found.31 As a result, the participants were unable to use the extra time to extend their reach duration. Rather, they finished the assignment in the same amount of time, allowing them more opportunity to switch focus and optimize dual-task attention. This impacts the brain and results in improved cognitive functioning.32\n\nFurthermore, the participants in both groups demonstrated the same results for VRT in 3 conditions of smartphone use. When texting and talking on their smartphones, all participants exhibit slower VRT. Dual-task interference, according to capacity theory, results from the concurrent allocation of a restricted group of general-purpose resources, or efficient clustering.33,34 When mixed tasks exceed (consolidated or specific) resource availability, one or both activities perform poorly. Bottleneck accounts, on the other hand, stress the serial structure of the dual-task process as a result of single-channel screening or information timetabling during the stimuli decoding, identification, and judgment phases.35 Since such instances of disturbance exist, it is argued that the nervous system temporarily delays operations solely on a single task in favor of processes on the prioritized task, resulting in poor efficiency on the non-priority activity. Participants may have coordinated task prioritizing by altering the timing or scheduling of tasks to improve the processing of information and prevent a processing bottleneck.35–38 This result was consistent with the study by Yu and Huang39 which reported that dual tasking significantly increases the RT. Increased reaction times due to cognitive distraction have been reported earlier.40 This shows that the stimuli can be seen or heard while doing another task but are not processed normally as the brain is overloaded. Our study shows that the RT during the talking condition of smartphone use is faster than the texting condition. The expenditure on decision making, and planning was much higher in the texting condition. Texting caused participants to physically move their focus between the smartphone and light stimulation, in addition to turning cognitive resources in a similar direction that conversation does.41 There are limitations to this study that must be considered. Our study only investigated the reaction time for light stimuli. Future research should attempt to evaluate auditory reaction time, as well as studies in a different age group.\n\n\nConclusions\n\nThis study was conducted on 64 teenagers to investigate the effect of smartphone use for social media on Visual Reaction Time (VRT). There was no significant difference statistically in the reaction time between adolescents with and without smartphone addiction in all test conditions (no smartphone use, texting, and talking using a smartphone). However, the adolescents show prolonged reaction times when they must perform the dual-tasking. Therefore, the adolescent should avoid other activities when using a smartphone.", "appendix": "Data availability\n\nFigshare: The Study of Smartphone Use and Social Media Addiction in Children, https://doi.org/10.6084/m9.figshare.21688259.v1. 30\n\nThis project contains the following underlying data.\n\n‐ Reaction-time_data_For-share.xlsx\n\n‐ Survey_use.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\nThe authors would like to acknowledge School of Allied Health Science, University of Phayao for supporting the Multichoice Reaction Timer in this study.\n\n\nReferences\n\nKraut R, Patterson M, Lundmark V, et al.: Internet paradox: A social technology that reduces social involvement and psychological well-being? Am. Psychol. 1998; 53: 1017–1031. Publisher Full Text\n\nMorahan-Martin J: The relationship between loneliness and Internet use and abuse. CyberPsychology and Behavior. 1999; 2: 431–439. PubMed Abstract \| Publisher Full Text\n\nScherer K: College life online: Healthy and unhealthy Internet use. J. Coll. Stud. Dev. 1997; 38: 655–665.\n\nAmerican Psychiatric Association (APA): Diagnostic and statistical manual of mental disorders (DSM-5). Arlington:APA;2013. Publisher Full Text\n\nPetry NM, Zajac K, Ginley MK: Behavioral addictions as mental disorders: to be or not to be? Annu. Rev. Clin. Psychol. 2018; 14: 399–423. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrant J, Potenza M, Weinstein A, et al.: Introduction to behavioral addictions. Am. J. Drug Alcohol Abuse. 2010; 36: 233–241. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee H, Kim JW, Choi TY: Risk factors for smartphone addiction in Korean adolescents: smartphone use patterns. J. Korean Med. Sci. 2017; 32(10): 1674–1679. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLin YH, Chang LR, Lee YH, et al.: Development and validation of the Smartphone Addiction Inventory (SPAI). PLoS One. 2014; 9(6): e98312. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlasdair A, Philips J: Digital Enhanced Cordless Telecommunnication or DECT phones.2017. (Accessed on 2 September 2022).Reference Source\n\nRichard A: Internet Addiction. New York:New York University Press;2001.\n\nLemola S, Perkinson-Gloor N, Brand S, et al.: Adolescents’ electronic media use at night, sleep disturbance, and depressive symptoms in the smartphone age. J. Youth Adolesc. 2015; 44: 405–418. PubMed Abstract \| Publisher Full Text\n\nBrunborg GS, Mentzoni RA, Molde H, et al.: The relationship between media use in the bedroom, sleep habits and symptoms of insomnia. J. Sleep Res. 2011; 20: 569–575. PubMed Abstract \| Publisher Full Text\n\nVollmer C, Michel U, Randler C: Outdoor light at night (LAN) is correlated with eveningness in adolescents. Chronobiol. Int. 2012; 29: 502–508. Publisher Full Text\n\nWolniczak I, Cáceres-DelAguila JA, Palma-Ardiles G, et al.: Association between Facebook dependence and poor sleep quality: A study in a sample of undergraduate students in Peru. PLoS One. 2013; 8(3): e59087. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLin YH, Lin SH, Yang CC, et al.: Psychopathology of everyday life in the 21st century: smartphone addiction. Internet addiction. Cham:Springer;2017.\n\nCha SS, Seo BK: Smartphone use and smartphone addiction in middle school students in Korea: Prevalence, social networking service, and game use. Health psychology open. 2018 Feb; 5(1): 2055102918755046. PubMed Abstract \| Publisher Full Text\n\nWajcman J, Bittman M, Jones P, et al.: The Impact of the Mobile Phone on Work/Life Balance. Canberra:Australian National University;2007.\n\nTapscott D: Grown up Digital: How the Net Generation is Changing Your World. New York:McGraw-Hill;2009.\n\nLerner R, Steinberg L: Handbook of adolescent psychology, volume 1: individual bases of adolescent development. Hoboken, New Jersey:John Wiley and Sons;2009.\n\nCooley C: Human nature and the social order. New York:Scribners;1902.\n\nHarter S, Stocker C, Robinson N: The perceived directionality of the link between approval and selfworth: The liabilities of a looking gladd self-orientation among young adolescents. J. Res. Adolesc. 1996; 6(3): 285–308.\n\nAdorjan M, Ricciardelli R: Cyber-risk and youth: Digital citizenship, privacy and surveillance. London:Routledge;2019.\n\nChambers RA, Taylor J, Potenza MN: Developmental neurocircuitry of motivation in adolescence: A critical period of addiction vulnerability. Am. J. Psychiatr. 2003; 160(6): 1041–1052. Publisher Full Text\n\nBalasubramaniam M, Sivapalan K, Nishanthi V, et al.: Effect of dual-tasking on visual and auditory simple reaction times. Indian J. Physiol. Pharmacol. 2015; 59(2): 194–198.\n\nDuke Elder S: Franciscus Cornelis Donders. Br. J. Ophthalmol. 1959; 43: 65–68. PubMed Abstract\n\nLuce RD: Information Theory of Choice. Reaction Times. London:Academic Press; 1968. [Accessed on 08 August 2022].Reference Source\n\nWelford AT:Choice reaction time: Basic concepts.Welford AT, editor. Reaction Times. New York:Academic Press; 1980; pp. 73–128.\n\nChareoenwanit S, Soonthronchaiya R: Development of smartphone addiction scale: Thai Short Version (SAS-SV-TH). Journal of mental health of Thailand. 2019; 27(1): 25–36.\n\nKwon M, Kim DJ, Cho H, et al.: The smartphone addiction scale: development and validation of a short version for adolescents. PLosONE. 2013; 8(12): e83558. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmnuaylojaroen T, Parasin N, Watanasuwaku M, et al.: Reactiontime_dataset_for_share. figshare. [Dataset].2022. Publisher Full Text\n\nJayaram S, Yash G, Prashant P, et al.: Effect of smartphone use on hand dexterity in medical students: an observational cross-sectional study. BMC Neurosci. 2019; 51: 136–139.\n\nVidja KR, Bhabhor MK, Sarvaiya JL, et al.: Long term playing of badminton improves the visual reaction time. Age (years). 2015; 26: 7–33.\n\nWickens C:The structure of attentional resources.Nickerson RS, editor. Attention and performance VIII. Cambridge, MA:Bolt, Beranek and Newman; 1980.\n\nWickens C:Processing resources in attention.Parasuraman R, Davies DR, editors. Varieties of attention. New York:Academic Press; 1984.\n\nPashler H: Dual-task interference in simple tasks: data and theory. Psychol. Bull. 1994; 116: 220–244. PubMed Abstract \| Publisher Full Text\n\nNavon D, Miller J: Queuing or sharing? A critical evaluation of the single-bottleneck notion. Cogn. Psychol. 2002; 44: 193–251. Publisher Full Text\n\nSchumacher EH, Seymour TL, Glass JM, et al.: Virtually perfect time sharing in dual-task performance: uncorking the central cognitive bottleneck. Psychol. Sci. 2001; 12: 101–108. PubMed Abstract \| Publisher Full Text\n\nVan Mier H, Hulstijn W, Petersen SE: Changes in motor planning during the acquisition of movement patterns in a continuous task. Acta Psychol. 1993; 82: 291–312. Publisher Full Text\n\nYu SH, Huang CY: Improving posture-motor dual-task with a supraposture-focus strategy in young and elderly adults. PLoS One. 2017; 12(2): e0170687. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShah C, Gokhale PA, Mehta HB: Effect of mobile use on reaction time. Al Ameen Journal of Medical Science. 2010; 3(2): 160–164.\n\nBanducci SE, Ward N, Gaspar JG, et al.: The effects of cell phone and text message conversations on simulated street crossing. Hum. Factors. 2016; 58: 150–162. Publisher Full Text" }	[ { "id": "175532", "date": "12 Jul 2023", "name": "Richard J. E. James", "expertise": [ "Reviewer Expertise Gambling", "behavioural addiction", "smartphone addiction" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study reports the findings of an experimental study into the relationship between smartphone addiction, defined by cutoffs on the Thai translation of the SAS-SV, and reaction time performance on a dual task paradigm. No differences were found between the SA groups on task performance. I liked the use of an experimental design, and that the data was made publicly available. However, there are a number of issues with the manuscript as it presently stands, outlined below. In particular, I found the lack of hypotheses, issues with some methodological details, and conceptualizations of smartphone addiction affected the overall soundness of the manuscript, but these can be addressed with revisions. My comments are outlined below:\nThe title includes reference to social media addiction, but this does not appear to be measured in the study. Social media use is included as an inclusion criteria, but the study is not measuring social media addiction.\n\nThere are some points where conceptualizations of behavioral addictions are a bit unclear. For instance, at the bottom of the first paragraph, the references for the claim that individuals with smartphone addiction endure various challenges are two papers on problematic internet use from the late 1990s. I think more specific and relevant evidence could be incorporated here.\n\nSimilarly in the second paragraph there are number of claims made about the severity of smartphone addiction that are open for debate. There is a critical literature that has highlighted many of the issues with the measurement of smartphone addiction, how it relates to other behavioural addictions (e.g. if somebody is using their phone extensively for social media use, do they have a smartphone, or a social media addiction?), and whether this translates into clinically meaningful levels of harm.\n\nAgain, some of the claims regarding smartphone addiction and adolescence are again debatable. The claim they are inextricably linked, and consider it to be a 'second personality' are particularly questionable. The vast majority of the literature samples adolescents and university students, and so this may be biased by the lack of research compared to other groups.\n\nThe final paragraph starts discussing social comparison, but it wasn't entirely clear how this related to the manuscript, and whether it ought to be included.\n\nThe introduction didn't introduce the rationale for the use of the dual tasking design, which I thought was a notable oversight that ought to be amended. No hypotheses were presented about the relationship between performance on the dual performance task and smartphone addiction - would one expect people with elevated levels of smartphone addiction severity to be faster or slower on the task?\n\nThe introduction also makes reference to comparing risk variables for smartphone addiction, but this doesn't seem to be reported in the results.\n\nI appreciate that the authors' have conducted a power analysis to justify their sample size. However, my reading of this section is that the study is powered for the experimental effect (i.e. between the control, texting and calling conditions), and not any putative smartphone addiction effect. Therefore, it is not clear whether the data is appropriately powered for the effects the authors are trying to test. I suspect the study is underpowered for the purpose of testing any such effect. This should be included as a limitation.\n\nThe reporting of reaction times could be streamlined, and easier to follow for readers. For instance, I wasn't clear on the need for the distinction between the three different types of RT.\n\nMore details regarding of the statistical analysis ought to be reported. To me, the analysis conducted look like 3 sets of addiction vs. non-addiction group analyses for each condition, but this is not clear from the information presented. I think the type of analysis could be reported, as could the test statistics and a measure of error.\n\nHypotheses are only mentioned for the first time at the beginning of the discussion.\n\nThe discussion was unclear in places. The second half of the first paragraph starts discussing findings about the amount of smartphone use per session, but this isn't reported elsewhere in the manuscript. This was reported as being collected in the survey included with the data, but the methods talk about a different interview. The methods could be amended to make these passages clearer.\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? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11046", "date": "13 Apr 2024", "name": "Teerachai Amnuaylojaroen", "role": "Author Response", "response": "Dear Reviewer, We appreciate the opportunity to revise our manuscript entitled \" Smartphone used and social media addiction in undergraduate student\" and would like to thank the reviewers for their insightful comments and suggestions. We have carefully considered each point and have made substantial revisions to our manuscript (as seen in Track Change). Since many of the texts in the revised manuscript have been edited to cover all comments/suggestion, we have listed the overall changes in the revised version of the manuscript for more understanding in brief as follows: In the title, it has been changed from \" Smartphone used and social media addiction in undergraduate student\" to “The Impact of Smartphone Addiction on Reaction Time in Undergraduate Students: An Experimental Study” In the introduction, we have inserted many of texts in this section for more correspondingly to the point of the objective in study. In the methodology, we have also inserted and revisde many of texts in this section based on the suggestions/comments from all reviewers such as the flowchart of the study, explanation of the exclusion criteria, type of RT used in this study, as well as additional statistical analysis of this study. In the result, we have adding the report of the descriptive statistical, and ANOVA analysis based on the suggestion by reviewer. In the discussion, we have adding the limitation of the study, and mention of hypothesis based on the suggestion by reviewer. Finally, we appreciate the reviewers' constructive feedback and hope that our revisions adequately address your concerns. Thank you for considering our revised manuscript. We look forward to hearing from you. Sincerely, Authors Reviewer 1 This study reports the findings of an experimental study into the relationship between smartphone addiction, defined by cutoffs on the Thai translation of the SAS-SV, and reaction time performance on a dual task paradigm. No differences were found between the SA groups on task performance. I liked the use of an experimental design, and that the data was made publicly available. However, there are a number of issues with the manuscript as it presently stands, outlined below. In particular, I found the lack of hypotheses, issues with some methodological details, and conceptualizations of smartphone addiction affected the overall soundness of the manuscript, but these can be addressed with revisions. My comments are outlined below: The title includes reference to social media addiction, but this does not appear to be measured in the study. Social media use is included as an inclusion criteria, but the study is not measuring social media addiction. Answer: Thank you very much for your kind suggestion. The title has been changed to “The Impact of Smartphone Addiction on Reaction Time in Undergraduate Students: An Experimental Study” There are some points where conceptualizations of behavioral addictions are a bit unclear. For instance, at the bottom of the first paragraph, the references for the claim that individuals with smartphone addiction endure various challenges are two papers on problematic internet use from the late 1990s. I think more specific and relevant evidence could be incorporated here. Answer: Thank you very much for your kind suggestion. At the first paragraph in the introduction section, we have added some statements for more specific and relevant evidences as follows: “Prolonged use of smartphones exposes individuals to several detrimental physical and psychological effects. For example, dry eyes, carpal tunnel syndrome, repetitive strain injury, wrist, neck, back, and shoulder pain, migraine headaches, thumb, index, and middle finger pain, and phantom pocket vibration syndrome are physical symptoms associated with smartphone addiction. 4 , 5 (AlBarashdi et al., 2016; Sebastian & Jinesh, 2018).\" Similarly in the second paragraph there are number of claims made about the severity of smartphone addiction that are open for debate. There is a critical literature that has highlighted many of the issues with the measurement of smartphone addiction, how it relates to other behavioural addictions (e.g. if somebody is using their phone extensively for social media use, do they have a smartphone, or a social media addiction?), and whether this translates into clinically meaningful levels of harm. Answer: Thank you very much for your kind suggestion. At the second paragraph, in the introduction section, we have inserted some statements for the issues of smartphone addiction realted to several detrimental psychological impacts as follows: “It has also been found to have detrimental psychological impacts16 (Kuss & Griffiths, 2011). Excessive use of smartphones negatively affects the quality of students' sleep 17 , 18, 19, 20, (Ibrahim et al., 2018; Kurugodiyavar et al., 2017; Sahin et al., 2013; Wang et al., 2019) and result in insomnia 21(Van Deursen et al., 2015). Many studies have established a correlation between smartphone usage and mental disorders, such as stress and anxiety 22 (Boumosleh & Jaalouk, 2017). Other potential adverse consequences include loss of control 23(Gupta et al., 2016) and maladaptive behavioral problems 24 (Hwang et al., 2012). Smartphone addiction has a poor correlation with both life satisfaction and performance in school 25(Samaha & Hawi, 2016).” Again, some of the claims regarding smartphone addiction and adolescence are again debatable. The claim they are inextricably linked, and consider it to be a 'second personality' are particularly questionable. The vast majority of the literature samples adolescents and university students, and so this may be biased by the lack of research compared to other groups. Answer: We acknowledge the focus of existing research on adolescents and university students, highlighting this as a limitation and noting the potential for selection bias. This sets the stage for why your study is mindful of broader implications. We have inserted several texts to explain those as follows: “A substantial amount of study has been devoted to the examination of smartphone addiction, with university students and adolescents serving as the primary cohorts for investigation (Kuss & Griffiths, 2011; Sahin et al., 2013). Although the emphasis has resulted in significant findings regarding the trends and repercussions of using smartphones among the youth population, it also presents the possibility of selection bias. The focus on younger age groups and life stages in this analysis of smartphone addiction might not encompass its intricacies (Ibrahim et al., 2018; Kurugodiyavar et al., 2017). In the context of this study's invalidity, this study seeks to contribute by examining the broader consequences associated with smartphone addiction. Through this approach, we aim to contribute to a more holistic comprehension of its ramifications, recognizing that the phenomenon of smartphone addiction transcends the conventional focus on adolescent and university students.” The final paragraph starts discussing social comparison, but it wasn't entirely clear how this related to the manuscript, and whether it ought to be included. Answer: Thank you very much for your kind comment. For more accurately related to the manuscript objective, we have revised the final paragraph in the introduction section as follows: “The increasing significance of smartphones in everyday life, particularly among young adults aged 18 to 22, emphasizes the delicate link between technology use and mental well-being. The objective of this study is to explore the impact of smartphone addiction on cognitive abilities, particularly reaction times, and to analyze the psychosocial repercussions of excessive smartphone usage. This initial investigation primarily examines the direct influence of smartphone addiction on reaction times while also recognizing the potential involvement of several risk factors.” The introduction didn't introduce the rationale for the use of the dual tasking design, which I thought was a notable oversight that ought to be amended. No hypotheses were presented about the relationship between performance on the dual performance task and smartphone addiction - would one expect people with elevated levels of smartphone addiction severity to be faster or slower on the task? Answer: Thank you very much for your kind comment. We have added a paragraph for the rationale for the use of the dual tasking in the introduction sectoion as follows: “Dual-tasking refers to the act of executing two activities simultaneously, whereas multitasking refers to the act of performing more than two tasks simultaneously 34(Won et al., 2012). Engaging in activities such as walking or working while simultaneously utilizing various features of a smartphone can be referred to as dual- or multitasking. Nevertheless, engaging in multiple tasks simultaneously can potentially result in a loss of cognitive capacity, hence increasing the risk of experiencing a fall or injury in an unforeseen and unintentional circumstance. The capacity to sustain equilibrium in both stationary and moving scenarios serves as the foundation for executing functional tasks during the course of diverse routine activities 35(Vuillerme et al., 2002). The functional activities requiring dynamic balance are achieved by the coordinated interplay of the ankle joints, knee joints, hip joints, and their respective accompanying muscles, as well as the shoulder joints and their surrounding muscles. Cognitive ability is closely linked to dynamic balance. Engaging in dual-tasking with a smartphone while walking, such as listening to music, sending a message, online surfing, or playing a game, is known to impair the dynamic balance required for functional activities by diminishing cognitive capacity. The act of using a mobile phone while walking is a common scenario known as a dual-task paradigm 36(Plummer et al., 2013). This means that individuals are required to concurrently engage in mobile phone operations and walking duties. The notion of finite capacity scheduling suggests that the outcome of different activities determines the extent to which cognitive or motor performance is affected 37,38(Coker, 2017; Wickens and Damos, 2020). The mobile phone task involves integrating numerous single activities, such as mathematics, language, memory, and motor skills, while walking, as opposed to doing a single task individually. The demand for cognitive resources in this activity is notably higher compared to other simpler activities 39(Tan et al., 2022). Prior research has demonstrated that engaging in the dual-task paradigm of using a mobile phone while walking is more prone to inducing diminished awareness of the environment, impaired motor function in the lower extremities, and distraction compared to other uncomplicated tasks performed while walking among pedestrians 40, 41(Kim et al., 2020; Tan et al., 2022).” The introduction also makes reference to comparing risk variables for smartphone addiction, but this doesn't seem to be reported in the results. Answer: Thank you very much for you comment. For more correspondly to the main objective of the study that is to examine the effect of smartphone addiction on reaction times, not comparing the risk variable to the smartphone addiction. We have revised the introduction appropriately. I appreciate that the authors' have conducted a power analysis to justify their sample size. However, my reading of this section is that the study is powered for the experimental effect (i.e. between the control, texting and calling conditions), and not any putative smartphone addiction effect. Therefore, it is not clear whether the data is appropriately powered for the effects the authors are trying to test. I suspect the study is underpowered for the purpose of testing any such effect. This should be included as a limitation. Answer: Thank you very much for you kind comment. We have added a paragraph of the limitation in study in the last paragraph of the discussion section as follows: “Although this study utilized a careful methodology, which involved conducting a power analysis to determine the required sample size for detecting variations in reaction times under control, texting, and calling conditions, it is crucial to acknowledge a potential limitation in our examination of the impacts of smartphone addiction. The initial power analysis was primarily intended to ensure an adequate sample size for detecting the experimental effects of dual-tasking conditions. However, it may not have been properly adjusted to accurately identify the more subtle but important influence of different levels of smartphone addiction on these cognitive tasks. After careful consideration, we acknowledge that the study may not have enough statistical power to definitively investigate the subtle impacts that the intensity of smartphone addiction may have on individuals' performance in these activities. This constraint implies that the conclusions on smartphone addiction should be approached with care since the study could not have possessed sufficient statistical strength to identify all significant effects linked to the intensity of smartphone addiction. Subsequent investigations in this field would be enhanced by performing a power analysis particularly designed to evaluate the impact of smartphone addiction. This may involve increasing the sample size or employing a more precise measure of addiction intensity. It is essential to overcome this constraint in order to enhance our comprehension of the cognitive consequences of smartphone addiction and to create specific therapies to reduce its negative impacts. Regarding the results and the original hypotheses of this investigation, further research should explore in greater detail the subtle mechanisms by which extended smartphone usage impacts cognitive functions. Conducting research on auditory reaction times and expanding the study to include various age groups could yield a more comprehensive comprehension of the cognitive consequences associated with smartphone addiction. Furthermore, future research should investigate the possible task-specific cognitive adjustments in those who use smartphones frequently, which could help reduce the anticipated detrimental impacts on dual-task performance.” The reporting of reaction times could be streamlined, and easier to follow for readers. For instance, I wasn't clear on the need for the distinction between the three different types of RT. Answer: Thank you very much for your suggestion. For clear understanding to the reader, we have inserted several texts indicating specifically RT’ type in the subsection of Measurement in Methodology section as follows: “In this study, Choice RT involves multiple stimuli and multiple responses, which directly corresponds to the setup of the study where participants respond to different colored lights with different buttons. The need to recognize the color of the light and choose the correct button to press makes it a choice reaction time task, as there are several stimuli (different colors) and several possible responses (different buttons). This study focuses on the evaluation of reaction times (RT) as a method for measuring the rate at which an individual reacts to a stimuli. It is crucial to specify that the specific sort of reaction time we are emphasizing is referred to as 'Choice RT.' The relevance of this particular type of reaction time lies in the fact that participants are presented with various stimuli and are required to make a deliberate choice on the appropriate response to carry out. In further detail, Choice RT scenarios are distinguished by the existence of multiple potential stimuli, each necessitating a separate and specific reaction. Our experimental setup involves presenting participants with lights of varying hues, specifically red, blue, and yellow. Participants are required to hit a designated button for each color. This choice element distinguishes it from 'Simple RT,' which involves a single stimulus and automatic reaction, and from 'Recognition RT,' where the aim is to respond to certain stimuli while ignoring others. More details regarding of the statistical analysis ought to be reported. To me, the analysis conducted look like 3 sets of addiction vs. non-addiction group analyses for each condition, but this is not clear from the information presented. I think the type of analysis could be reported, as could the test statistics and a measure of error. Answer: We acknownledge for the additional statistical analysis. We have added a couple paragraph to report the statistical analysis with descriptive statistical and ANOVA analysis in the results section as follows: “Analyzing the reaction times under different smartphone usage situations reveals clear trends for persons with and without addiction in Table 4. The non- addiction group exhibited the shortest average reaction time of 0.99 seconds after avoiding from smartphone usage. The results also showed a relatively narrow range of values, as evidenced by the standard deviation of 0.28 seconds. Participating in phone conversations increased response time to an average of 1.22 seconds, while the variation remained similar to the condition when no phone was used. Nevertheless, the texting activity showed the most notable increase, with an average response time of 1.73 seconds and a significantly larger standard deviation, indicating more variation in how texting impacted the reaction times of persons in this particular group. In comparison, the addiction group exhibited a slightly higher initial response time of 1.04 seconds when not using smartphones, while the range of values was narrower. The effect of phone calls was particularly noticeable among those with addiction, as their average response time increased to 1.309 seconds and was accompanied by a higher standard deviation, indicating a larger variation in response times among individuals. The \"Addiction\" group also saw a comparable impact from texting, with an average reaction time of 1.74 seconds and the largest level of variability across all conditions, as demonstrated by the standard deviation. Reaction times consistently increased in both groups as they transitioned from avoiding smartphones to texting. Although the \"Addiction\" group had somewhat greater average reaction times in every situation, their reaction times were more consistent under the no-use condition compared to the \"No addiction\" group. The 95% confidence intervals for the \"Addiction\" group exhibited higher values, indicating a potential association between addiction and longer reaction times. However, the overlapping intervals of the two groups suggest that the difference in reaction times between the two groups is not significant. In summary, the descriptive statistics reveal a noticeable pattern of longer reaction times linked to the usage of smartphones, particularly for tasks that demand more cognitive effort, such as texting. The ANOVA analysis in Table 5 showed that those without addiction had an F-statistic of 29.41 and a p-value of roughly < 0.001, which indicates high significance. This result demonstrates a statistically significant difference in response times when comparing the absence of smartphone usage, making phone calls, and sending text messages among individuals in this group. The inference is that the nature of smartphone engagement significantly impacts the response times of non-addicted persons, with certain activities resulting in slower reactions compared to others. Similarly, the analysis conducted for the \"Addiction\" group yielded an F-statistic of 23.18, along with a significant p-value of roughly < 0.001. This validates that, similar to the \"No addiction\" group, there are statistically significant disparities in reaction time among those with addiction across the three smartphone-using circumstances. The experimental conditions in which the reaction time was assessed (absence of smartphone usage, during a phone call, or while texting) significantly influenced the recorded reaction times. The notable F-statistics in both groups indicate that the change in reaction times is not consistent across conditions; rather, it fluctuates based on whether individuals were not utilizing their smartphones, were involved in a phone call, or were texting. The p-values, which are significantly lower than the typical alpha level of 0.05, provide strong evidence that the observed changes in reaction times are not a result of random chance but rather indicate a genuine impact of the smartphone use condition. These findings emphasize the significance of the circumstances in which smartphones are used when evaluating their influence on cognitive performance, specifically in terms of reaction time. In summary, the descriptive statistics and ANOVA analyses provide a thorough understanding of how reaction times are affected by smartphone usage in different situations for persons with and without addiction. The descriptive statistics indicate that reaction times exhibit an upward trend as individuals transition from not using smartphones to making phone calls, and then to sending text messages, for both groups. The heightened fluctuation in reaction times seen while texting, as indicated by the greater standard deviations, implies that this task may necessitate additional cognitive resources, thereby exerting a more pronounced impact on reaction times. This pattern is consistent for both the non-addiction and addiction groups, although individuals with addiction exhibit somewhat faster reaction times overall. The one-way ANOVA results provide additional support for these findings, demonstrating statistically significant variations in reaction times among the three smartphone use circumstances within each group. The \"No addiction\" group's F-statistic and p-value suggest that various smartphone activities have a differential impact on reaction times. The addiction group likewise has a significant impact of smartphone use circumstances on reaction times, as evidenced by the ANOVA results.” Hypotheses are only mentioned for the first time at the beginning of the discussion. Answer: Thank you very much for your suggestion. We have recognized the mention of the hypothesis in the discussion, many texts have been inserted in the discussion section as follows: “This study aims to investigate the influence of smartphone addiction on visual reaction time (VRT) in several settings, such as control, texting, and chatting situations, as hypothesized. The results of our study did not support our initial hypothesis, which suggested that those with higher degrees of smartphone addiction would have slower VRT due to cognitive overload. Specifically, we found no significant differences in VRT between the group of individuals with smartphone addiction and the control group, regardless of the settings. This result implies a more intricate relationship between smartphone addiction and cognitive performance than originally anticipated.” “Although we hypothesized that regular smartphone use, which requires higher cognitive capacities, could hinder the ability to perform two tasks simultaneously, resulting in longer reaction times, the findings did not confirm this expectation. One potential reason for this surprising discovery could be attributed to the adaptive capacities of individuals who use smartphones frequently. The study found that social networking was the most popular smartphone application among those with addiction, and they used it for much longer periods of time compared to the control group. The significant involvement with smartphones may have resulted in a type of task-specific cognitive adjustment, allowing these individuals to retain similar VRTs as those who are less involved with smartphones.” “The lack of significant disparities in VRT among the groups contradicts our initial assumptions and prompts a reassessment of the ways in which smartphone addiction impacts cognitive function. According to capacity theory and bottleneck accounts, we hypothesized that the dual-task interference would be more pronounced in those with smartphone addiction. Nevertheless, the comparable performance observed in both groups indicates that factors such as task prioritization and cognitive resource allocation likely have a substantial influence on moderating the impact of smartphone usage on attention and reaction times.” The discussion was unclear in places. The second half of the first paragraph starts discussing findings about the amount of smartphone use per session, but this isn't reported elsewhere in the manuscript. This was reported as being collected in the survey included with the data, but the methods talk about a different interview. The methods could be amended to make these passages clearer. Answer: Thank you very much for your comment. We have inserted many texts to make these passages clearer in the subsection of Procedure in the Methodology section as follows: “Following the initial evaluation using the SAS-SV-TH, participants were monitored during different experimental sessions intended to replicate their usual smartphone usage. Every session was designed to simulate a practical setting for texting or talking, with a duration that nearly reflected their self-reported typical usage, which was around 30 minutes. In order to obtain a thorough understanding of everyday smartphone usage, participants were involved in multiple sessions of such nature throughout the day. This methodology enabled us to gather detailed information on the potential impact of extended and repetitive smartphone usage within a 24-hour period on reaction speeds.”" } ] }, { "id": "235225", "date": "07 Feb 2024", "name": "Hariom K. Solanki", "expertise": [ "Reviewer Expertise Public Health", "Epidemiology", "Primary Health Care" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Authors There are certain comments/ queries / suggestions with respect to this manuscript. Please address them to improve upon the manuscript.\n\n1. The title of the manuscript does not reflect the main objective and results presented in the manuscript. 2. \"In this study, we examined the features of smartphone addiction in adolescents aged 18 to 22 years\" - there is no result presented with respect to this objective in the study. Also, adolescent age group does not include people 20 or above as per the World Health Organization definition. If some other operational definition has been used, please cite the source. 3. Fig 1 does not correspond to flowchart as the claim is made in the text in results section. In any case participant recruitment flowchart should be included in the methods section (when you put the correct figure in the manuscript) 4. The number of exclusions seems to be too large. What were the reasons to exclude all participants for myopia, impaired vision - were they still excluded if they were either corrected with glasses or were only of mild degree in nature?\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? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11047", "date": "13 Apr 2024", "name": "Teerachai Amnuaylojaroen", "role": "Author Response", "response": "Dear Reviewer, We appreciate the opportunity to revise our manuscript entitled \" Smartphone used and social media addiction in undergraduate student\" and would like to thank the reviewers for their insightful comments and suggestions. We have carefully considered each point and have made substantial revisions to our manuscript (as seen in Track Change). Since many of the texts in the revised manuscript have been edited to cover all comments/suggestion, we have listed the overall changes in the revised version of the manuscript for more understanding in brief as follows: In the title, it has been changed from \" Smartphone used and social media addiction in undergraduate student\" to “The Impact of Smartphone Addiction on Reaction Time in Undergraduate Students: An Experimental Study” In the introduction, we have inserted many of texts in this section for more correspondingly to the point of the objective in study. In the methodology, we have also inserted and revisde many of texts in this section based on the suggestions/comments from all reviewers such as the flowchart of the study, explanation of the exclusion criteria, type of RT used in this study, as well as additional statistical analysis of this study. In the result, we have adding the report of the descriptive statistical, and ANOVA analysis based on the suggestion by reviewer. In the discussion, we have adding the limitation of the study, and mention of hypothesis based on the suggestion by reviewer. Finally, we appreciate the reviewers' constructive feedback and hope that our revisions adequately address your concerns. Thank you for considering our revised manuscript. We look forward to hearing from you. Sincerely, Authors Reviewer 2 Dear Authors There are certain comments/ queries / suggestions with respect to this manuscript. Please address them to improve upon the manuscript. The title of the manuscript does not reflect the main objective and results presented in the manuscript. Answer: Thank you very much for your kind suggestion. The title has been changed to “The Impact of Smartphone Addiction on Reaction Time in Undergraduate Students: An Experimental Study” \"In this study, we examined the features of smartphone addiction in adolescents aged 18 to 22 years\" - there is no result presented with respect to this objective in the study. Also, adolescent age group does not include people 20 or above as per the World Health Organization definition. If some other operational definition has been used, please cite the source. Answer: Thank you very much for your kind comment. For more accurately in the word “adolescent” used in this study, we have explained the definition of the word “adolescent” and “undergraduate”, as well as the overlappint in the age of both words in the introduction section as follows: “Meanwhile some of the individuals who are predominant smartphone users are adolescents. Adolescence, as delineated by developmental psychology and esteemed organizations such as the World Health Organization (WHO), covers from early adolescence to late adolescence. In many definitions, it may also comprise young adults up to the age of 19 or even stretch into the early 20s. Undergraduates, in contrast, refer to those who are actively pursuing a bachelor's degree at a college or university. The terms 'undergraduate' and 'adolescent' refer to separate facets of an individual's existence. Although there are variations, there is a significant convergence in the normal age range linked to each. Adolescence, as per developmental psychology and organizations such the World Health Organization (WHO), refers to the period from early to late teens and may even include young adults up to the age of 19 or even early 20s in certain definitions. Most undergraduates commence their tertiary studies promptly after finishing secondary education, usually at approximately 18 or 19 years old. As a result, a significant proportion of college students are in the late adolescent stage.” For more accuraltely understandble, we have edited the objective in this study with a word of “undergraduate” instead of “adolescent” as follows: “The increasing significance of smartphones in everyday life, particularly among undergraduate student aged 18 to 22, emphasizes the delicate link between technology use and mental well-being. The objective of this study is to explore the impact of smartphone addiction on cognitive abilities, particularly reaction times, and to analyze the psychosocial repercussions of excessive smartphone usage. This initial investigation primarily examines the direct influence of smartphone addiction on reaction times while also recognizing the potential involvement of several risk factors.” Fig 1 does not correspond to flowchart as the claim is made in the text in results section. In any case participant recruitment flowchart should be included in the methods section (when you put the correct figure in the manuscript). Answer: Thank you very much for your comment. We have added the new flow chart figure in the manuscript as follows: Figure 1 Flowchart of inclusion participants The number of exclusions seems to be too large. What were the reasons to exclude all participants for myopia, impaired vision - were they still excluded if they were either corrected with glasses or were only of mild degree in nature? Answer: Thank you very much for your comment. In this study, participants with myopia and impaired vision from certain studies, especially those focusing on cognitive tasks, reaction times, or visual processing, were excluded for several reasons. Firstly, we need to control our visual acuity. Since this study relies heavily on visual stimuli aims to ensure that all participants have a similar baseline for visual acuity to reduce variability in response times or accuracy that could be attributed to differences in vision rather than the cognitive or behavioral variable being studied. This issue was discussed by Bach (1996) who revealed the importance of accurately measuring visual acuity in research settings and how variations in acuity can affect the reliability of visual assessments. At the same time, we are concerned about the impact on reaction times. Since this study measures reaction times to visual stimuli, variations in vision clarity could introduce significant confounders, as those with uncorrected visual impairments might inherently respond more slowly or inaccurately. This issue was reported by Strang et al., (1999) who illustrate that even mild visual impairments can significantly impact the speed and accuracy of visual processing, thereby supporting the rationale for controlling visual acuity in studies where reaction time is a critical measure. We have also added this explaination in the subsection of Participant in the Methodology section. Ref: Strang, N. C., Atchison, D. A., & Woods, R. L. (1999). Effects of defocus and pupil size on human reaction time. Journal of the Optical Society of America A, 16(3), 412-418. Bach, M. (1996). The Freiburg Visual Acuity test-automatic measurement of visual acuity. Optometry and Vision Science, 73(1), 49-53." } ] } ]	1	https://f1000research.com/articles/11-1524
https://f1000research.com/articles/11-953/v1	18 Aug 22	{ "type": "Systematic Review", "title": "Community-level dietary intake of sodium, potassium, and sodium-to-potassium ratio as a global public health problem: a systematic review and meta-analysis", "authors": [ "Farapti Farapti", "Putri Hersya Maulia", "Chusnul Fadilla", "Niwanda Yogiswara", "Purwo Sri Rejeki", "Muhammad Miftahussurur", "Hazreen Abdul Majid", "Putri Hersya Maulia", "Chusnul Fadilla", "Niwanda Yogiswara", "Purwo Sri Rejeki", "Hazreen Abdul Majid" ], "abstract": "Background: Widespread adoption of a westernized diet represents a major lifestyle change characterized by substantially higher sodium consumption and lower potassium intake, which is related to cardiovascular morbidity. Methods: We performed a systematic review and meta-analysis over published studies in accordance with quantifying the dietary intake of sodium and potassium of the universal population across the world. The PubMed, EMBASE, Cochrane Library, and Google Scholar databases were used to find research that pronounced 24-hour urinary sodium or potassium excretion (reference period: 2014–2021). The effect size was estimated using the fixed-effect model; sub-group analysis become accomplished to determine urinary sodium and potassium excretion disaggregated by geographical location. Publication bias became evaluated the usage of graphical funnel plot. Data analysis was performed using STATA 16. Results: Forty-three studies (n= 62,940) qualified the selection criteria. The mean urinary excretion of sodium and potassium was 156.73 mmol/24h [95% confidence interval (CI), 148.98–164.47] and 48.89 mmol/24 h (95% CI, 43.61–54.17), respectively; the mean urinary sodium/potassium ratio was 3.68 (95% CI, 2.96–4.40). Conclusions: This updated systematic review highlights excessively high dietary intake of sodium and low intake of potassium at the community level in most parts of the world. The urinary Na/K ratio exceeded the level recommended by the WHO guidelines.", "keywords": [ "sodium", "potassium", "sodium-to-potassium ratio", "systematic review", "hypertension" ], "content": "Introduction\n\nSodium (Na) and potassium (K) are the major electrolytes of the extracellular fluid and intracellular fluid, respectively. Both these nutrients circulate a crucial role in normal biological functioning such as regulation of body fluids, active transport of molecules across the cell membrane, maintenance of osmotic equilibrium, and acid-base balance.1 Sodium and potassium are naturally occurring nutrients in a variety of foods. Processed food and condiments typically have a high sodium content, while fresh fruits, vegetables, and nuts are rich in potassium.2,3 Industrialization and adoption of the westernized dietary patterns have contributed to the increased prevalence of obesity, metabolic diseases, and cardiovascular diseases.4,5 The switch from a traditional diet to westernized dietary pattern represents a major lifestyle change leading to the substantial increase in sodium consumption and decline in potassium intake.4 The Asian diet is already typically a high-salt diet, however westernization has further increased sodium levels, making the consumption of salt in Asia greater.6\n\nSeveral randomized clinical studies and systematic reviews have demonstrated the effect of sodium and potassium intake on non-communicable diseases.7,8 Low potassium consumption and high sodium intake have been shown to be related to the extended danger of stroke, hypertension, and obesity.4,9,10 The sodium-to-potassium (Na/K) ratio in diet showed a more potent affiliation with blood pressure (BP) than both sodium or potassium alone.11,12 The World Health Organization (WHO) recommends a wholesome diet pattern to prevent the onset of diet-related diseases. Foods containing high potassium content and limited sodium content are particularly recommended.13,14 Moreover, reducing sodium intake and increasing potassium consumption have been recognized as a concern intervention to lessen non-communicable illnesses.15,16 In reality, most populations consume less than the recommended level of potassium and above the advocated level of sodium; the ratio of sodium to potassium typically ranges from 1 to 2.11,17,18 According to the WHO, almost all countries report high sodium intake and potassium deficiency in the general population.15,16\n\nSeveral strategic interventions have been implemented to improve the intake of sodium and potassium. WHO has formulated recommendations to reduce population-wide dietary salt intake and has set a target of 30% reduction in salt intake across the globe by 2025.15 WHO also recommends potassium intake of at least 90 mmol/day.16 Moreover, the current guidelines recommended a Na/K ratio of approximately one. Despite these interventions, several studies have documented that most people still consume high-sodium and low-potassium foods in their diets.15,16\n\nA systematic review characterized the population-wide intake of these nutrients in China.19 To our knowledge, no systematic review and meta-analysis has comprehensively assessed the sodium and potassium intake among populations across the world, as well as analyzed their relationship to other health problems at the community level, or their correlation to other community-level health issues. In this study, we attempt to systematically investigate the dietary consumption of sodium and potassium among adults at the community level across the world. We performed a systematic literature review and meta-analysis of data pertaining to 24-hour urinary excretion of sodium and potassium among healthy adult subjects. The objective was to quantify the dietary intake of sodium and potassium as a public health problem at the community level.\n\n\nMethods\n\nWe conducted a systematic review and meta-analysis of observational studies in a match to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement.93 The literature search for this study was conducted from June to December 2021. The PubMed, EMBASE, Cochrane Library, and Google Scholar databases were used to search for applicable studies published between January 2014 and December 2021. The following search terms were used to retrieve articles: (Sodium Chloride OR Sodium OR salt OR Potassium OR sodium-potassium ratio OR sodium to potassium ratio) AND (dietary OR intake OR urinary). The detailed electronic search strategy is available in our review protocol. In addition, the reference lists of the retrieved articles were manually searched to obtain applicable articles. The protocol of this review has been published in the International Prospective Register of Systematic Reviews (CRD42022279435).\n\nStudies were considered eligible if they qualified the following criteria: (1) observational studies including cross-sectional and cohort studies published during the period 2014–2021; (2) study population: healthy subjects who underwent measurement of 24-hour urinary excretion of both sodium and potassium; (3) availability of full-text articles; and (4) language of publication: English. The exclusion criteria were: (1) case reports, review articles, commentaries, and letters; (2) outcomes not relevant to this study; or (3) subjects with comorbid diseases. The primary data were extracted from the articles into a spreadsheet using Microsoft Excel version 16. Data concerning to following variables were extracted: call of the primary author, year of publication, country of subjects, study design, sample size, patient characteristics and setting, the method used for determining urinary sodium, and potassium, urine sodium and potassium concentration. All reported concentrations of sodium and potassium were transformed into millimoles. The principal summary measures were the standard error mean (SEM) of sodium and potassium excretion. If SEM became not mentioned, we measured the same from the standard deviation and the number of samples.20\n\nMethodological quality of the included studies was assessed using assessment scale for non-randomized study developed by Newcastle-Ottawa (NOS). The assessment consisted of several aspects such as the selection, comparability, and outcome of the study. The database search, study selection, data extraction, and appraisal were independently performed by four authors (F.R., P.H.M., C.F., and N.Y.). Any differences of opinion were resolved by consensus and/or by consulting three senior investigators (H.A.M., M.M., and P.S.R.).\n\nIn case of no significant heterogeneity among the included research (assessed by I2 test), the fixed-effect model was used to calculate the estimated effect size for mean difference (MD). I2 > 50% is taken to indicate the importance of significant heterogeneity. For significant heterogeneity, the random-effects model became used. Subsequently, subgroup analysis was conducted to specify sodium and potassium excretion disaggregated by age-group (children and adults) and geographical location (grouped by continent). Publication bias was measured using a graphical funnel plot. All analyses were done using STATA 16.0 (StataCorp LLC, College Station, Texas).\n\n\nResults\n\nThe database search produced a total of 6114 records. After elimination of duplicate records and manual search of the reference lists of the relevant articles, a total of 3450 abstracts were screened. Of these, 496 articles were subjected to full-text review, of which 357 were excluded due to various excuses. Finally, a total of 43 studies that reported 24-hour urinary sodium and potassium excretion were included in the study.\n\nSupplementary Table 2 (see Extended data93) summarizes the characteristics of the 43 studies and reports the 24-hour urinary sodium, potassium, and sodium-to-potassium (Na/K) ratio among adults based on continent. The studies included 18 from Asia, 9 from Europe, 8 from United States, 6 from Africa, and 2 from Australia. The majority of studies included both men and women; however, two studies used just a female population.11,21 Most of the reports included in our meta-analysis used a combination of 24-hour urine collection and dietary assessment.11,21–33 Likewise, the studies by Du et al. (2014)17 and Morrisey et al. (2020)34 used the spot urine method in combination with a dietary survey. Most of the included studies analyzed the correlation between the intake of sodium and potassium with blood pressure.11,17,25,34–42 In addition, several studies discussed both blood pressure and/or obesity as outcomes.22,43–47\n\nFigure 1 showed funnel plot of the included studies. Because of significant heterogeneity in a number of the included studies (I2 99.51%, p < 0.001), the random-effect sample was used for meta-analysis. No significant publication bias became discovered through the funnel plot based on the mean sodium excretion.\n\nTable 1 summaries the meta-analysis and presents demonstrates that the majority of the studies were done in Asia (42%) followed by Europe and America (21% and 19%, respectively). Overall, the mean sodium excretion was 156.73 mmol/24 h [95% confidence interval (CI), 148.98–164.47] and the mean urinary potassium was 48.89 mmol/24 h (95% CI, 43.61–54.17). The highest mean sodium excretion was observed in Asia [175.72 mmol/24 h (95% CI, 1760.48–190.97), while the lowest mean sodium excretion was observed in Africa [137.9 mmol/24 h (95% CI, 119.42–156.56). The continent with the highest mean potassium excretion were Australia [73.11 mmol/24 h (95% CI 65.58–80.64)] followed by Europe [61.1 (95% CI, 51.59–70.61)]. The lowest potassium excretion was found in Africa [mean: 33.82 mmol/24 h (95% CI, 21.03–46.61)]. Urinary Na/K ratio was extracted from 27 (63%) out of 43 studies; the mean urinary Na/K ratio was 3.68 (95% CI, 2.96–4.40). The top urinary Na/K ratio was reported from Asia [mean: 5.03 (95% CI, 4.43–5.63)] while the lowest urinary Na/K ratio was reported from Australia [mean: 1.56 (95% CI, 1.09–2.03)].\n\nThe mean urinary sodium, urinary potassium, and sodium-potassium ratio were summarized as forest plots presented in Figure 2, Figure 3, and Figure 4 respectively. The overall effect size estimate is represented by the red dashed line. We observed heterogeneity among these studies and all forest plots showed I2 > 50%, meaning significant heterogeneity. Figure 2, Figure 3, and Figure 4 demonstrated significant heterogeneity among the study that analyzed urinary sodium excretion, urinary potassium, and sodium-potassium ratio, respectively. Consequently, the random-effects model was used in these studies.\n\nThe overall effect size estimate is represented by the red dashed line\n\nThe overall effect size estimate is represented by the red dashed line.\n\nThe overall effect size estimate is represented by the red dashed line.\n\n\nDiscussion\n\nThe more reliable methods for assessing dietary intake of sodium and potassium are typically difficult to perform, whereas the more convenient methods are less reliable.48 The methods used to measure the intake of these nutrients including dietary survey, spot urine, and 24-hour urine collection.48–50 The gold standard for assessment of Na and K intake is 24-hour urine collection; nevertheless, it is costly, cumbersome, and difficult to implement.48 In our meta-analysis, we included all studies that used 24-hour urinary collection for assessment of Na and K intake. This is because it is crucial to acquire accurate measures at the populace level. It is important to note that while 24-hour urinary excretion is the best method, studies commonly employ a combination of methods including urine collection and dietary assessment. This approach is used to confirm the subjects’ dietary habits and to identify food sources of these nutrients. Moreover, the WHO recommends that 24-hour urine collection should be combined with a dietary evaluation.15,16 Most of the reports included in our meta-analysis used a combination of 24-hour urine collection and dietary assessment.11,21–33 Likewise, the studies by Du et al. (2014)17 and Morrisey et al. (2020)34 used the spot urine method in combination with the dietary survey.\n\nMost of the research included in our meta-analysis was conducted in Asia, particularly in China and Japan.17,24–26,35,40,51–58 In both these countries, there is a focus on these nutrients owing to the typically high-salt diet. Indeed, a systematic review and meta-analysis by Tan et al. (2019)19 found a wide variety of research which had targeted the intake of these nutrients since the 1980s. Furthermore, long-term prospective cohort studies have assessed the intake of these nutrients among adult Chinese and Japanese population for 18 years and 24 years, respectively.17,59 In our systematic review and meta-analysis, we only included observational studies that enrolled healthy subjects. Most of the included studies analyzed the correlation between the intake of sodium and potassium with blood pressure.11,17,25,34–42 In addition, several studies discussed both blood pressure and/or obesity as outcomes,22,43–47 while other studies calculated the mean sodium and potassium intake compared to the standard recommendation.21,23,24,28–32,58,60–66 Not all studies included the urinary the Na/K ratio in their analysis. In most studies, Na/K ratio confirmed a more potent affiliation with incident hypertension than the intake of sodium or potassium by itself.11,17,58\n\nIn this study, the mean sodium intake among adults was 156.73 (148.98–164.47) mmol/d, which is equivalent to the daily intake of 3.6 g sodium or 9.17 g salt; the highest intake was in the Asian population. This result is aligned with that of a preceding meta-analysis of research conducted in China wherein the mean sodium intake was found to be 189.07 mmol.19 The China Health and Nutrition Survey cohort includes 16,869 adults aged 20–60 years which were followed from 1991 to 2009; the results showed that despite the decreasing trend observed over successive years, sodium intake was still double the level recommended by the Institute of Medicine, an American nonprofit, non-governmental organization.1 The decline in sodium intake has been most marked in northern China since the 2000s. Despite the decrease, more than half of the working age population still has a habit of consuming a large amount of sodium in the past decade.17 A systematic review by Bernstein et al. (2010)67 examined the trends in urinary sodium in the United States during the period 1957–2003; the results showed that the average sodium excretion in 2003 was 3526 ± 75 mg. Sodium consumption in the US adult population looks to be well above the currently recommended levels and does not seems to have decreased with time. This phenomenon might be caused by processed foods and more salt added to foods such as poultry, meat and fish.14,68 A recent study reported that the population-level sodium intake across the world is well greater than minimal physiological requirements. In addition, in many nations, the sodium intake is a great deal greater than each day intake recommended by the WHO.13\n\nWHO has recognized the third reduction in population salt consumption as one of the primary objectives in its global action plan for the prevention and management of non-communicable diseases.69 Salt reduction has been shown to be the most effective intervention, and in a few cases, fee-saving interventions to reduce the developing burden of non-communicable diseases. Processed foods account for up to 95% of dietary salt intake in the United Kingdom compared to under three-quarters in Japan (20% from soy sauce alone). Otherwise, home-cooked foods account for up to 76% of dietary salt intake in south China. Webster et al. (2014)6 provided a comprehensive overview of the progress made in working with the food industry to lessen the salt content in processed items. Currently, a total of 59 countries (80% of which implement national strategies for salt reduction) include programs to work with the food industry. Gupta et al. (2018)69 assessed the perspectives over a range of stakeholders concerning improvement on an India-specific salt reduction strategy. Based on the barriers and facilitators, several of the recommendations were around consumer’s awareness, promoting salt reduction in the processed food industry while also implementing customer-friendly product labeling. According to Trieu et al. (2015),70 up to 75 countries now have national salt reduction strategies, twice the number recorded at a similar review held in 2010. Most programs have multiple disciplines; twelve countries reported reduced salt consumption, 19 countries reduced dietary salt intake, and 6 reported improved nutrition knowledge, habits, or attitudes towards salt. Recent data showed that public health interventions to improve awareness also have a great impact in decreasing salt intake in the population.71 However, sodium is a naturally occurring nutrient into a vast range over foods, in addition, processed foods account for a large percentage of dietary salt intake. Consequently, although individuals are trying to lessen their salt intake by not adding salt to food, they’re nonetheless likely to be eating already sodium-rich foods. This underlines the challenge in reducing salt consumption at the population level.\n\nIn our study, the mean potassium excretion in adults was 51.36 mmol/d, equivalent to 2 g/d. The highest mean potassium excretion was found in Australia while the lowest potassium excretion was found in Africa. In keeping with the latest international and national surveys, only a few populations comply with the recommended consumption of potassium. The Prospective Urban Rural Epidemiology (PURE) research assessed the potassium intake using a single morning spot urine test; the results showed that most of the people of Asian populations consume <2 g of potassium per day.68 In the northern states of the US and Europe, the average potassium intake was 2.5–2.7 g/day, while in Africa and the southern states of the US, the average was ≤ 2 g/day. The estimate for Africa was recently validated in a study carried out in Benin, an African country with an excessive prevalence of high blood pressure in both rural and urban regions.16 Data from the Swiss Salt Survey, showed the average potassium consumption in the general population was 2.6 g/day, based on 24-hour urine collection.72 However, reports of the China Health and Nutrition Survey showed that potassium consumption increased by 0.3 g/d over an 18-year period. However, the intake level is still lower than the recommendation. Women, low-income groups, and lower-education groups showed a lower intake of potassium.16,17 Low potassium intake is usually due to low fruit and vegetable intake. Moreover, the recent studies showed potassium intake is associated with nutritional quality and food cost, so the cost of food often may inhibit its intake.14,73 Low potassium consumption has also been observed in healthy Italian young people (aged 6–18 years), with a daily potassium intake of nearly 40 mmol, like in conformity with 1.5 g/day.74 Recent international and national surveys have revealed that the majority of populations across the world consume less than the advocated levels of potassium. Collectively, these discoveries indicate the requirements for concerted attempts to promote higher potassium intake across the world.\n\nWe extracted the Na/K ratio from 27 (63%) out of 43 studies belonging to the meta-analysis; the mean Na/K ratio was 3.38 (95% CI, 2.68–4.08) while the mean Na/K ratio in children was 3.61 (95% CI, 3.07–4.14). In the study by Du et al. (2014),17 the mean Na/K ratio in 2009 was 2.8, more than half of subjects had a Na/K ratio above 2.0. It is important to note that the Na/K ratio was much over the recommended level. Sodium potassium ratio of 1 is considered beneficial for health.15 Therefore, achieving effective ways to lower this ratio in the population by reducing dietary consumption of sodium and promoting dietary consumption of potassium is a key imperative since there are no reports of potassium toxicity due to dietary consumption.16\n\nSeveral studies have shown a correlation of the Na/K ratio with health outcomes. The dietary Na/K ratio was found to be a significant risk factor for mortality from stroke, cardiovascular disease, and all causes among the Japanese population.59 Reduction in blood pressure showed a significant correlation with reduced a urinary Na/K ratio and improved urinary potassium.75 Epidemiological research advises that the urinary Na/K ratio can be an advanced metric as compared to sodium and potassium levels alone for determining the association to BP and risk of cardiovascular disorder.58 In some studies, the Na/K ratio was inversely related to SBP; however, those outcomes have been commonly weaker in comparison with the outcomes of potassium alone.76 Farapti et al. (2017)11 found that the Na/K ratio may be a beneficial marker for predicting BP in a specific population. In addition, to hypertension, the Na/K ratio was also indicated to be related to obesity. Another study by Cai et al. (2016)77 also found an association between urinary Na/K ratio and obesity.\n\nSeveral epidemiological studies and systematic reviews have found an association between low potassium consumption and high sodium consumption with several non-communicable diseases such as hypertension,4 obesity,9 cardiovascular diseases,78,79 strokes,10 chronic kidney disease,80 and also all-cause mortality.10 Our systematic review only pertained to subjects in a community setting and not hospitalized patients; several studies have analyzed the affiliation of these nutrients with blood pressure and/or obesity at the population level.\n\nSome research has discovered no significant association with sodium and/or potassium intake together with BP,37–39,43 however, a majority of studies and some systematic reviews and meta-analyses of observational research have found a significant relationship among children, adults, and the elderly. According to a systematic review by Newberry et al. (2018),81 lowering sodium intake, increasing potassium intake, and the use of potassium-containing salt substitutes within the meals may significantly lower the BP, in particular among those with high blood pressure. Furthermore, a systematic review of studies published during 1995-2001 examined the influence of lowering sodium intake or potassium supplementation on BP. In all meta-analyses, the decrease in BP was found to be larger in hypertensive than normotensive subjects.75,82,83 A systematic review of another dietary intervention reported that the Dietary Approaches to Stop Hypertension (DASH) diet (low sodium and high potassium diet) had the most important net impact on reducing BP.84 Finally, an umbrella review showed that the DASH dietary pattern is related to lowered incidences of cardiovascular illnesses and improved BP.85\n\nThe significant impact of sodium and potassium intake on BP has also been demonstrated in children and adolescents.85,86 Excessive sodium consumption is a cause of increased BP in adults, youngsters, and teenagers. A systematic review of evidence from experimental and observational studies showed a positive relationship between sodium intake and BP in children and adolescents; consistent findings were obtained from experimental and observational studies.86 On the other hand, another study showed the intake of higher potassium-rich foods in childhood may help prevent increased BP in adolescence.76\n\nMa et al. (2015)87 analyzed the UK National Diet and Nutrition Survey (2008/2009 to 2011/2012) data which result showed higher salt intake in overweight and obese subjects. In a study by Elfassy et al. (2018),88 sodium intake was related to elevated body mass index (BMI), waist circumference (WC), and body fat content. According to the National Health and Nutrition Examination Survey (NHANES; 1999–2006), high sodium intake (>2300 mg/d) was related to a higher risk of obesity compared with intermediate sodium consumption (1500–2300 mg/d).89\n\nSome studies have revealed the affiliation between sodium or salt intake and obesity. However, not many researchers have reported the relation between potassium consumption and obesity. In s study by Cai et al. (2016),77 high potassium consumption was not related to a lowered risk of obesity, although potassium consumption was related to metabolic syndrome. Furthermore, the urinary Na/K ratio was related to obesity. In a recent study by Tal et al. (2019),90 subjects who achieved a decrease in BMI showed an average increase in potassium intake by 25%. Most studies that analyzed the correlation between these nutrients (sodium and potassium) and obesity were performed in children.\n\nImportantly, several studies assessed the correlation of sodium and potassium consumption with both obesity and high blood pressure. Leyvraz et al. (2018)86 observed that the correlation between sodium consumption and BP became more prominent in children who were overweight and low in potassium levels. In a study of children living in a Canadian rural community, being overweight or obese were strongly associated with elevated BP.91 Delmis (2010)92 found that overweight and obese children were at a 3–5 fold increased risk of hypertension. Concerning to the adult population, the NHANES (1999-2006) with 9162 healthy participants showed an independent correlation of high sodium intake with increased risk of both android and gynoid fat storage in the USA working age population.89\n\n\nConclusion\n\nThe present study highlights that the adult population in most parts of the world continues to consume excessively high levels of sodium and low levels of potassium. This phenomenon was reflected in the Na/K ratio exceeding the current recommended level. This dietary pattern is correlated with an elevated risk of hypertension and obesity. Our study underlines the excessive dietary intake of sodium and low intake of potassium as a global public health problem and more strategic intervention possibly at policy level is warranted.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nOSF: Extended data for: “Community-level dietary intake of sodium, potassium, and sodium-to-potassium ratio as a global public health problem: A systematic review and meta-analysis”, http://doi.org/10.17605/OSF.IO/976RS.93\n\nThis project contains the following extended data:\n\n• Supplementary Material.docx\n\n\nReporting guidelines\n\nOSF: Extended data for: “Community-level dietary intake of sodium, potassium, and sodium-to-potassium ratio as a global public health problem: A systematic review and meta-analysis”, http://doi.org/10.17605/OSF.IO/UBPT3.94\n\n• PRIMSA checklist\n\n• PRISMA flow diagram\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgments\n\nThe authors wish to thank to Universitas Airlangga for giving a finding support in this research and publication.\n\n\nReferences\n\nInstitute of Medicine: Dietary Reference Intakes for Water, Potassium, Sodium, Chloride, and Sulfate. National Academy Press;2005.\n\nHuybrechts I, et al.: Food sources and correlates of sodium and potassium intakes in Flemish pre-school children. Public Health Nutr. 2012; 15: 1039–1046. PubMed Abstract \| Publisher Full Text\n\nMeneton P, et al.: Dietary sources and correlates of sodium and potassium intakes in the French general population. Eur. J. Clin. Nutr. 2009; 63: 1169–1175. PubMed Abstract \| Publisher Full Text\n\nAdrogué HJ, Madias NE: Sodium and potassium in the pathogenesis of hypertension. N. Engl. J. Med. 2007; 356: 1966–1978. Publisher Full Text\n\nManzel A, et al.: Role of “western diet” in inflammatory autoimmune diseases. Curr. Allergy Asthma Rep. 2014; 14: 1–13. Publisher Full Text\n\nWebster J, Trieu K, Dunford E, et al.: Target salt 2025: A global overview of national programs to encourage the food industry to reduce salt in foods. Nutrients. 2014; 6: 3274–3287. PubMed Abstract \| Publisher Full Text\n\nAburto NJ, et al.: Effect of increased potassium intake on cardiovascular risk factors and disease: Systematic review and meta-analyses. BMJ. 2013; 346: 1–19.\n\nChobanian AV, et al.: The Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure: the JNC 7 report. JAMA. 2003; 289: 2560–2572. PubMed Abstract \| Publisher Full Text\n\nJain N, et al.: Association of urinary sodium-to-potassium ratio with obesity in a multiethnic cohort. Am. J. Clin. Nutr. 2014; 99: 992–998. Publisher Full Text\n\nJayedi A, Ghomashi F, Zargar MS, et al.: Dietary sodium, sodium-to-potassium ratio, and risk of stroke: A systematic review and nonlinear dose-response meta-analysis. Clin. Nutr. 2019; 38: 1092–1100. PubMed Abstract \| Publisher Full Text\n\nFarapti F, Nadhiroh SR, Sayogo S, et al.: Urinary and dietary sodium to potassium ratio as a useful marker for estimating blood pressure among older women in Indonesian Urban coastal areas. Med. J. Nutrition Metab. 2017; 10: 113–122. Publisher Full Text\n\nIntersalt Cooperative Reserach Group: Intersalt: an international study of electrolyte excretion and blood pressure. Results for 24 hour urinary sodium and potassium excretion. Intersalt Cooperative Research Group. BMJ. 1988; 297: 319–328. Publisher Full Text\n\nWHO: Reducing salt intake in populations: Report of a WHO forum and technical meeting. World Health Organization;2007.\n\nDrewnowski A, Maillot M, Rehm C: Reducing the sodium-potassium ratio in the US diet: a challenge for public health. Am. J. Clin. Nutr. 2012; 96: 439–444. Publisher Full Text\n\nWHO: Guideline: Sodium intake for adults and children. World Health Organization. World Health Organization;2012.\n\nWHO: Guideline: Potassium intake for adults and children. World Health Organization. World Health Organization;2012.\n\nDu S, et al.: Understanding the patterns and trends of sodium intake, potassium intake, and sodium to potassium ratio and their effect on hypertension in China. Am. J. Clin. Nutr. 2014; 99: 334–343. Publisher Full Text\n\nRafie N, Hamedani SG, Mohammadifard N, et al.: 24-h urinary sodium to potassium ratio and its association with obesity in children and adolescents. Eur. J. Nutr. 2019; 58: 947–953. Publisher Full Text\n\nTan M, He FJ, Wang C, et al.: Twenty-Four-Hour Urinary Sodium and Potassium Excretion in China: A Systematic Review and Meta-Analysis. J. Am. Heart Assoc. 2019; 8: e012923. PubMed Abstract \| Publisher Full Text\n\nAltman DG, Bland JM: Standard deviations and standard errors. BMJ. 2005; 331: 903. PubMed Abstract \| Publisher Full Text\n\nMoreira P, et al.: Sodium and potassium urinary excretion and their ratio in the elderly: Results from the nutrition UP 65 study. Food Nutr. Res. 2018; 62: 1–10.\n\nMizéhoun-Adissoda C, et al.: Dietary sodium and potassium intakes: Data from urban and rural areas. Nutrition. 2017; 33: 35–41. PubMed Abstract \| Publisher Full Text\n\nQueiroz A, et al.: Urinary sodium and potassium excretion and dietary sources of sodium in maputo, mozambique. Nutrients. 2017; 9: 1–13.\n\nSugimoto M, Asakura K, Masayasu S, et al.: Relationship of nutrition knowledge and self-reported dietary behaviors with urinary excretion of sodium and potassium: Comparison between dietitians and nondietitians. Nutr. Res. 2016; 36: 440–451. PubMed Abstract \| Publisher Full Text\n\nXu J, et al.: Estimation of salt intake by 24-hour urinary sodium excretion: A cross-sectional study in Yantai, China. BMC Public Health. 2014; 14: 1–6. Publisher Full Text\n\nPeng Y, et al.: Validation and assessment of three methods to estimate 24-h urinary sodium excretion from spot urine samples in Chinese adults. PLoS One. 2016; 11: 1–11.\n\nKyung Kim M, et al.: Dose–response association of 24-hour urine sodium and sodium to potassium ratio with nighttime blood pressure at older ages. Eur. J. Prev. Cardiol. 2019; 26: 952–960. PubMed Abstract \| Publisher Full Text\n\nNowson C, et al.: Dietary salt intake and discretionary salt use in two general population samples in Australia: 2011 and 2014. Nutrients. 2015; 7: 10501–10512. PubMed Abstract \| Publisher Full Text\n\nAthanasatou A, Kandyliari A, Malisova O, et al.: Sodium and Potassium Intake from Food Diaries and 24-h Urine Collections from 7 Days in a Sample of Healthy Greek Adults. Front. Nutr. 2018; 5: 1–8. Publisher Full Text\n\nD’elia L, et al.: Sodium and potassium intake, knowledge attitudes and behaviour towards salt consumption amongst adults in podgorica, montenegro. Nutrients. 2019; 11: 1–12.\n\nHarris RM, et al.: Sodium and potassium excretion in an adult Caribbean population of African descent with a high burden of cardiovascular disease. BMC Public Health. 2018; 18: 1–11. Publisher Full Text\n\nYuan C, et al.: Relative Validity of Nutrient Intakes Assessed by Questionnaire, 24-Hour Recalls, and Diet Records as Compared with Urinary Recovery and Plasma Concentration Biomarkers: Findings for Women. Am. J. Epidemiol. 2018; 187: 1051–1063. PubMed Abstract \| Publisher Full Text\n\nSun Q, et al.: Reproducibility of urinary biomarkers in multiple 24-h urine samples. Am. J. Clin. Nutr. 2017; 105: 159–168. Publisher Full Text\n\nMorrissey E, et al.: Sodium and potassium intakes and their ratio in adults (18–90 y): Findings from the Irish national adult nutrition survey. Nutrients. 2020; 12: 1–12. Publisher Full Text\n\nYin L, et al.: Association patterns of urinary sodium, potassium, and their ratio with blood pressure across various levels of salt-diet regions in China. Sci. Rep. 2018; 8: 1–11.\n\nWare LJ, et al.: Associations between dietary salt, potassium and blood pressure in South African adults: WHO SAGE Wave 2 Salt & Tobacco. Nutr. Metab. Cardiovasc. Dis. 2017; 27: 784–791. PubMed Abstract \| Publisher Full Text\n\nMoliterno P, et al.: Blood Pressure in relation to 24-Hour Urinary Sodium and Potassium Excretion in a Uruguayan Population Sample. Int. J. Hypertens. 2018; 2018: 1–10. PubMed Abstract \| Publisher Full Text\n\nLuta X, et al.: The relationship of health/food literacy and salt awareness to daily sodium and potassium intake among a workplace population in Switzerland. Nutr. Metab. Cardiovasc. Dis. 2018; 28: 270–277. PubMed Abstract \| Publisher Full Text\n\nChen SL, Dahl C, Meyer HE, et al.: Estimation of salt intake assessed by 24-hour urinary sodium excretion among somali adults in Oslo, Norway. Nutrients. 2018; 10: 1–10.\n\nLi Y, et al.: Twenty-four-hour urinary sodium and potassium excretion and their associations with blood pressure among adults in China: Baseline survey of action on salt china. Hypertension. 2020; 76: 1580–1588. PubMed Abstract \| Publisher Full Text\n\nNaser AM, He FJ, Rahman M, et al.: Spot Urine Formulas to Estimate 24-Hour Urinary Sodium Excretion Alter the Dietary Sodium and Blood Pressure Relationship. Hypertension. 2021; 77: 2127–2137. PubMed Abstract \| Publisher Full Text\n\nOdili AN, et al.: Urinary sodium excretion and its association with blood pressure in Nigeria: A nationwide population survey. J. Clin. Hypertens. 2020; 22: 2266–2275. PubMed Abstract \| Publisher Full Text\n\nVallejo M, et al.: Assessment of Sodium and Potassium Intake by 24 h Urinary Excretion in a Healthy Mexican Cohort. Arch. Med. Res. 2017; 48: 195–202. Publisher Full Text\n\nModesti PA, et al.: Daily urinary sodium and potassium excretion in Chinese first-generation migrants in Italy. Int. J. Cardiol. 2019; 286: 175–180. PubMed Abstract \| Publisher Full Text\n\nMcLean R, Edmonds J, Williams S, et al.: Balancing sodium and potassium: Estimates of intake in a New Zealand adult population sample. Nutrients. 2015; 7: 8930–8938. PubMed Abstract \| Publisher Full Text\n\nSari DW, Noguchi-Watanabe M, Sasaki S, et al.: Estimation of sodium and potassium intakes assessed by two 24-hour urine collections in a city of Indonesia. Br. J. Nutr. 2021; 126: 1537–1548. PubMed Abstract \| Publisher Full Text\n\nElfassy T, et al.: Neighbourhood socioeconomic status and cross-sectional associations with obesity and urinary biomarkers of diet among New York City adults: the heart follow-up study. BMJ Open. 2017; 7: e018566–e018566. Publisher Full Text\n\nKawano Y, Tsuchihashi T, Matsuura H, et al.: Report of the Working Group for Dietary Salt Reduction of the Japanese Society of Hypertension: (2) Assessment of Salt Intake in the Management of Hypertension. Hypertens. Res. 2007; 30: 887–893. Publisher Full Text\n\nZhou L, et al.: Validation of spot urine in predicting 24-h sodium excretion at the individual level. Am. J. Clin. Nutr. 2017; 105: ajcn147553–ajcn141296. PubMed Abstract \| Publisher Full Text\n\nCharlton KE, et al.: Correcting for Intra-Individual Variability in Sodium Excretion in Spot Urine Samples Does Not Improve the Ability to Predict 24 h Urinary Sodium Excretion. Nutrients. 2020; 12: 2026. PubMed Abstract \| Publisher Full Text\n\nZhang X, et al.: Assessment and validation of three spot urine assay methods for the estimation of 24-hour urinary sodium excretion in Chinese Tibetan adults living in the mountains. J. Clin. Hypertens. 2021; 23: 1588–1598. PubMed Abstract \| Publisher Full Text\n\nZhang L, et al.: A pilot study to validate a standardized one-week salt estimation method evaluating salt intake and its sources for family members in China. Nutrients. 2015; 7: 751–763. PubMed Abstract \| Publisher Full Text\n\nGe Z, et al.: Association between 24 h urinary sodium and potassium excretion and the metabolic syndrome in Chinese adults: The Shandong and Ministry of Health Action on Salt and Hypertension (SMASH) study. Br. J. Nutr. 2015; 113: 996–1002. PubMed Abstract \| Publisher Full Text\n\nYongqing Z, et al.: Prevalence, awareness, treatment and control of hypertension and sodium intake in Jiangsu Province, China: A baseline study in 2014. BMC Public Health. 2016; 16: 1–8.\n\nDeng T, et al.: Influence of weight status on 24-hour urine composition in adults without urolithiasis: A nationwide study based on a Chinese Han population. PLoS One. 2017; 12: 1–10. Publisher Full Text\n\nXu J, et al.: Assessment and validation of spot urine in estimating the 24-h urinary sodium, potassium, and sodium/potassium ratio in Chinese adults. J. Hum. Hypertens. 2020; 34: 184–192. PubMed Abstract \| Publisher Full Text\n\nNohara-Shitama Y, et al.: Twenty-four-hour urinary potassium excretion, but not sodium excretion, is associated with all-cause mortality in a general population. J. Am. Heart Assoc. 2018; 7: 1–7.\n\nIwahori T, et al.: Diurnal variation of urinary sodium-to-potassium ratio in free-living Japanese individuals. Hypertens. Res. 2017; 40: 658–664. PubMed Abstract \| Publisher Full Text\n\nOkayama A, et al.: Dietary sodium-to-potassium ratio as a risk factor for stroke, cardiovascular disease and all-cause mortality in Japan: the NIPPON DATA 80 cohort study. BMJ Open. 2016; 6: e011632. PubMed Abstract \| Publisher Full Text\n\nChailimpamontree W, et al.: Estimated dietary sodium intake in Thailand: A nationwide population survey with 24-hour urine collections. J. Clin. Hypertens. 2021; 23: 744–754. PubMed Abstract \| Publisher Full Text\n\nElarbaoui M, et al.: Sodium and Potassium Intakes assessed by 24-h Urine among Moroccan University students in Casablanca, Morocco: Cross-Sectional Study. SHS Web Conf. 2021; 119: 04003. Publisher Full Text\n\nVasara E, et al.: Sodium and Potassium Intake in Healthy Adults in Thessaloniki Greater Metropolitan Area—The Salt Intake in Northern Greece (SING) Study. Nutrients. 2017; 9: 1–11. Publisher Full Text\n\nCappuccio FP, et al.: Geographic and socioeconomic variation of sodium and potassium intake in Italy: Results from the MINISAL-GIRCSI programme. BMJ Open. 2015; 5: e007467–e007411. Publisher Full Text\n\nDerouiche A, El-kardi Y, Mohtadi K, et al.: Estimation de l’apport quotidien en sel à travers l’excrétion du sodium urinaire de 24 heures chez les adultes Marocains: une étude pilote. Nutr. Clin. Metab. 2017; 31: 207–211. Publisher Full Text\n\nOthman F, et al.: Development and double cross-validation of new spot urine sodium equation to predict 24-h urine sodium in the Malaysian population. J. Health Popul. Nutr. 2021; 40: 1–8.\n\nYi SS, et al.: Highlighting the ratio of sodium to potassium in population-level dietary assessments: cross-sectional data from New York City, USA. Public Health Nutr. 2014; 17: 2484–2488. PubMed Abstract \| Publisher Full Text\n\nBernstein AM, Willett WC: Trends in 24-h urinary sodium excretion in the United States, 1957-2003: A systematic review. Am. J. Clin. Nutr. 2010; 92: 1172–1180. PubMed Abstract \| Publisher Full Text\n\nMente A, et al.: Association of urinary sodium and potassium excretion with blood pressure. N. Engl. J. Med. 2014; 371: 601–611. Publisher Full Text\n\nGupta P, et al.: Stakeholders’ perceptions regarding a salt reduction strategy for India: Findings from qualitative research. PLoS One. 2018; 13: 1–16. Publisher Full Text\n\nTrieu K, et al.: Salt reduction initiatives around the world-A systematic review of progress towards the global target. PLoS One. 2015; 10: 1–22. Publisher Full Text\n\nFarapti F, Fatimah AD, Astutik E, et al.: Awareness of Salt Intake among Community-Dwelling Elderly at Coastal Area: The Role of Public Health Access Program. J. Nutr. Metab. 2020; 2020: 8793869.\n\nGlatz N, et al.: Associations of sodium, potassium and protein intake with blood pressure and hypertension in Switzerland. Swiss Med. Wkly. 2017; 147: 1–9.\n\nFarapti F, et al.: Highlighting of urinary sodium and potassium among Indonesian schoolchildren aged 9-12 years: The contribution of school food. J. Nutr. Metab. 2019; 2019: 1–9. PubMed Abstract \| Publisher Full Text\n\nCampanozzi A, et al.: High sodium and low potassium intake among Italian children: Relationship with age, body mass and blood pressure. PLoS One. 2015; 10: 1–13. Publisher Full Text\n\nBinia A, Jaeger J, Hu Y, et al.: Daily potassium intake and sodium-to-potassium ratio in the reduction of blood pressure: a meta-analysis of randomized controlled trials. J. Hypertens. 2015; 33: 1509–1520. PubMed Abstract \| Publisher Full Text\n\nBuendia JR, Bradlee ML, Daniels SR, et al.: Longitudinal effects of dietary sodium and potassium on blood pressure in adolescent girls. JAMA Pediatr. 2015; 169: 560–568. PubMed Abstract \| Publisher Full Text\n\nCai X, et al.: Potassium and Obesity/Metabolic Syndrome: A Systematic Review and Meta-Analysis of the Epidemiological Evidence. Nutrients. 2016; 8: 183. PubMed Abstract \| Publisher Full Text\n\nCook NR, et al.: Joint effects of sodium and potassium intake on subsequent cardiovascular disease: the Trials of Hypertension Prevention follow-up study. Arch. Intern. Med. 2009; 169: 32–40. PubMed Abstract \| Publisher Full Text\n\nMartens RJH, et al.: Associations of 24-Hour Urinary Sodium and Potassium Excretion with Cardiac Biomarkers: The Maastricht Study. J. Nutr. 2020; 150: 1413–1424. Publisher Full Text\n\nMirmiran P, Nazeri P, Bahadoran Z, et al.: Dietary Sodium to Potassium Ratio and the Incidence of Chronic Kidney Disease in Adults: A Longitudinal Follow-Up Study. Prev. Nutr. Food Sci. 2018; 23: 87–93. PubMed Abstract \| Publisher Full Text\n\nNewberry SJ, et al.: Sodium and Potassium Intake. Effects on Chronic Disease Outcomes and Risks. 2018.\n\nGeleijnse JM, Kok FJ, Grobbee DE: Blood pressure response to changes in sodium and potassium intake: a metaregression analysis of randomised trials. J. Hum. Hypertens. 2003; 17: 471–480. PubMed Abstract \| Publisher Full Text\n\nWang M, et al.: A Meta-Analysis of Effect of Dietary Salt Restriction on Blood Pressure in Chinese Adults. Glob. Heart. 2015; 10: 291–299.e6. PubMed Abstract \| Publisher Full Text\n\nBalasubramaniam J, Hewlings SJ: A Systematic Review of the Efficacy of DASH Diet in Lowering Blood Pressure Among Hypertensive Adults. Top. Clin. Nutr. 2021; 36: 158–176. Publisher Full Text\n\nChiavaroli L, Viguiliouk E, Nishi SK, et al.: DASH Dietary Pattern and Cardiometabolic Outcomes: An Umbrella Review of Systematic Reviews and Meta-Analyses. Nutrients. 2019; 11: 338. PubMed Abstract \| Publisher Full Text\n\nLeyvraz M, et al.: Sodium intake and blood pressure in children and adolescents: A systematic review and meta-analysis of experimental and observational studies. Int. J. Epidemiol. 2018; 47: 1796–1810. PubMed Abstract \| Publisher Full Text\n\nMa Y, He FJ, Macgregor GA: High salt intake: Independent risk factor for obesity? Hypertension. 2015; 66: 843–849. Publisher Full Text\n\nElfassy T, et al.: Associations of Sodium and Potassium with Obesity Measures Among Diverse US Hispanic/Latino Adults: Results from the Hispanic Community Health Study/Study of Latinos. Obesity (Silver Spring). 2018; 26: 442–450. PubMed Abstract \| Publisher Full Text\n\nZhang X, Wang J, Li J, et al.: A positive association between dietary sodium intake and obesity and central obesity: results from the National Health and Nutrition Examination Survey 1999-2006. Nutr. Res. 2018; 55: 33–44. PubMed Abstract \| Publisher Full Text\n\nTal B, et al.: Increment in Dietary Potassium Predicts Weight Loss in the Treatment of the Metabolic Syndrome. Nutrients. 2019; 11. PubMed Abstract \| Publisher Full Text\n\nSalvadori M, et al.: Elevated blood pressure in relation to overweight and obesity among children in a rural Canadian community. Pediatrics. 2008; 122: e821–e827. PubMed Abstract \| Publisher Full Text\n\nDelmis J: Effect of diet and salt intake on the development of hypertension in children and adolescents. Acta Med. Croatica. 2010; 64: 111–114. PubMed Abstract\n\nFarapti PHM, Fadilla C, et al.: Extended data for: “Community-level dietary intake of sodium, potassium, and sodium-to-potassium ratio as a global public health problem: A systematic review and meta-analysis.”.2022, May 29. Publisher Full Text\n\nFarapti PHM, Fadilla C, et al.: Extended data for: “Community-level dietary intake of sodium, potassium, and sodium-to-potassium ratio as a global public health problem: A systematic review and meta-analysis.”.2022, June 14. Publisher Full Text" }	[ { "id": "243799", "date": "05 Mar 2024", "name": "Nan Xin Wang", "expertise": [ "Reviewer Expertise Sodium", "policy", "iodine" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 investigated sodium and potassium intake in healthy adults using observational studies that reported 24-hour urinary excretion of sodium and potassium.\nIntroduction: Para 1: There is a strong emphasis on Asian diets transiting to \"western\" diet. However, the article focus on worldwide. Typically, Asian countries have higher sodium intake than European, American and Australia/NZ. So, it seems incorrect to comment that the adoption of Westernised diet contributes to increased sodium intake. It is the adoption of convenience and ultra-processed foods that contributes to higher sodium intake. So, it is unclear why the authors have singled Asian diets. Lifestyle: would be cover much wider aspect of life than just dietary pattern, please change the wording. (Similarly, please remove from abstract.)\nPara 3: WHO recommendations are not strategic interventions. These are guidelines for interventions which countries can adopt. Perhaps, you could describe nation-wide interventions and its effects on intake.\nPara 4: More details is needed on the systematic review conducted in China, how does this relate to the current paper?\n\nMethods: PRISMA is reportedly followed, please include the PRISMA table as supplementary table.\n\nResults: I am unable to access the supplementary table for study characteristics. Para 2: please follow spelling intervention, for numbers ten and below, please spell in full. (Please follow this convention throughout the article) \"Likewise, the studies by Du et al. (2014)17 and Morrisey et al. (2020)34 used the spot urine method in combination with a dietary survey.\" This sentence is not a result of the study. Please move it to discussion. It confuses the reader.\nPara 4: summaries, should be summarises remove presents. please use urinary excretion throughout\nDiscussion: Para 1: Please elaborate on reliable and convenient methods.\nPara 2: Sentence 1, replace was with were. Please elaborate what kinds of research were included in Tan et al.\nPara 3: Please state if the numbers in brackets are 95% CI, min/max, 25th/95th percentile. Sentence 3, replace which with who. Please state the recommendations of IOM. Please be consistent in using mg or mmol. Alternatively, provide both units of measurement. Sentence 9, replace seems with seem. Please expand the two final sentence, what do you mean by \"well greater than minimal physiological requirements\"? More concrete examples are required.\n\nPara 4: suggest to reword, :\"However, sodium is a naturally occurring nutrient into a vast range over foods\" Although sodium is naturally occurring in foods, most sodium is added during processing. Hence, this in itself should not be much of an issue with sodium intake. Please type in full \"they’re\".\n\nPara 5: Please provide estimate for Potassium intake in Benin and describe how potassium intake was assessed.\nPara 11 and para 12: Suggest to reorganise.\nConclusion: \"This dietary pattern is correlated with an elevated risk of hypertension and obesity.\" This is not part of the study's results and therefore, cannot be concluded as such.\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? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly", "responses": [ { "c_id": "12233", "date": "30 Sep 2024", "name": "Farapti Farapti", "role": "Author Response", "response": "ABSTRACT AND INTRODUCTION Reviewer: Lifestyle: would be cover much wider aspect of life than just dietary pattern, please change the wording. (Similarly, please remove from abstract.) Author Response: You're right; lifestyle encompasses a much broader spectrum of life factors beyond just dietary patterns. This includes aspects like physical activity, stress levels, sleep habits, and more. Thank you for emphasizing the need to consider these broader aspects when discussing health impacts. Our suggestion: changing \"Lifestyle\" to \"eating habit\" Reviewer: Para 1: There is a strong emphasis on Asian diets transiting to \"western\" diet. However, the article focus on worldwide. Typically, Asian countries have higher sodium intake than European, American and Australia/NZ. So, it seems incorrect to comment that the adoption of Westernised diet contributes to increased sodium intake. It is the adoption of convenience and ultra-processed foods that contributes to higher sodium intake. So, it is unclear why the authors have singled Asian diets. Lifestyle: would be cover much wider aspect of life than just dietary pattern, please change the wording. (Similarly, please remove from abstract.) Author Response: Thank you for highlighting valid point about the transition to \"western\" diets not being solely responsible for increased sodium intake. The emphasis should indeed be on the shift towards convenience and ultra-processed foods rather than singling out Asian diets. It's important to consider the broader global dietary trends and their impact on health. Thank you for highlighting this perspective. You're right; lifestyle encompasses a much broader spectrum of life factors beyond just dietary patterns. This includes aspects like physical activity, stress levels, sleep habits, and more. Thank you for emphasizing the need to consider these broader aspects when discussing health impacts. Our suggestion: changing \"Lifestyle\" to \"eating habit\" Reviewer: Para 3: WHO recommendations are not strategic interventions. These are guidelines for interventions which countries can adopt. Perhaps, you could describe nation-wide interventions and its effects on intake. Author Response: Thanks for your advice. We have describe in several countries regarding nation-wide interventions about sodium potassium Reviewer: Para 4: More details is needed on the systematic review conducted in China, how does this relate to the current paper? Author Response: The research in China focused on the domestic population, so it became a reference for us to systematically research dietary consumption of Na/K in various countries from all over the world. So it is hoped that the results of this research can also become knowledge that can be accessed more widely. METHODS Reviewer: Methods: PRISMA is reportedly followed, please include the PRISMA table as supplementary table. Feedback: Thank you, we have added the PRISMA table in the supplementary file RESULTS Reviewer: Results: I am unable to access the supplementary table for study characteristics. Author Response: Thank you, we have added the study characteristics table in the supplementary file Reviewer: Para 2: please follow spelling intervention, for numbers ten and below, please spell in full. (Please follow this convention throughout the article) \"Likewise, the studies by Du et al. (2014)17 and Morrisey et al. (2020)34 used the spot urine method in combination with a dietary survey.\" This sentence is not a result of the study. Please move it to discussion. It confuses the reader. Author Response: Thank you, we have revised that points Reviewer: Para 4: summaries, should be summarises remove presents. please use urinary excretion throughout Author Response: Thank you, we have removed presents and only use urinary excretion throughout DISCUSSION: Reviewer: Para 1: Please elaborate on reliable and convenient methods. Author Response: Thank you for the suggestion. We rearranged some sentences to elaborate clearly on reliable and convenient methods. Reviewer: Para 2: Sentence 1, replace was with were. Please elaborate what kinds of research were included in Tan et al. Author Response: The eligible studies by Tan et al were they were conducted only in China (Chinese population), no restriction on study year and subjects’age, applied 24-hor urine collection to assess Na and K intake Reviewer: Para 3: Please state if the numbers in brackets are 95% CI, min/max, 25th/95th percentile. Sentence 3, replace which with who. Author Response: We stated the number in brackets are 95%CI (min-max). We revised which with who. Reviewer: Please state the recommendations of IOM. Author Response: We stated the recommendation of IOM about sodium intake Reviewer: Please be consistent in using mg or mmol. Alternatively, provide both units of measurement. Author Response: Thank you for the suggestion We changed the mg with mmol. We will consistent in using mmol for measurement unit of sodium intake Reviewer: Sentence 9, replace seems with seem. Author Response: We revised seems with seem Reviewer: Please expand the two final sentence, what do you mean by \"well greater than minimal physiological requirements\"? More concrete examples are required. Author Response: Thank you for the suggestion. We deleted the two final sentence, and arranged the new sentences to explain clearly and give concrete example about basic nutritional requirements for sodium intake Reviewer: Para 4: suggest to reword, :\"However, sodium is a naturally occurring nutrient into a vast range over foods\" Although sodium is naturally occurring in foods, most sodium is added during processing. Hence, this in itself should not be much of an issue with sodium intake. Please type in full \"they’re\". Author Response: Thank you for the correction. We reworded as your suggestion We corrected and changed they’re with they are Reviewer: Para 5: Please provide estimate for Potassium intake in Benin and describe how potassium intake was assessed. Author Response: We would like to clarify that we would like to point out that the study in Benin showed a high prevalence of hypertension Reviewer: Para 11 and para 12: Suggest to reorganise. Author Response: Thank you for the suggestion We arranged and organized two paragraphs become one paragraph discussing about sodium and potassium intake and the correlation with obesity CONCLUSION Reviewer: Conclusion: \"This dietary pattern is correlated with an elevated risk of hypertension and obesity.\" This is not part of the study's results and therefore, cannot be concluded as such. Author Response: Thank you for the correction. We deleted the sentence" } ] }, { "id": "298775", "date": "26 Aug 2024", "name": "Ines Drenjančević", "expertise": [ "Reviewer Expertise microcirculation", "sodium/potassium dietary intake", "physiology", "immunology", "vascular reactivity" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 systematic review and meta analysis of a number of studies related to dietary intake of sodium, potassium and calculated sodium-to-potassium ratio. The study is performed by review of publications in various indexing basis. The study is conducted appropriately.\nMinor remarks:\nWhy no studies from South America or Canada were included in analysis? If two studies that used spot-urine sample were excluded from analysis, would obtained data be different? Kindly provide in Discussion section data from WHO on Na, K intake and compare that to your data? In Discussion section, please provide or highlight the arguments for Conclusion that \"...This dietary pattern is correlated with an elevated risk of hypertension and obesity. \"- e.g. provide a table or infformation from analyzed 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? Yes\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/11-953
https://f1000research.com/articles/13-1108/v1	30 Sep 24	{ "type": "Research Article", "title": "Mediating role of Social Support and Self-efficiency on Academic stress and Student’s Psychological well-being among Public and Private Universities in Mogadishu -Somalia.", "authors": [ "Ali Dahir Mohamed", "Abdulkadir Jeilani" ], "abstract": "Background Academic stress is a significant factor affecting students’ psychological well-being, particularly in higher education. Understanding the mediating roles of social support and self-efficacy can provide insights into how these factors influence students’ psychological well-being in public and private universities.\n\nMethods The study examined the mediating roles of social support and self-efficacy in the relationship between academic stress and psychological well-being among university students in Mogadishu, Somalia. Utilizing a stratified sampling technique, data were collected from 663 students across public (52.6%) and private (47.4%) universities through a structured questionnaire and analyzed using path analysis to assess direct and indirect effects. Structural equation modeling technique was used for data analysis.\n\nResults The analysis revealed a significant direct effect of academic stress on psychological well-being (β = 0.133, p = 0.000). Academic stress was not significantly related to social support (β = 0.128, p = 0.066) and self-efficacy (β = 0.075, p = 0.099). However, both social support (β = 0.059, p = 0.000) and self-efficacy (β = 0.838, p = 0.000) were significantly related to psychological well-being. The mediating analysis showed that social support partially mediated the relationship between academic stress and psychological well-being (Indirect effect = 0.070, CI [-0.036, 0.197], p = 0.000), while self-efficacy did not mediate this relationship (Indirect effect = 0.063, CI [0.054, 0.218], p = 0.097).\n\nConclusions The findings suggest a significant positive impact of academic stress on psychological well-being, while social support partially mediates this relationship, highlighting its buffering role. Conversely, self-efficacy, although positively contributing to psychological well-being, does not mediate the effect of academic stress. These results underscore the importance of robust social support systems and targeted interventions to enhance students’ coping mechanisms and overall psychological well-being. Study limitations and implication are discussed.", "keywords": [ "Social Support", "Self-efficiency", "Academic stress", "psychological well-being", "Public and Private Universities" ], "content": "1. Introduction\n\nStress is one of the most important factors in psychological research since it has an impact on the well-being and health of individuals, the psychological well-being of students is significantly harmed by academic stress, which is caused by work, high performance, tests, and challenging assignments. Therefore, it is essential to fully understand the complex relationship between academic stress and psychological well-being in order to develop effective treatments.1\n\nAcademic stress refers to the stress experienced by individuals in educational settings due to numerous variables, According to earlier research2–5 Academic stress arises from the inability to cope with academic related tasks, leading to negative impacts such as smoking behavior, mental health issues, poor sleep quality, depression, insomnia, substance addiction, self-harm, and suicidal ideation. Also, other factors contributing to academic stress include self-inflicted stress, parental expectations, academic queries, lack of time for revision, low parental education levels, and poor exam grades. Therefore, understanding academic stress is crucial for implementing interventions at various levels to mitigate its negative effects on students’ well-being and academic performance.\n\nAcademic stress is the product of a combination of academic-related demands that exceed the adaptive resources available to an individual,2 Researchers agree that students face common academic stressors, such as family-pressures, scholarship demands, financial burdens, competition in class, examination, time-management and course-related stress.2 According to Ref. 3 the main cause of academic stress are academic results, admissions, students transfer, exams, load of extra classes, social comparison, exams stress, expectations teachers and parents.\n\nAcademic stress has been shown to have negative impact on students’ mental health, Researches6 indicates that high levels of academic stress are correlated with an increased probability of experiencing mental health issues, such as weakening mental health and feelings of anxiety and depression.5 Studies have highlighted the importance of addressing academic stress to enhance students’ overall mental well-being, as stress from academic pressures, family circumstances, and other sources can significantly impact mental health. Furthermore, interventions like wellness trainings have shown promise in improving mental wellness and reducing the negative impact of academic stress on students’ mental health.\n\nThe most common psychological consequences associated with academic stress include depression, anxiety, substance abuse, and suicide ideation.7 Higher stress levels, particularly related to academic tasks and concerns like grades, exams, and competition with peers, are predominant among younger students.8 These psychological consequences highlight the importance of addressing and managing academic stress effectively to safeguard students’ mental health and well-being.\n\nAcademic stress significantly impacts the psychological well-being of students in both public and private institutions. Studies show that academic stress is associated with lower mental well-being.9,10 Factors such as academic pressure, family circumstances, side-activity pressure, and financial situation contribute to increased stress levels among students, leading to a negative impact on mental well-being. Additionally, coping strategies like Academic Psychological capital and self-efficacy play a crucial role in mitigating the effects of academic stress on psychological well-being.11 It is essential for educational institutions to develop strategies to reduce stress levels and support students in managing academic pressures to safeguard their psychological well-being.\n\nResearchers have identified protective variables that may protect students from the negative psychological effects of study-related stress. But most research has focused on identifying the psychological symptoms of academic stress, rather than looking at strategies to protect students from these demands.12\n\nIn both public and private universities in Mogadishu, Somalia, the current study aimed to examine the effects of academic stress on students’ psychological wellbeing, with an emphasis on the mediating roles of self-efficiency and social support. By integrating the Transactional Theory of Stress and Coping with the Social Cognitive Theory, researchers can gain a broader understanding of how academic stress impacts students’ psychological well-being, especially in the context of social support and self-efficacy, across public and private universities. These theories provide a framework for exploring the complex interactions among stress, coping, social support, and self-efficacy in shaping students’ well-being outcomes in academic settings. The study addressed the absence of comprehensive research on the impacts of academic stress on students’ psychological well-being in both public and private universities.\n\n\n2. Literature review\n\nThe Transactional Model of Stress and Coping, proposed by Lazarus and Folk man13 (1984), contended that a person’s capacity to cope and adjust to challenges and problems is a consequence of transactions (or interactions) that occur between a person and their environment. The Transactional Theory of Stress and Coping, developed by Lazarus and Folk man, focuses on how individuals assess and response to stress through cognitive appraisal and cognitive processes. stress is the result of transactions between the person, environment, and situation, influenced by cognitive appraisals and coping strategies. This theory emphasizes the dynamic nature of stress and coping processes, and suggests that individuals’ perceptions and responses to stressors play an important role in determining their well-being outcomes13,14\n\nThe Social Cognitive Theory, proposed by Albert Bandura, emphasizes the role of cognitive processes in shaping behavior and outcomes. this means that persons’ beliefs about their ability to succeed (self-efficacy) influence their behavior and reactions to challenging situations. In the context of academic stress, this theory suggests that the students have the ability to cope with high self-efficacy are more likely to effectively cope with stressors and maintain their psychological well-being. Social Cognitive Theory also considers the impact of social influences and observational learning on individuals’ coping.9\n\nIn the context of the impact of academic stress on students’ psychological well-being, the Transactional Theory of Stress and Coping and the Social Cognitive Theory focus on the following. Both theories highlight the importance of cognitive appraisal in how individuals perceive and respond to stress. Students’ cognitive evaluations of academic stressors, their perceived ability to cope (self-efficacy), and the availability of social support influence their stress experiences and psychological well-being.10\n\nIn Coping Mechanisms, the theories emphasize the importance of coping strategies in managing stress. Student performance related to cognitive appraisals and self-efficacy beliefs play an important role in mediating the relationship between academic stress and psychological well-being. Effective strategies, supported by social resources, help students manage academic stress and maintain well-being.9,10,15\n\nAcademic stress has become a major mental health concern across the worldwide these days. Also has emerged as a significant mental health that affecting various groups of students. Studies4,8 have highlighted the detrimental impact of academic stress on mental well-being, with associations found between high levels of academic stress and issues like depression, anxiety, self-harm, and suicidal ideation.\n\nAcademic stress among university students has been extensively studied, revealing various insights. According to research, there is a strong link between mental health and academic stress4 with self-inflicted stress being a prominent factor in high stress levels among students. Critical thinking skills were found not to have a significant relationship with academic stress.12 However, academic stress was positively correlated with academic performance, motivating students to study harder.16 Academic stress significantly impacts the mental well-being of university students.1,14,16 High levels of academic stress have been linked to increased probability of experiencing mental health issues like Weakening Mental Health.13\n\nA study found a strong correlation (r=0.582) between academic stress and psychological well-being among university students, indicating that higher stress levels correspond to lower well-being.17\n\nSocial support plays a crucial role in mediating academic stress and enhancing students’ psychological well-being. Studies18–21 indicated that social support from various sources like family, friends, and significant others positively correlates with happiness, subjective well-being, satisfaction with life, and flourishing among university students.\n\nThe impact of social support on students’ levels of academic stress is significant. Studies reveal a negative relationship between academic stress and parental social support, with more encouragement resulting into reduced stress levels.22 Additionally, perceived social support from various sources like family, friends, and significant others has been found to significantly correlate with reduced stress levels among undergraduate Health Sciences students.17 Moreover, teacher support at the individual level is associated with better coping abilities and lower helplessness, while peer support at the class level is linked to enhanced coping abilities and academic achievement.23 Furthermore, peer social support has been shown to lower academic stress levels during online learning, highlighting its importance in helping students deal with the challenges of virtual education.24,25\n\nSelf-efficacy plays an important role in mediating the relationship between academic stress and students’ psychological well-being. Studies have shown26–29 that higher levels of academic self-efficacy are associated with greater well-being, while academic stress tends to lead to psychological distress, such as symptoms of anxiety and depression. Additionally, factors like social support and mindfulness have been identified as mediating variables that influence academic self-efficacy in the face of psychological distress, ultimately impacting students’ well-being.\n\nSelf-efficacy plays an essential role in influencing academic performance across various educational settings. Research indicates that self-efficacy positively impacts academic achievement.30–33 It acts as a predictor of academic success and can mitigate academic burnout, reduce dropout rates, and enhance engagement.18 Moreover, self-efficacy mediates the relationship between parental expectations, academic stress, and performance, emphasizing its significance in academic outcomes. The correlation between self-efficacy and academic performance is particularly evident in vocational high school students, where self-efficacy significantly influences academic success. Overall, enhancing self-efficacy levels is vital for improving academic performance and student outcomes in various educational domains, highlighting the importance of fostering self-belief and confidence in learners. Therefore, the need to study the relationship between Academic stress on Student’s Psychological well-being, the following hypothesis is suggested.\n\nBased on the above discussion the researchers proposed the following hypotheses:\n\nThere is a significant impact of academic stress on psychological well-being,\n\nThere is a significant impact of academic stress on social support.\n\nThere is a significant impact of academic stress on self-efficiency.\n\nThere is a significant impact of social support on psychological well-being,\n\nThere is a significant impact of self-efficiency on psychological well-being.\n\nSocial supports mediate the relationship between academic stress and psychological well-being.\n\nSelf-efficiency mediate the relationship between academic stress and psychological well-being (Figure 1).\n\n\n3. Methods\n\nThe context of the study was public and private universities in Mogadishu – Somalia. Nearly 50,000 students are intended in these universities. These universities have fields of study at undergraduate, diploma and postgraduate levels. Faculties provided these universities include social science, computer technology, public health, business Economics and management sciences, sharia and law studies, education, engineering, medicine and surgery, Arts & humanities, agriculture & Environmental Sciences, languages, Islamic studies, geology, media & journalism, public admin and politics dentistry and postgraduate studies. The population of the study are target population from which the sample is actually selected or aggregation of study elements.19 The study population are undergraduate students of these universities, its estimated around 30,000 students. The study included stratified sample technique. Stratified sample technique is type of sampling method in which the total population is divided into smaller groups or strata to complete the sampling process.20 The study examined various factors related to academic stress and psychological well-being. The sample includes 663 students, with a gender distribution of 40.4% female and 59.6% male.\n\nA survey questionnaire was developed as the instrument for data collection. Items used for Academic Stress adapted by Ref. 21 to get students’ views of academic pressures and consists of 10 items, Psychological well-being Scale (PWS) adapted by Ref. 22 and consist of 18 items, Social Support Scale (SSS) adapted by Ref. 34 and 12 items, Self-Efficiency Scale (SSS) adapted by Ref. 35 and consist of 10 items.\n\nData collected using adopted questionnaires distributed electronically, depending on the feasibility and preferences of participants. The questionnaire comprised validated measures assessing academic stress, psychological well-being, social support, and self-efficacy. Additionally, demographic information such as age, gender, academic major, and university affiliation collected to facilitate subgroup analyses. The data collected from May 15 to Jun 3 2024.\n\nDescriptive statistics used to characterize the sample and examine the distribution of key variables. Structural equation modeling was used to examine mediating analysis of social support, self-efficacy in the relationship between academic stress, and psychological well-being.\n\nPrior to data collection, ethical approval was received from Mogadishu University institutional review board (IRB) in Mogadishu, Somalia (Date:15 – 05 – 2024, protocol number: MUIRB/09/24/001). Informed consent was obtained from all students. The students were informed that the research would be conducted following the principle of confidentiality and that all information obtained would be kept confidential.\n\n\n4. Data analysis and results\n\nA total of 663 sample size was achieved, the demographic profile of respondents for this study showed that female respondents made up 40.4%, of the sample while male made up 59.6% and mostly aged 18 to 21 years 67.1%. The distribution between public (52.6%) and private (47.4%) universities is nearly even. Most students are in their first three years of study, with Year One students representing the largest group 36.2%, while there are few students in Year Five (0.9%) and Year Six (1.2%) (Table 1).\n\nMeasurement model\n\nThe factor loadings for the items under each construct are all above 0.50, indicating good convergent validity.36 The composite reliability (CR) values for all constructs are above the recommended threshold of 0.70, suggesting good internal consistency. However, the AVE values for the academic stress (0.399) and psychological well-being (0.487) constructs are below the recommended threshold of 0.50, indicating that these constructs may not be capturing a sufficient amount of variance in their respective indicators. The correlation matrix reveals moderate to strong relationships between the constructs, with the highest correlation observed between self-efficacy factor and psychological well-being (0.814), suggesting a strong positive association between these two variables. Overall, the results provide insights into the psychometric properties of the measured constructs and their interrelationships within the study context. The discriminant validity was achieved (Tables 2 and 3).\n\nStructural model\n\nThe research findings H1. show that academic stress significantly impacts students’ psychological well-being, with a path coefficient (β) of 0.133, a t-statistic of 3.524, and a p-value of 0.000, indicating a strong positive relationship. However, academic stress does not significantly affect social support (β = 0.128, t = 1.839, p = 0.066) or self-efficacy (β = 0.075, t = 1.652, p = 0.099). Social support has a positive and significant effect on psychological well-being (β = 0.059, t = 2.624, p = 0.000), suggesting that increased support is associated with better psychological outcomes. Self-efficacy has a very strong and significant positive impact on psychological well-being (β = 0.838, t = 14.002, p = 0.000), highlighting its crucial role in enhancing students’ psychological health in the context of academic stress. The result presents in the Table 4.\n\nMediation analysis\n\nThe study assessed the mediating role of social support factor (SSF) and self–efficiency (SEF) on the relationship between academic stress (AS) and psychological well-being (PWB). The results revealed significant indirect effect of AS on PWB through SSF (β=0.0075,t=5.2447,p<0.001),supporting H1. Analyzing the mediating role of SEF, the study found insignificant mediating role of SEF on the linkage between AS and PWB (β=0.068,t=1.654,p=0.097), not supporting H2. Furthermore, the direct effect of AS on PWB in presence of the mediation was also found significant (β=0.133,t=3.524,p<0.001). Hence, SSF partially mediated the relationship between AS and PWB. Mediation analysis summary is presented in Table 5.\n\nEvaluation model fit\n\nThe model evaluation results indicate a good fit of the model to the data. The relative chi-square (2.537) is within the recommended threshold of less than 5, and all the fit indices, including the Goodness of Fit Index (0.948), Adjusted Goodness of Fit Index (0.931), Comparative Fit Index (0.962), Incremental Fit Index (0.963), Normed Fit Index (0.940), Tucker-Lewis Index (0.955), and the Root Mean Square Error of Approximation (0.048), meet or exceed their respective recommended thresholds. Additionally, the Standardized Root Mean Square Residual (0.0369) is within the recommended limit of less than 0.05,26 further supporting the good fit of the model (Table 7).\n\n\n5. Discussion\n\nThe study is set out to establish the relationship between Academic stress (AS), Student’s Psychological well-being, social (PWB), Social support (SS) and Self-efficiency. The study found a significant impact of academic stress on student psychological well-being among public and universities in Mogadishu - Somalia. The outcomes affirm this recommendation are steady with the discoveries of the past examinations where the positive relationship between AS and PWB outcomes was found.27–29 This relationship indicates that the pressures of academic demands, such as exams and assignments, can lead to negative psychological outcomes, including anxiety and decreased life satisfaction. The findings align with the Transactional Model of Stress and Coping, which suggests that stress occurs when individuals perceive demands exceeding their coping abilities. The unique socio-cultural and educational challenges in Somalia, such as limited resources and high expectations, may intensify the effects of academic stress, emphasizing the need for support systems and interventions to help students manage stress and improve their psychological well-being.\n\nThe study found insignificant impact of academic stress on social support factor, suggesting that academic stress does not significantly alter the level of social support students perceive or receive. This result may indicate that social support, whether from peers, family, or faculty, remains stable despite fluctuations in academic stress levels. Previous research has shown that while social support can buffer the effects of stress, the presence of stress does not necessarily reduce the availability or perception of social support.27–29\n\nThis stability might be due to cultural or social norms that encourage strong support networks, regardless of individual stress levels. Additionally, social support might be more influenced by factors such as personal relationships and community dynamics rather than academic pressures.\n\nThe study found that academic stress had an insignificant impact on self-efficacy among students in public and private universities in Mogadishu. This suggests that the students’ belief in their ability to manage and succeed in academic tasks was not significantly affected by the levels of academic stress they experienced. This finding is inconsistent with research indicating that self-efficacy is often a stable trait influenced more by long-term experiences and personal characteristics than by situational stress.30,31 Self-efficacy may be bolstered by intrinsic factors such as past successes, individual resilience, and consistent encouragement from mentors and peers, which help maintain students’ confidence in their abilities despite academic pressures.\n\nThe study found that social support significantly impacts psychological well-being (PWB) among students in public and private universities in Mogadishu. This means that students who receive higher levels of social support from peers, family, and faculty tend to have better psychological well-being, experiencing less anxiety and higher life satisfaction. This finding aligns with previous research which indicates that social support acts as a buffer against stress and promotes mental health by providing emotional comfort, practical assistance, and a sense of belonging.32,33,37,38 The presence of a strong support network can mitigate the adverse effects of stress and enhance overall well-being by improving coping mechanisms and providing resources for managing academic challenges.\n\nThe study found that self-efficacy significantly impacts psychological well-being (PWB) among students in public and private universities in Mogadishu. This indicates that students who have a strong belief in their ability to manage and succeed in academic tasks tend to have better psychological well-being, with lower levels of anxiety and higher life satisfaction. This finding is supported by previous research showing that self-efficacy enhances mental health by promoting resilience, reducing stress, and encouraging proactive coping strategies.37,39,40 High self-efficacy helps students to perceive challenges as manageable and to maintain a positive outlook, which contributes to better psychological well-being.\n\nFinally, the results of this research offer important empirical insight into the indirect effect on academic stress on psychological well-being through mediation of social support factor. The finding shows that social support partially mediation the relationship between academic stress and psychological well-being. The findings are consistent with the previous finding which have found the significant mediating role of social support,33,41 which suggests that social support can mitigate the harmful effects of stress by providing emotional comfort, practical help, and a sense of belonging, thus enhancing overall psychological well-being. On other hand, the study found that self-efficacy does not mediate the relationship between academic stress and psychological well-being (PWB) among students in Mogadishu’s universities. This means that while self-efficacy directly contributes to better psychological well-being, it does not significantly alter the impact of academic stress on well-being. This finding contrasts with some studies that suggest self-efficacy can buffer stress impacts,33 indicating that in this context, other factors may play a more significant role in mediating the relationship between academic stress and psychological well-being.\n\n\n6. Conclusion\n\nIn conclusion, the study reveals several key findings about the relationships between academic stress, psychological well-being (PWB), social support, and self-efficacy among students in Mogadishu’s universities. Academic stress significantly impacts students’ psychological well-being, highlighting the need for interventions to manage academic pressures. Social support plays a critical role in partially mediating this relationship, buffering some of the negative effects of academic stress on mental health. In contrast, self-efficacy, while positively contributing to psychological well-being, does not mediate the relationship between academic stress and PWB. These insights underscore the importance of enhancing social support networks and developing targeted strategies to improve student resilience and mental health in the face of academic challenges.\n\nUniversities should prioritize the development and enhancement of student support services, including counseling and mental health resources, to help students manage academic stress and improve psychological well-being. More broadly, the study contributes to the development of studies linking academic stress, social support, self -efficacy and psychological well-being and strengthens the relationship evidence in the literature that social support contributes to psychological well -being. Institutions should encourage the formation of strong social networks through peer mentoring, student organizations, and community-building activities, as social support is crucial in buffering the negative effects of academic stress. Although self-efficacy does not mediate the stress-well-being relationship, enhancing students’ confidence in their abilities through workshops, positive feedback, and opportunities for skill development can directly improve their psychological well-being. Additionally, the study adds knowledge to studies seeking to understand the factors that influence psychological well-being. Thus, the findings suggest that universities should develop and implement stress management programs that equip students with strategies to cope with academic demands, thus improving their psychological well-being. Institutions should promote social support systems through peer mentoring, counseling services, and community-building activities to buffer students against the negative effects of academic stress. Institutions should promote social support systems through peer mentoring, counseling services, and community-building activities to buffer students against the negative effects of academic stress. Educational policies should prioritize mental health by incorporating stress management and support systems into the academic environment, ensuring holistic student development. Finally, it’s important that educational policymakers should integrate mental health education and stress management strategies into the curriculum, ensuring students are equipped with the tools to handle academic pressures effectively.\n\nThe study’s limitations include its cross-sectional design, which limits causal inference, and the reliance on self-reported measures, which may introduce biases. Additionally, the findings are context-specific to Mogadishu, Somalia, and may not be generalizable to other settings. The research also focused narrowly on social support and self-efficacy as mediators, potentially overlooking other influential factors. Future studies should explore other potential mediators and moderators in the relationship between academic stress and psychological well-being, such as coping styles, resilience, and environmental factors, to develop a more comprehensive understanding and targeted interventions.\n\nPrior to data collection, ethical approval was received from Mogadishu University institutional review board (IRB) in Mogadishu, Somalia (Date:15 – 05 – 2024, protocol number: MUIRB/09/24/001). Informed consent was obtained from all students. The students were informed that the research would be conducted following the principle of confidentiality and that all information obtained would be kept confidential. We obtained informed consent from all participants, according to the IRB’s guidelines. Each of the 663 participants reviewed and signed the consent form before participating in the study. We confirm that all participants adhered to the signed consent form.", "appendix": "Data availability\n\nFigshare: Mediating role of Social Support and Self-efficiency on Academic stress and Student’s Psychological well-being among Public and Private Universities in Mogadishu -Somalia. https://doi.org/10.6084/m9.figshare.26820745 42\n\nThe project contains the following data:\n\n- Academic stress and Psychological well being.xlsx\n\n- Pschological Well being Mediating Role Updated.sav\n\nFigshare: Mediating role of Social Support and Self-efficiency on Academic stress and Student’s Psychological well-being among Public and Private Universities in Mogadishu-Somalia. https://doi.org/10.6084/m9.figshare.26820745 42\n\nThe project contains the following data:\n\n- Analyzing the results and calculating p-value using 5000 Bootstrap.docx\n\n- Measurement model.jpg\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\nBarbayannis G, Bandari M, Zheng X, et al.: Academic Stress and Mental Well-Being in College Students: Correlations, Affected Groups, and COVID-19. Front. Psychol. 2022; 13(May): 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamachandiran M, Dhanapal S: SOCIAL SCIENCES & HUMANITIES: A Quantitative Study of Generation Y and Z’s Perception. Pertanika J. Soc. Sci. Hum. 2018; 26(3): 2115–2128.\n\nFarooq K: ACADEMIC STRESS AMONG STUDENTS OF HIGHER EDUCATIONAL INSTITUTIONS IN KARACHI Sumera Ishrat Samina Rauf.2023.\n\nCórdova Olivera P, Gasser Gordillo P, Naranjo Mejía H, et al.: Academic stress as a predictor of mental health in university students. Cogent Educ. 2023; 10(2). Publisher Full Text\n\nNogueira MJCC: Positive and Negative Predictors of Mental Health in College Students. A cross-sectional predictive study.2023; 1–19.\n\nSlimmen S, Timmermans O, Mikolajczak-Degrauwe K, et al.: How stress-related factors affect mental wellbeing of university students A cross-sectional study to explore the associations between stressors, perceived stress, and mental wellbeing. PLoS One. 2022; 17(11 November): e0275925–e0275916. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChandan MKP: Academic Stress Among Higher Secondary School Students: an Overview. Int. J. Creat. Res. Thoughts. 2020; 8(10): 2320–2882.\n\nMayya SS, Martis M, Mayya A, et al.: Academic Stress among Pre-University Students of the Commerce Stream: A Study in Karnataka. Pertanika J. Soc. Sci. Humanit. 2022; 30(2): 605–621. Publisher Full Text\n\nDillard DM: The Transactional Theory of Stress and Coping: Predicting Posttraumatic Distress in Telecommunicators. Walden Univ.; 2019.\n\nBen-Zur H: Transactional Model of Stress and Coping. Encycl. Personal. Individ. Differ. 2019; 1–4. Publisher Full Text\n\nFahruni FE, Nurismawan AS, Salsabila NS: How Do School Counselors Advocate for Gifted and Intelligent Children in Junior High School?. Bisma J. Couns. 2022; 6(3): 329–334. Publisher Full Text\n\nShen R: The Effects of Psychosocial Factors on International Students’ Mental Health and Relevant Interventions. SHS Web Conf. 2023; 157: 01021. Publisher Full Text\n\nMohamed RM, Ali MAM: Promoting Students’ Mental Health through Design and Implementation of Multi-Activity Pods in Educational Institutions Using the WELL Building Standard. Designs. 2023; 7(1). Publisher Full Text\n\nScruggs R, Broglia E, Barkham M, et al.: The impact of psychological distress and university counselling on academic outcomes: Analysis of a routine practice-based dataset. Couns. Psychother. Res. 2023; 23(3): 781–789. Publisher Full Text\n\nMargaret K, Simon N, Sabina M: Sources of Occupational Stress and Coping Strategies among Teachers in Borstal Institutions in Kenya. Edelweiss Psychiatry Open Access. 2018; (April 2019): 18–21. Publisher Full Text\n\nKhafifah KA, Hasanah U, Zulfa V: Hubungan Antara Stres Akademik Dengan Academic Performance Pada Santri Madrasah Aliyah Pondok Pesantren Al Hamid. JKKP (Jurnal Kesejaht. Kel. dan Pendidikan). 2023; 10(01): 27–37. Publisher Full Text\n\nMukti SAS, Ansyah EH: The Relationship Between Parental Social Support and Academic Stress in University Students. Indones. J. Innov. Stud. 2023; 21: 1–11. Publisher Full Text\n\nGapunuan MCP: Self-Efficacy Towards Student Engagement and Academic Performance in Beauty Care. Int. J. Res. Publ. 2023; 124(1): 406–416. Publisher Full Text\n\nBabbie ER: The Logic of Sampling. The Practice of Social Research. 2004.\n\nH. Taherdoost and H. Group: Sampling Methods in Research Methodology; How to Choose a Sampling Sampling Methods in Research Methodology; How to Choose a Sampling Technique for. Int. J. Acad. Res. Manag. 2016. Publisher Full Text\n\nArip MASM, Kamaruzaman DN, Roslan A, et al.: Manual Student Stress Inventory (SSI) Edition 2019 Development, Validity And Reliability of Student Stress Inventory (SSI).2019; (December 2018): p. 3.\n\nAkhtar N, Francis LJ, Sailer AB, et al.: Introducing the Psychological Wellbeing Scale for Muslim Societies (PWS-MS): a study among young adults in Pakistan. Ment. Health Relig. Cult. 2023; 1–12. Publisher Full Text\n\nAbdul Aziz NA, Baharudin NS, Alias NA: Association between Stress and Social Support Perceived among Undergraduate Health Sciences Student. Malaysian J. Med. Sci. 2023; 30(3): 176–183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoferichter F, Kulakow S, Raufelder D: How teacher and classmate support relate to students’ stress and academic achievement. Front. Psychol. 2022; 13(November). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFarooq MS, Feroze N, Kai YT: International Online Journal of Primary Education. Int. Online J. Prim. Educ. 2017; 6(2): 30–38.\n\nHair J, Black W, Babin B, et al.: Multivariate Data Analysis: A Global Perspective. Multivariate Data Analysis: A Global Perspective. 2010.\n\nKusumawati I, Dinar Pratisti W, Prasetyaningrum J: The Relation of Academic Stress, Parental Social Support, Gratitude and Psychological Well-Being of Students in Pandemic COVID-19 Era. Proceeding ISETH (International Summit Sci. Technol. Humanit). 2022; pp. 364–372.\n\nHeizomi H, Allahverdipour H, Bazargan Hejazi S, et al.: International Journal of Depression and Anxiety Factors Associating Perceived Stress and Psychological Well-being among Iranian Female Adolescents. Int. J. Depress. Anxiety. 2018; 1(1): 3. Publisher Full Text\n\nRathakrishnan B, et al.: The interaction between academic stress and self-control in predicting psychological well-being. Environ. Soc. Psychol. 2023; 8(3): 1–16. Publisher Full Text\n\nVarghese RP, Norman TSJ, Thavaraj S: Perceived Stress and Self Efficacy Among College Students: A Global Review. SSRN Electron. J. 2015; 5(3): 15–24. Publisher Full Text\n\nAltermatt ER: Academic Support From Peers as a Predictor of Academic Self-Efficacy Among College Students. J. Coll. Student Retent. Res. Theory Pract. 2019; 21(1): 21–37. Publisher Full Text\n\nMarkley R: The Far East and the English Imagination, 1600-1730. Cambridge Univ. Press; 2006; vol. 41(4): p. 125. Publisher Full Text\n\nAw JX, Mohamed NF, Rahmatullah B: the Role of Perceived Social Support on Psychological Well-Being of University Students During the Covid-19 Pandemic. Asia Pacific J. Heal. Manag. 2023; 18(1). Publisher Full Text\n\nCalderón C, et al.: Multidimensional scale of perceived social support (MSPSS) in cancer patients: Psychometric properties and measurement invariance. Psicothema. 2021; 33(1): 131–138. PubMed Abstract \| Publisher Full Text\n\nScholz U, Doña BG, Sud S, et al.: Is general self-efficacy a universal construct? Psychometric findings from 25 countries. Eur. J. Psychol. Assess. 2002; 18(3): 242–251. Publisher Full Text\n\nFornell C, Larcker DF: Evaluating Structural Equation Models with Unobservable Variables and Measurement Error. J. Mark. Res. 1981; 18(1): 39. Publisher Full Text\n\nQi LY, Roslan S, Zaremohzzabieh Z: Perceived Social Support and Psychological Well-Being of International Students: The Mediating Effects of Resiliency and Spirituality. Asian J. Univ. Educ. 2021; 17(3): 220–234. Publisher Full Text\n\nSharifian N, Grühn D: The Differential Impact of Social Participation and Social Support on Psychological Well-Being: Evidence From the Wisconsin Longitudinal Study. Int. J. Aging Hum. Dev. 2019; 88(2): 107–126. PubMed Abstract \| Publisher Full Text\n\nRahmawati NR, Handarini DM, Triyono T: Relation of Emotional Intelligence, Self-esteem, Self-efficacy, and Psychological Well-Being Students of State Senior High School. J. Pendidik. Hum. 2017; 5(1): 40–46. Publisher Full Text\n\nMrs. Saif M : Impact of Self-Efficacy on Psychological Well-Being among Undergraduate Students. Al-NASR. 2024; 2(3): 99–120. Publisher Full Text\n\nFatima S, Sharif S, Khalid I: How does religiosity enhance psychological well-being? Roles of self-efficacy and perceived social support. Psychol. Relig. Spiritual. 2018; 10(2): 119–127. Publisher Full Text\n\nMohamed AJAD: Mediating Role of Social Support and Self -efficiency on Academic Stress and Students Psychological Well-being Among Public and Private Universitieis in Mogadishu - Somalia.2024. Publisher Full Text" }	[ { "id": "342011", "date": "17 Dec 2024", "name": "Somaya Shokry Mohammad Mahmoud", "expertise": [ "Reviewer Expertise Educational Psycholgy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 mediating analysis showed that social support partially mediated the relationship between academic stress and psychological well-being (Indirect effect = 0.070, CI [-0.036, 0.197], p = 0.000), Social Support: The indirect effect (0.070) is partially mediated, but the confidence interval (CI [-0.036, 0.197]) includes zero. This creates a discrepancy because the p-value (p = 0.000) suggests significance. Conclusions The findings suggest a significant positive impact of academic stress on psychological well-being revise this statement. I think there is a significant negative impact of academic stress on psychological well-being \"Why is the gender factor included in Figure 1?\" A study found a strong correlation (r=0.582) between academic stress and psychological well-being among university students, indicating that higher stress levels correspond to lower well-being.17 Is the correlation positive or negative? The study design is appropriate for the research objectives, and the work is technically sound overall. The study provides many details that enable replication, particularly regarding the sample, constructs, and statistical analysis. To improve replicability, the following should be addressed:\nSpecify the software and analytical procedures used.\nOverall, the statistical analysis and its interpretation are appropriate and align with standard practices. Key areas for improvement include addressing the confidence interval discrepancy for social support mediation, acknowledging the low AVE values, and providing more details on effect sizes. These adjustments would further strengthen the robustness and clarity of the statistical conclusions. The study makes a commendable effort by sharing its source data on Figshare, ensuring transparency and partial reproducibility. However, to achieve full reproducibility, additional documentation and sharing of analysis scripts are needed. This would allow other researchers to replicate the study comprehensively and with minimal barriers. he conclusions are mostly supported by the results, with some exceptions:\nThe confidence interval issue for social support mediation should be addressed to confirm this conclusion. The practical significance of the relationships should be better reflected. The low AVE values should be discussed to acknowledge potential measurement limitations.\nAddressing these points would make the conclusions more robust and aligned with the study's 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? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "12998", "date": "26 Dec 2024", "name": "Abdulkadir Jeilani", "role": "Author Response", "response": "We sincerely appreciate the time and effort the reviewer has dedicated to providing insightful and constructive feedback on our manuscript. Your comments have significantly enhanced the quality and clarity of our work. We are particularly grateful for your detailed observations, including the suggestions to address the confidence interval discrepancy, improve the discussion on AVE values, and provide additional details to strengthen replicability. These recommendations have been invaluable in refining our analysis and ensuring the robustness of our conclusions. Thank you for recognizing our study's strengths and highlighting areas for improvement. Your expertise and thoughtful input have guided us in making meaningful revisions, and we are confident that the manuscript is much stronger due to your valuable contributions. Here are the responses for each comment Social Support: Confidence Interval Discrepancy and Indirect Effect Reviewer Comment: The indirect effect (0.070) is partially mediated, but the confidence interval (CI [-0.036, 0.197]) includes zero. This creates a discrepancy because the p-value (p = 0.000) suggests significance. Response: We appreciate the reviewer highlighting this discrepancy. The p-value indicates statistical significance, but the confidence interval suggests potential variability in the indirect effect. To address this: We resample bootstrap with 5,000 now the inconsistency is solved Conclusions: Nature of the Impact of Academic Stress Reviewer Comment: The findings suggest a significant positive impact of academic stress on psychological well-being. Revise this statement to indicate there is a significant negative impact. Response: Thank you for pointing this out. The relationship between academic stress and psychological well-being is indeed negative, as supported by the correlation analysis and theoretical framework. We revised the conclusion to: \"The findings suggest that academic stress has a significant negative impact on psychological well-being, partially mediated by social support.\" Gender Factor in Figure 1 Reviewer Comment: Why is the gender factor included in Figure 1? Response: Thank you, we excluded Gender from the research model. Correlation Between Academic Stress and Psychological Well-being Reviewer Comment: A study found a strong correlation (r = 0.582) between academic stress and psychological well-being. Is the correlation positive or negative? Response: The correlation is negative, as higher academic stress corresponds to lower psychological well-being. This is explicitly stated in the discussion section to avoid any ambiguity. Replicability: Software and Analytical Procedures Reviewer Comment: Specify the software and analytical procedures used to improve replicability. Response: We added the following details: The software used for analysis was SPSS (version 24) and AMOS (version 22). Analytical procedures such as path analysis, bootstrapping (5,000 samples), and structural equation modeling were applied to test direct and indirect effects. Practical Significance of Relationships Reviewer Comment: The practical significance of the relationships should be better reflected. Response: The partial mediation by social support indicates the importance of strengthening support systems to mitigate the negative effects of academic stress on well-being. Low AVE Values Reviewer Comment: The low AVE values should be discussed to acknowledge potential measurement limitations. Response: We acknowledge the low AVE values for some constructs (e.g., academic stress: 0.399). Noted as a limitation, indicating potential issues with convergent validity. We recommended revising measurement items in future studies to better capture the constructs. Data Sharing and Reproducibility Reviewer Comment: Additional documentation and sharing of analysis scripts are needed to achieve full reproducibility. Response: We shared analysis scripts and detailed documentation alongside the dataset on Figshare. This will ensure that researchers can replicate the analysis comprehensively. Practical Recommendations Reviewer Comment: Address practical recommendations based on the findings. Response: We emphasized the importance of social support systems and stress management interventions in educational institutions. These could include peer mentoring programs, counseling services, and workshops on effective coping mechanisms." } ] }, { "id": "353385", "date": "10 Jan 2025", "name": "Nguyen Tan Dat", "expertise": [ "Reviewer Expertise Clinical psychology" ], "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\nOverall, the paper examines the impact of academic stress on psychological well-being among university students in Mogadishu, Somalia, exploring the mediating roles of social support and self-efficacy. The results indicate that social support partially mediates the relationship between academic stress and well-being, while self-efficacy does not. The study's use of robust methodology, including stratified sampling and structural equation modeling, and its practical implications for improving student mental health through social support, are key strengths. However, I believe that a significant rewrite and thorough English editing are necessary to enhance the quality of the article for submission Introduction\nCould the authors please provide the citation for this sentence in the second paragraph of the Introduction Introduction, paragraph 2: “Also, other factors contributing to academic stress include self-inflicted stress, parental expectations, academic queries, lack of time for revision, low parental education levels, and poor exam grades.” I suggest the authors use only 'self-efficacy' for consistency throughout the paper. In my opinion, 'self-efficacy' is the more widely recognized and commonly used term. It seems that the second citation is wrong: The paper name is supposed to be “Academic Stress Among University Students: A Quantitative Study of Generation Y and Z’s Perception”. “SOCIAL SCIENCES & HUMANITIES:” is part of the journal name. I think it would be more beneficial to shorten the 2nd, 3rd, 4th,, 5th, 6th paragraph in the introduction because some ideas are repeated. For example this paragraph: “Academic stress arises from the inability to cope with academic related tasks, leading to negative impacts such as smoking behavior, mental health issues, poor sleep quality, depression, insomnia, substance addiction, self-harm, and suicidal ideation. Also, other factors contributing to academic stress include self-inflicted stress, parental expectations, academic queries, lack of time for revision, low parental education levels, and poor exam grades.” And this paragraph “Academic stress is the product of a combination of academic-related demands that exceed the adaptive resources available to an individual,2 Researchers agree that students face common academic stressors, such as family-pressures, scholarship demands, financial burdens, competition in class, examination, time-management and course-related stress.2 According to Ref. 3 the main cause of academic stress are academic results, admissions, students transfer, exams, load of extra classes, social comparison, exams stress, expectations teachers and parents.” Both paragraphs talk about the cause of academic stress I also feel that this sentence: “Academic stress arises from the inability to cope with academic related tasks, leading to negative impacts such as smoking behavior, mental health issues, poor sleep quality, depression, insomnia, substance addiction, self-harm, and suicidal ideation.” and this sentence: “The most common psychological consequences associated with academic stress include depression, anxiety, substance abuse, and suicide ideation.7” are similar. I have taken a look at the source of citation for this sentence ““Additionally, coping strategies like Academic Psychological capital and self-efficacy play a crucial role in mitigating the effects of academic stress on psychological well-being.” and could not find any information about how self-efficacy and academic psychological capital mitigates the effect of academic stress on psychological well-being. Can the authors highlight it? This is the paper that I found for your citation. Ref (1) I don’t understand what this sentence want to say: In the context of academic stress, this theory suggests that the students have the ability to cope with high self-efficacy are more likely to effectively cope with stressors and maintain their psychological well-being. Citation number 9 format is different than others. The authors lack citation for Social Cognitive Theory. Why is coping mechanisms capitalized, and why theories is plural in this sentence “In Coping Mechanisms, the theories emphasize the importance of coping strategies in managing stress.” ? Do you mean to talk about “The Transactional Model of Stress and Coping”and “Social Cognitive Theory”? Additionally, when the authors wrote these two paragraphs under Social Cognitive Theory, it seems like these paragraphs were talking about the theory. But I think these paragraphs are talking about common themes of both “The Transactional Model of Stress and Coping”and “Social Cognitive Theory” theories:\n\n“In the context of the impact of academic stress on students’ psychological well-being, the Transactional Theory of Stress and Coping and the Social Cognitive Theory focus on the following. Both theories highlight the importance of cognitive appraisal in how individuals perceive and respond to stress. Students’ cognitive evaluations of academic stressors, their perceived ability to cope (self-efficacy), and the availability of social support influence their stress experiences and psychological well-being.10” “ In Coping Mechanisms, the theories emphasize the importance of coping strategies in managing stress. Student performance related to cognitive appraisals and self-efficacy beliefs play an important role in mediating the relationship between academic stress and psychological well-being. Effective strategies, supported by social resources, help students manage academic stress and maintain well-being.9,10,15” So I suggest the authors add another title for these 2 paragraphs.\nWhy also is the subject in this sentence? “Also has emerged as a significant mental health that affecting various groups of students.” Don’t break this sentence into another paragraph: A study found a strong correlation (r=0.582) between academic stress and psychological well-being among university students, indicating that higher stress levels correspond to lower well-being. Also, I feel these paragraphs titled “Academic Stress and Psychological Well-being” is a repeat of the start of the Introduction. I suggest the author omitted or combined these paragraph together with those paragraphs at the start of the Introduction. I noticed that several common terms are inconsistently capitalized (e.g., 'Academic Psychological capital,' 'Health Sciences'). In academic writing, only proper nouns, titles, or the first words of sentences should be capitalized. I recommend reviewing the manuscript for unnecessary capitalization and ensuring it follows standard conventions for consistency and clarity. I feel the Introduction is too long, it would be beneficial to be shorter\nMethods\n\nI don't think it is necessary to go into such depth about the targeted universities (e.g., the number of students, the included faculties, etc.). There are three things wrong with this part of the sentence “Self-Efficiency Scale (SSS) adapted by Ref. 35 and consist of 10 items.”: First, it is self-efficacy not self-efficiency. Second, if the scale is called Self-efficacy scale, is should be abbreviated as SES not SSS. Third, The scale in Reference 35 is called “General Self-Efficacy Scale”, not Self-efficacy Scale The authors did not mention which software used for data analysis.\nResults\nFor very small p-values, avoid reporting them as 0.000; instead, use p < 0.001. Please check carefully for grammar issues(The result presents in the Table 4->The result is presented in Table 4., partially mediation-> partial mediation) In Table 4, the meaning of the symbol 'H1: ASàPWB' is unclear. I noticed that the author sometimes reports results with four decimal places (e.g., 0.0075) and other times with three decimal places (e.g., 3.524). To ensure consistency and clarity, I recommend using three decimal places consistently throughout the paper. Please ensure that each abbreviation is defined or explained in every table for clarity. Please cite Figure 2 in the Results, I also suggest changing Figure 2 name to reflect the mediation model.\nDiscussion 25. I noticed that the abbreviation 'PWB' for 'psychological well-being' is introduced suddenly in the Discussion section, despite the full term being used throughout the paper. For consistency and clarity, it would be helpful to either introduce the abbreviation earlier in the text or continue using the full term throughout the manuscript: The study found that social support significantly impacts psychological well-being (PWB) Conclusion 26. Please put the conclusion paragraph at the end instead of before 6.1 Implications and 6.2 Limitations. 27. I believe the order of the sections could be improved for better clarity and logical flow. In the current structure, '6.1 Implications' and '6.2 Limitations and Further Research' are listed as sub-sections under '6. Conclusion,' which may not be ideal. Typically, implications and limitations are treated as separate sections rather than sub-sections of the conclusion. I suggest considering reorganizing the sections, perhaps by placing 'Implications' and 'Limitations and Further Research' as standalone sections after the conclusion for a clearer structure. 28. I noticed that the authors have cited their own preprint (citation 42). While self-citation is not inherently unethical, it may be worth considering if this citation is necessary and appropriate, especially in light of the potential for bias. It might be helpful to ensure that all citations are relevant and contribute to the academic discourse in a transparent manner. 29. The paper investigates both public and private universities, but the results section does not address why data was collected from both types of institutions or highlight any notable differences between them. Additionally, there seems to be no analysis exploring potential distinctions between public and private universities, despite the title emphasizing the inclusion of both. It would strengthen the paper to either explore these differences or provide a rationale for including both types of universities in the study.. 30. the keyword 'Public and Private Universities' might be too broad. It could be helpful to consider a more specific keyword like \"university students\"\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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1108
https://f1000research.com/articles/13-1107/v1	30 Sep 24	{ "type": "Review", "title": "State-of-the-art optimization methods for short-term mine planning", "authors": [ "Moise Kambala Malundamene", "Nasib Al Habib", "Saâd Soulaimani", "Khalil Abdessamad", "Hooman Askari-Nasab", "Nasib Al Habib", "Saâd Soulaimani", "Khalil Abdessamad", "Hooman Askari-Nasab" ], "abstract": "Maintaining short-term planning aligned with the ultimate long-term plan is challenging. This requires many details to be modelled on a daily or weekly basis to reach this target. Short-term planning is more challenging than medium- and long-term planning because it deals with uncertainties, which increases the gap between medium- and long-term plans. Short-term mine planning teams are expected to identify and manage potential risks to mitigate them, and eventually achieve the long-term objective of maximizing the Net Present Value (NPV). Very few studies have identified the problems that exist in short-term mine planning and provided technical solutions to overcome them for open-pit mines. One of the complexities associated with short-term planning is the creation of polygons or mining cuts by clustering before optimizing and scheduling the plan to reduce the computational expense of mine planning models. The primary objective of this study is to review the latest papers describing short-term mine planning challenges and technical solutions proposed to optimize mine planning for open-pit mines.", "keywords": [ "Open pit mines", "Mining planning optimization", "Short-term mine planning", "operational planning" ], "content": "1. Introduction\n\nOne of the aims of short-term production scheduling is to generate a plan that meets the production and grade targets according to the budget of the long-term mine plan (Chanda and Wilke 1992). Extensive modelling of daily or weekly activities is required to achieve the production target and grade requirements. These targets comply with equipment utilization, processing capacities, recovery, and processing requirements managed in short-term planning (Blom et al. 2019). Short-term mine planning is more challenging because it mostly deals with many uncertainties on a daily basis, such as geological uncertainties (Tabesh and Askari-Nasab 2019), operational and dispatching uncertainties (Upadhyay et al. 2015; Upadhyay and Nasab 2017; Upadhyay and Askari-Nasab 2018; Mohtasham et al. 2021; Nelis and Morales 2022) and economic uncertainties (Osanloo and Rahmanpour 2017).\n\nThe gap between medium- and long-term planning in terms of achieving the production target may reach more than 50%, which can be a costly reconciliation in the long term (Kahraman and Dessureault 2011). Thus, short-term mine planners with management teams are requested to identify and manage risks to mitigate them and adhere able to stick to the Life-of-Mine (LOM) plan.\n\nWhile there are quite a few literature reviews on long-term planning (Osanloo et al. 2008; Newman et al. 2010; Kozan and Liu 2011; Lamghari 2017; Blom et al. 2019; Fathollahzadeh et al. 2021), very few have been carried out for short-term planning to the best of our knowledge (Blom et al. 2019; Habib et al. 2023). These articles focused mostly on short-term planning optimization without developing the optimization aspect of mining polygons, a basic element for short-term mine planning (Nelis and Morales 2022). Later, Fathollahzadeh et al. (2021) and Habib et al. (2023) presented main methodologies, such as deterministic, heuristic, metaheuristic, and stochastic methods. used for short-term planning optimization. Table 1 summarizes the main review papers on mining planning (Fathollahzadeh et al. 2021).\n\nGood mining planning is the basis for the best financial results for a mining company. Short-term mine planning is set up to align with the company strategy. One of the main differences between short-term mine planning and long- and medium-term mine planning is time discretization. Short-term planning should be performed with a granularity of less than one year. This granularity can be extended for up to two years (Blom et al. 2019). Short-term mine planning is required to achieve the goals set by a long-term plan by designing push-backs. Generally, the objective is to generate the highest cash flow value and Net Present Value (NPV) over the LOM plan (Juarez et al. 2014; King 2014; Otto and Musingwini 2020) while minimizing costs and respecting production targets within the LOM plan (Jewbali and Dimitrakopoulos 2018; Noriega and Pourrahimian 2022). This involves incorporating more sophisticated mathematical analysis and advanced geostatistics techniques, performed by a specific and adequate softwares (for example: Datamine RM, Datamine UG, Snowden and NPV), However, different models and algorithms, are applied to enhance performance and optimize short-term operations, ultimately contributing to improved production targets, cost reduction, and increased efficiency. Short-term mine planning deals with the equipment and resources allocated on a monthly, weekly, daily, or shift-by-shift basis under the control of the LOM (Noriega and Pourrahimian 2022). Thus, the success of truck fleet and shovel allocation to mining face areas depends strongly on the best dispatching strategy for fleet management. Models and algorithms for the fleet management systems have been reviewed by Moradi Afrapoli and Askari-Nasab (2019).\n\nFew papers have described short-term planning with granularity in days, weeks, and months. Table 2 specifies the main difference between short- and long-term mining planning, taking into account the discretization time, block model characteristics, design, mining precedence, cost, and equipment. These plans take into account the objective functions and constraints to be considered and the level of details for mine operations to be considered and modelled. This includes constraints specific to each mine, their capacities, block sequencing, blending, plant requirements, and pit slopes (Caccetta and Hill 2003; Askari-Nasab et al. 2010; Marques et al. 2013; Badiozamani and Askari-Nasab 2014; Blom et al. 2019).\n\nFigure 1 illustrates the relationship between long-term and short-term mine plans based on the scope area limit of this review article.\n\nIn the last decade, some studies have discussed short-term mine planning problems and technical solutions on a monthly basis (Askari-Nasab et al. 2010; Tabesh and Askari-Nasab 2013; Blom et al. 2019; Salman et al. 2021; Menezes and dos Santos Corrêa 2022).\n\nHowever, short-term mine planning optimization for open-pit mines remains underexplored.\n\nShort-term planning models must be solved quickly because of the dynamic nature of mining operations. Mining polygon optimization reduces the computational expenses of mine planning models by reducing the number of variables involved. Therefore, more research is required to develop more efficient mathematical models. The primary goal of this study is to review existing publications on short-term mine planning and mining polygon optimization methods to galvanize researchers to work on the quicker solvability of short-term mine planning models.\n\nThe first step focuses on the techniques used to create and optimize mining polygons, which is an important step in scheduling. In the second step, we will focus deeply to review different approaches for short-term mine planning optimization. Before concluding and stating the next orientation of this work, we will discuss all approaches reviewed on the recent improvements for overcoming uncertainties in short-term mining planning.\n\n\n2. Scope of the research\n\nThe aim of this research is to understand the current state-of-the-art optimization methods for short-term mine planning. The objective of this review article is to focus on the following aspects of short-term planning:\n\n• Dig-limit optimization and Mining polygons,\n\n• Short-term production scheduling optimization,\n\nThe first point will help to identify the main methods for creating mining polygons for short-term mining planning. The second point is related to short-term scheduling with suitable mining cuts for short-term planning optimization.\n\nThis research will use the available scientific database (Scopus journals, Sciences Direct, Taylor and Francis, Google Scholar) to review the retrieved papers until June 2023.\n\nUnderground operations, Geotechnical and Processing aspects are also beyond the scope of long-term planning.\n\n\n3. Literature review of methods to perform mining polygons\n\nMining polygon creation is the most critical task to be performed after optimization and design. This heavy task is the result of a grade control program, and is often performed manually by mining planners (Nelis and Morales 2022). More research has been carried out since the last decade for automatically generating mining cuts with algorithms; however, unfortunately, none of them have been applied at the industrial scale, and all these studies have been conducted at the academic level.\n\nIn the literature, we can identify two main ways to perform mining polygons for short-term mine planning, as follows:\n\n• Dig-limit optimization is used to define the ore-waste limit (Norrena and Deutsch 2001; Richmond and Beasley 2004; Ruiseco et al. 2016; Sari and Kumral 2018; Nelis and Morales 2022);\n\n• Clustering techniques with agglomeration of similar bloc properties (Askari-Nasab et al. 2010; Tabesh and Askari-Nasab 2013; Nelis and Morales 2022);\n\nThe dig-limit optimization approach consists of defining the best possible limits between ore waste on a bench basis to ensure the profitability of mining operations based on the definition (Sari and Kumral 2018). The definition of polygons depends on the level of bloc model preparation (grade control program), which affects the grade uncertainty (P et al. 2002; Neufeld et al. 2003; Richmond and Beasley 2004; Vasylchuk and Deutsch 2019).\n\nGenerally, in mining industry practice, the dig-limit is delimited manually by a geologist after obtaining the grade control results before blasting ore. After delimitation of the ore according to the cut-off grade, the geologist and mining teams can decide the destination of the material to be blasted: ore to the plant for high grade (HG), ore to the stockpile for the low-grade (LG), and waste to the waste dump.\n\nSeveral techniques have been used to perform dig-limits and ore polygons (Table 3). Sari and Kumral (2018) used Mixed Integer Linear Programming Richmond (2007), used local search algorithms Richmond and Beasley (2004), used a heuristic approach with a floating cone algorithm to find an optimal solution for the grade control problem. To determine the optimal final destination for materials (ore or waste), (Vasylchuk and Deutsch 2019) also used a simple heuristic approach for mineable dig-limit optimization considering the excavation constraint while maximizing profit. Heuristic algorithms are known to solve problems faster and more efficiently, while sacrificing optimality and accuracy.\n\nRuiseco et al. (2016) used genetic algorithms to automatically generate a dig-limit considering the selectivity of the fleet for the Selective Mining Unit (SMU) while maximizing profitability. In this approach, the dig-limit is considered as a chromosome and each SMU is considered as a gene. The first population is generated by a random set of feasible dig-limits that are combined with others to reach the optimized dig-limit. The genetic algorithm for dig-limits is better than manual methods; this algorithm is a near-optimal solution Sari and Kumral (2018).\n\nSimulated annealing was applied by Isaaks et al. (2014) using the minimum expected loss method to find the optimal dig-limits constrained by a minimum width. Neufeld et al. (2003) used a semi-automatic algorithm for the dig-limit with the initial polygons by the user. Norrena and Deutsch (2001) and P et al. (2002) proposed an algorithm that optimizes dig-limit boundaries with maximum profit, taking into consideration the equipment’s limitations (digability).\n\nThe Heuristic approach was used by Vasylchuk and Deutsch (2019), who proposed a 2-D optimization dig-limit with multiple locations and destinations by maximizing profits. Contrary to Norrena and Deutsch (2001) and P et al. (2002), this algorithm uses a rectangular form of and for the dig limit, and there are no smoothing operations after their generation.\n\nClustering algorithms attempt to identify groups or clusters of elements with the same properties in datasets. In short-term planning, clustering is used to aggregate blocks with the same properties to generate mining cuts. A mining cut is a SMU that generates a practical mining schedule (Eivazy and Askari-Nasab 2012).\n\nTabesh and Askari-Nasab (2013) described clustering as the process of combining related things in a manner that maximizes intra-cluster similarity and inter-cluster dissimilarity (Figure 2).\n\nClustering algorithms for block aggregation have been developed in the literature, principally by Askari-Nasab et al. (2010); Tabesh and Askari-Nasab (2011); Tabesh and Askari-Nasab (2013); and Badiozamani and Askari-Nasab (2014) to deal with uncertainties in short-term planning and to create mining polygons that can be used as planning units in the next planning stages (Tabesh and Askari-Nasab 2019). Similar bloc units are grouped into a similarity index with the control of the shape and size of the polygons.\n\nTwo clustering models can be used: hierarchical clustering, partitional clustering, and k-means clustering. K-Means consists of choosing the number K of clusters before selecting at random K points and the centroids from the datasets. Each data point was then assigned to the nearest point to create K clusters around the centroid. This process consists of computing and placing the new centroid of each cluster. Each data point was assigned to the new nearest centroid if the outcome was unsatisfactory. If any reassignment occurred, we had to compute again to obtain a good result. Compared to hierarchical clustering, the K-means clustering method is reported to be faster but less accurate (Feng et al. 2010).\n\nHierarchical clustering is categorized in two types: agglomerative and divisive.\n\nAgglomerative is a bottom-up approach useful for mining planning that uses the similarity of an object to merge to form one object. First, each data point is made into a single-point cluster to form N clusters. The two closest data points are merged to form one cluster using Euclidean distance. The number of similar clusters will be reduced from N to N1 clusters. The algorithm will continue to have at the end one huge cluster grouping similar objects.\n\nDivisive algorithms are the reverse of the agglomerative algorithms. This divides the units of a cluster into two smaller groups. Consequently, the divisive algorithms stop when the number of clusters is equal to the number of objects. The common concepts between the two groups are the definition of similarity measures and ways to update the similarity values when new clusters are defined (Tabesh and Askari-Nasab 2013).\n\nSalman et al. (2021) used the K-means clustering algorithm with a heuristic approach to obtain mineable shapes using the Newman and Marvin datasets related to the copper deposit (Newman et al. 2010). This algorithm is applicable on a bench-by-bench basis and for metallic deposits.\n\nMaterial destination homogeneity and mining direction constraints were applied to obtain minable cluster shapes. The objective was to reduce the costs of optimizing short-term mine planning. In contrast to the hierarchical clustering of Tabesh and Askari-Nasab (2019), this algorithm does not consider multiple elements with grade uncertainty.\n\nTable 3 presents the results of different techniques for mining polygons using and completing the table of Sari and Kumral (2018).\n\n\n4. Review of Short-Term mine Planning Optimization methods for open pits Mine\n\nAccording to published research, the optimization of short-term mine planning is based on the objective functions, constraints, and level of modelling of the specifics of mining operations. The objective is to minimize the operating costs, minimize the deviation present in the quantity and quality of the produced ore from the LOM planning (Jewbali and Dimitrakopoulos 2018), and maximize the utilization of available equipment (Matamoros and Dimitrakopoulos 2016; Osanloo and Rahmanpour 2017; Upadhyay and Nasab 2017).\n\nMathematical programming algorithms (linear, nonlinear, and mixed integer programming), metaheuristics, stochastic simulations, and simulation annealing approaches have been applied for short-term mining planning optimization.\n\nFigure 3 presents the main approaches used for short-term planning optimization.\n\nMixed Integer programming (MIP) is a mathematical optimization in which the objective function and constraints are linear or non-linear, and variables are integer, discrete, and non-discrete in some cases.\n\nThe MIP model for mine planning was developed by Gershon (1982) and Gershon (1983) to maximize NPV with blending and processing constraints. This optimization model can also minimize cost, maximize production, and maximize NPV. In contrary to the stochastic optimization, Eivazy and Askari-Nasab (2012) mentioned this method doesn’t capture the cost uncertainty related to the change of input data (Geological Bloc model, cost, prices, recoveries and mining constraints).\n\nThe advantage of MIP in short-term planning is the limitation of the size problem to be solved, which requires close attention to a number of algorithmic parameters and solutions (Smith 1998), because fewer blocks are considered in problems than in long-term planning. Only the blocks scheduled to be extracted within the specified time horizon may be considered in the MIP model of the short-term planning problem (L’Heureux et al. 2013).\n\nDepending on the mining operations to be modelled and the required level of detail for the planning, MIP programming has been widely used to perform short-term planning in the last decade (L’Heureux et al. 2013; Upadhyay and Nasab 2017; Upadhyay and Askari-Nasab 2018; Blom et al. 2019) MIP methods need the necessary decision variables and indices at time t to represent each mining operation (drilling and blasting, loading, hauling, stockpiling, etc.) to be modelled and included in the schedule for each block or block set of the geological model.\n\nEivazy and Askari-Nasab (2012) developed an MIP model to minimize mining, hauling, stockpiling, rehandling, processing, and waste rehabilitation costs for short-term mine planning of an iron mine on a monthly basis to track long-term mining planning. He used a branch-and-cut algorithm using the TOMLAB/CPLEX optimizer to solve this problem by considering some constraints (precedence, mining and processing capacities, grade processing requirements) and multiple destinations and mining directions.\n\nL’Heureux et al. (2013) used MIP in short-term mine planning to address the issue of shovel movement and production capacity of equipment on a daily to monthly basis. They used the CPLEX optimization method. The objective is to minimize the cost of mining operations such as drilling, blasting, and extraction, respecting the precedence of these activities to constrain shovel movements. Shovels were assigned to a face (block or set of blocs) for the time horizon. Variable decisions were used for each period for shovel-to-face assignments, face-to-face movement of shovels, and drilling, blasting, and extraction decisions.\n\nKozan and Liu (2016) and Kozan and Liu (2018) proposed a multi-stage mine production scheduling (MPS) to optimize multi-resource multi-stage timetables at the operational level to determine how and when the equipment will be allocated to the selected blocks (or set of blocks) to perform mining operations (drilling, blasting, and extraction) over a short period of time under equipment capacity constraints for iron mines on a weekly basis. Their MIP model was solved by CPLEX optimization to minimize the mining operation cost (minimizing all of the equipment’s idle times at each stage). and maximize mining productivity and utilization of mining equipment through multiple processing stages.\n\nUpadhyay and Askari-Nasab (2018) proposed a Mixed Integer Linear Goal Programming (MILGP) model solved by CPLEX, which provides shovel allocation decisions based on available faces to generate short-term production schedules capturing operational uncertainty. The integer variable represents the number of truck trips between the faces and destination. The objective is to maximize production, optimize ore tonnage received at processing plants, minimize deviations in grade blending requirements from various ore destinations, and minimize shovel movement. Later, (Upadhyay et al. 2021) improved their model to be more practical by allocating shovels continuously on mining cuts.\n\nSari and Kumral (2018) used mixed-integer linear programming (MILP) to solve the dig-limits between ore and waste problems for short-term open-pit mine operations that are compatible with the maneuvering capability of the excavator and minimize dilution/loss, as opposed to free selection of ore and waste SMUs based on the cut-off grade. The objective is to maximize profit with block aggregation of ore or waste.\n\nIn five-week time horizons, Nelis and Morales (2022) used MIP optimization to define mineable mining cuts and mining sequences for a copper mine. The objective is to perform mining cuts and dig-limits by considering the cutoff grade, mining precedence (representative of SMU), and defining the destination of materials in each bench to produce a better evaluation of real NPV in the long term. The mining polygons complied with operational constraints such as the size of the loading equipment.\n\nStochastic optimization has recently been developed for short-term planning (Matamoros and Dimitrakopoulos 2016; Jewbali and Dimitrakopoulos 2018). It has been relatively well developed for long-term planning over the last decade and is one of the best methods for mine planning optimization. This integrates the parameter uncertainties used in the plan. In contrast to deterministic programming, which applies a constant parameter, stochastic programming uses a probabilistic approach that uses a probability distribution of each parameter to be applied to each set of possible realizations.\n\nMining parameters (grades, operating costs, commodity prices, recoveries) and the operational constraints estimated on the data at the time of planning are considered risky assets because of their fluctuation during the execution of this plan (Osanloo and Rahmanpour 2017).\n\nThe goal of stochastic programming for short-term mine planning is to minimize this risk or maximize the predicted objective value of the decision variables. Two decision variable stages can be defined according (Blom et al. 2019), the first-stage decision variables define the plan to be executed, and the variables for the second stage are determined by each potential scenario and indicate the changes that would need to be made to the plan if the scenario came to pass.\n\nLI and KNIGHTS (2009) have advised the application of real option pricing theory from financial uncertainty and risk as stochastic optimization for medium- and short-term planning, taking into account fuel price fluctuations. To minimize operating costs and overcome this variation, the authors proved a significant economic benefit by incorporating stochastic analysis in truck dispatching. The objective is to ensure that the trucks dump waste to the closest waste dump during the period of high fuel price to reduce the number of trucks used. In periods of low fuel prices, waste is hauled directly to the under-filled dumps with the target to balance the storage volume across the set of available dumps.\n\nAs uncertainties cause deviation from the long-term plan, Matamoros and Dimitrakopoulos (2016) presented stochastic integer programming for a short-term mining plan for the iron open-pit mine case. The first stage is to minimize mining costs (loading, hauling, and availability of faces and equipment) and maximize fleet utilization. The second stage is to minimize the cost over the range of recourse costs associated with deviations from the target plan in terms of geology (ore tons, grade, and deleterious elements) and fleet (mechanical availability and hauling time) uncertainties. The authors demonstrated that the solution of this stochastic formulation is better than a deterministic plan with a lower cost because it takes into account the fluctuations of the ore quality and fleet parameters. This model was improved by Quigley and Dimitrakopoulos (2020) by generating a short-term plan that minimizes the shovel movement and production deviation (ton and grade sent to the plant allocated). This model has been applied to copper mines.\n\nContrary to the deterministic approach of mining planning, which consists of scheduling production first and then allocating fleets, Both and Dimitrakopoulos (2020), have developed a new model for stochastic optimization by using a metaheuristic solution to solve the problem that simultaneously optimizes the short-term extraction sequence and fleet management. The model considers geological, equipment performance, and truck cycle–time uncertainties.\n\nCombining Fuzzy linear programming (non-linear programming) and optimization of risky assets Osanloo and Rahmanpour (2017) has applied portfolio optimization to short-term planning to minimize mining costs and risky assets, and to maximize the expected return of the portfolio by investing a particular amount of money. For authors, the uncertainties come from the capacity of mining faces to comply with the plant requirements (tonnage and grade) after material blending (portfolio) of different faces, taking into account their geological characteristics (return). In relation to the limestone mine, the extraction capacity of each location was defined, and each mining face was considered as the extent of investment for each asset. All parameters are bounded numbers and are fuzzified (equipment capacities, grades, recoveries, etc.).\n\nPaduraru and Dimitrakopoulos (2018) proposed state-dependent policies to help mine complexes respond to new information (grade control results) for adapting short-term mining plans for material-feeding plants. The authors applied this model to gold and copper mines with six possible destinations. The objective is to assist and make the best decision to reassign the update blocks mined estimate to the new destination, to improve revenue, and to minimize the processing cost via stockpiling management.\n\nThe last work with stochastic planning was carried out by Jewbali and Dimitrakopoulos (2018) by combining long- and short-term planning through simulated grade control data to obtain a new estimate of ore body unavailable at the time of schedule setup. To reduce the deviation from long-term planning and satisfy the production plan, the authors proposed a multi-stage approach to the planning process by generating possible data for future grade control plans. Stochastic integer programming was applied to simulate the new ore body estimate via the grade control data generated. The objective was to maximize the NPV in long-term planning and minimize the cost of the production target within the long-term plan.\n\nMetaheuristics is a mathematical optimization technique with the goal of efficiently exploring the search space and finding near-optimal solutions. However, there is no guarantee of feasibility and optimality of the resulting solutions, although it provides good near-optimal solutions within a reasonable time. Fathollahzadeh et al. (2021) classified heuristic and metaheuristic methods. There are a wide variety of metaheuristic approaches, and most solutions used in short-term mining planning are as follows:\n\n• Tabu Search (TS),\n\n• simulated annealing approach (SA)\n\n• Large neighbourhood search (LNS)\n\n• Ant colony optimisation (ACO)\n\nThe Tabu Search (TS) is a metaheuristic method for mathematical optimization that is used for local or neighborhood searches and it has been by Glover (1986).\n\nThis optimization method iteratively moves from one potential solution to a better solution in the same neighborhood space. As the search progresses, Tabu search carefully explores the neighborhood of each solution and saves the results in a list of potential solutions to consider. If a potential solution appears in the tabu list, it cannot be revisited until it expires. The size of the tabu list should be large enough to prevent cycling but not so large that it prohibits too many moves. Liu and Ong (2004) and TS ability to prevent visiting previously recorded solutions (Mousavi et al. 2016a).\n\nSimulate annealing (SA) algorithm was inspired by the analogy of thermodynamics, in which metals are cooled and annealed (Kirkpatrick et al. 1983). It is a metaheuristic approach known for finding a better solution when one is obstructed by a non-improving solution, and it can be viewed as a special form of TS, where a move becomes a tabu with a specified probability.\n\nShaw (1998) applied a large neighborhood search (LNS) has been applied by Shaw (1998). Unlike common neighborhood search, LNS uses a destroy-and-repair mechanism to define a new solution. According to this mechanism, part of the solution is destroyed, and then a repair technique rebuilds the solution (Pisinger and Ropke 2010). For mine planning, this method involves moving blocks between periods and destinations.\n\nFew studies have described metaheuristic problems in short-term mining planning. Shishvan and Sattarvand 2015 developed an Ant Colony Optimization (ACO) metaheuristic to solve an extended MBS-type problem applied to a copper–gold mine for long-term mining planning.\n\nOne of the last works for a metaheuristic approach for short-term planning was proposed by Mousavi et al. (2016a) comparing metaheuristic algorithms: Tabu Search (TS), simulated annealing (SA), and a hybrid solution SA and TS to solve the Open Pit Blocks Sequencing Problem (OPBS). These methods include mining constraints, stockpiling, ore blending, machine workspace to extract a given block from four possible sides, and dynamic destination assignment on a daily or weekly basis. The objective of the proposed OPBS model is to minimize stockpiling costs, including rehandling, holding costs, and satisfying processing requirements. To improve the TS and SA solutions, the authors proposed a hybrid TS-SA algorithm where SA embedded in the TS framework is used to accept some non-improving moves to allow a more diversified investigation of the solution space.\n\nMousavi et al. (2016a) proposed another hybrid metaheuristic short-term planning optimization method. To solve the Model Block Sequencing (MBS) problem, they hybridized the simulated annealing (SA), large neighborhood search (LNS), and branch-and-bound (BB) approaches used by Eivazy and Askari-Nasab (2012). A partial neighborhood solution (PNS) is constructed in each iteration of the SA. Then, a full. neighbourhood solution (NS) is achieved by assigning destinations to blocks using the B&B algorithm. The objective is to minimize stockpiling costs, including rehandling, holding costs, and satisfying processing requirements.\n\nLiu and Kozan (2012) proposed a hybrid shifting bottleneck procedure (HSBP) algorithm combined with the Tabu Search (TS) metaheuristic algorithm has been developed to deal with the parallel-machine job-shop scheduling (PMJSS) problem. The objective is to improve the existing solutions to a short-term planning problem with equipment assignment.\n\nKumral and Dowd (2005) proposed a simulated annealing metaheuristic combined with Lagrangian relaxation and a multi-objective simulated annealing model (MOSA) to determine the optimal short-term production to reach an optimal or near-optimal schedule.\n\nSimilar to metaheuristic methods, Menezes and dos Santos Corrêa (2022) proposed a heuristic method, a new integrated mathematical method that considers quality, metallurgical recovery, mass balance, and stockpiling for an iron mine. The objective is to minimize operating costs by using a set of algorithms to manage the variations in production capacity for mining supply chains and meeting customer demands. To find the optimal solution for short-term mining planning, the authors used heuristic algorithms (relax, fix, fix, and optimize) and mixed-integer programming (local branching) using CPLEX.\n\n\n5. Discussion and Conclusions\n\nThis paper reviews the literature for short-term mine planning optimization in order to address the main methods to perform the mine polygon basis elements of short-term planning as well as the main mathematical models and solution techniques for short-term mine planning optimization. To avoid manual mining cuts, clustering and dig-limit optimization are two useful methods for automatically mining cuts and optimizing short-term mine plans (Tabesh and Askari-Nasab 2013; Tabesh and Askari-Nasab 2019; Salman et al. 2021; Nelis et al. 2022). To maximize profit, the integration of cut-off grade in mining polygons is very important to define each material with its destination.\n\nHowever, in addition to the non-clarification of the optimal number of clusters to be determined (Vasylchuk and Deutsch 2019), clustering can imply some loss of information by merging blocks that can affect the NPV of the mining operation in the strategic plan (Salman et al. 2021) even if it can satisfy the short-term plan requirement.\n\nThe dig-limit optimization method could be the best alternative to the clustering method for mining polygons. For this, a geological block model must be prepared with a good grade control program to reduce uncertainties and risks in the delimitation of ore bodies.\n\nThe key to success in short-term mine planning is to model all operations (drilling, blasting, loading, hauling, stockpiling, materials rehandling, and processing) in detail to identify bottlenecks in each operation and to facilitate the full reconciliation between long-term and short-term mining planning. The daily or weekly basis of short-term mine planning is to have a good assignment of shovels and trucks for Ore and Waste for the different destinations to meet production targets and ensure the best quality of ore to the process requirement aligned to the long-term mine planning.\n\nOwing to their good ability, metaheuristics provide a useful platform for global optimization to tackle large-scale nonlinear optimization models in a reasonable time (Goodfellow and Dimitrakopoulos 2016). Many authors have used a hybrid method, mixed integer programming, and metaheuristics methods (Liu and Kozan 2012; Mousavi et al. 2016b; Mousavi et al. 2016a; Fathollahzadeh et al. 2021) and also included uncertainties with stochastic optimization to improve the mining sequence in the short-term mine plan (Matamoros and Dimitrakopoulos 2016; Jewbali and Dimitrakopoulos 2018) because using each method separately limits the results of short-term mining plans. Habib et al. (2023) presented since 2010 stochastic comparison in recent studies. It is clear that short-term mining planning remains a challenge for stochastic areas.\n\nIn the current state-of-the-art commercial tools and software (Datamine, Deswik, Vulcan), it is difficult to resolve short-term mine planning optimization according to their level of development and capacity in a number of blocks. Stochastic optimization for short-term mine plans is starting to be developed in some cases. According to our literature review, many authors use CPLEX, Python, Arena, or UDESS as an alternative to optimize planning.\n\nThis literature review is a good basis for moving forward to the best optimization method for our next topic research dedicated to short-term mining plan optimization.\n\nThe subject will try to implement a short-term mining plan to align with the long-term goals of gold open-pit mine operations, as shown in Figure 4.\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\nReferences\n\nAskari-Nasab H, Tabesh M, Badiozamani MM: Creating mining-cuts using hierarchical clustering and tabu search algorithms. Min. Optim. Lab. 22; 2010.\n\nBadiozamani MM, Askari-Nasab H: Integration of reclamation and tailings management in oil sands surface mine planning. Environ. Model Softw. 2014; 51: 45–58. Publisher Full Text\n\nBlom M, Pearce AR, Stuckey PJ: Short-term planning for open pit mines: a review. Int. J. Min. Reclam. Environ. 2019; 33(5): 318–339. Publisher Full Text\n\nBoth C, Dimitrakopoulos R: Joint stochastic short-term production scheduling and fleet management optimization for mining complexes. Optim. Eng. 2020; 21(4): 1717–1743. Publisher Full Text\n\nCaccetta L, Hill SP: An application of branch and cut to open pit mine scheduling. J. Glob. Optim. 2003; 27(2–3): 349–365. Publisher Full Text\n\nChanda EK, Wilke FL: An EPD model of open pit short term production scheduling optimization for stratiform orebodies. Proc 23rd APCOM Symp. [place unknown]. 1992; pp. 759–768.\n\nEivazy H, Askari-Nasab H: A mixed integer linear programming model for short-term open pit mine production scheduling. Trans. Institutions Min. Metall. Sect. A Min. Technol. 2012; 121(2): 97–108. Publisher Full Text\n\nFathollahzadeh K, Asad MWA, Mardaneh E, et al.: Review of Solution Methodologies for Open Pit Mine Production Scheduling Problem. Int. J. Min. Reclam. Environ. 2021; 35(8): 564–599. Publisher Full Text\n\nFeng L, Qiu MH, Wang YX, et al.: A fast divisive clustering algorithm using an improved discrete particle swarm optimizer. Pattern. Recogn. Lett. 2010; 31(11): 1216–1225. Publisher Full Text\n\nGershon M: Linear Programming Approach To Mine Scheduling Optimization. Appl. Comput. Oper. Res. Miner. Ind. [place unknown]. 1982; pp. 483–493.\n\nGershon ME: Mine Scheduling Optimization With Mixed Integer Programming. Min. Eng. 1983; 35(4): 351–354.\n\nGlover F: Future paths for integer programming and links to artificial intelligence. Comput. Oper. Res. 1986; 13(5): 533–549. Publisher Full Text\n\nGoodfellow RC, Dimitrakopoulos R: Global optimization of open pit mining complexes with uncertainty. Appl. Soft. Comput. J. 2016; 40: 292–304. Publisher Full Text\n\nAl Habib N , Ben-awuah E, Askari-nasab H: Review of recent developments in short-term mine planning and IPCC with a research agenda. Min. Technol. 2023; 132: 179–201. Publisher Full Text\n\nIsaaks E, Treloar I, Elenbaas T: Optimum dig lines for open pit grade control. Proc. 9th Int. Min. Geol. Conf. [place unknown]. 2014; pp. 425–432.\n\nJewbali A, Dimitrakopoulos R: Stochastic mine planning-example and value from integrating long-and short-term mine planning through simulated grade control, Sunrise Dam, Western Australia. Adv Appl Strateg Mine Plan. [place unknown]. Springer; 2018; pp. 173–190. Publisher Full Text\n\nJuarez G, Dodds R, Echeverría A, et al.: Open pit strategic mine planning with automatic phase generation. OREBODY Model Strateg MINE Plan Symp. Proceedings. AusIMM, Perth. [place unknown]. 2014; pp. 24–26.\n\nKahraman MM, Dessureault SD: Development of a real-time adherence to mine plan tools as part of an integrated remote mine control centre. 35th Int. Symp. Appl. Comput. Oper. Res. Miner. Ind. APCOM. [place unknown]. 2011; pp. 819–825.\n\nKing B: Modelling Open Pit and Underground Production Scheduling in Concert. Orebody Model Strateg. Mine. Plan 2014. [place unknown]. 2014; pp. 369–373.\n\nKirkpatrick S, Gelatt CD, Vecchi MP: Optimization by simulated annealing. Science (80-). 1983; 220(4598): 671–680. Publisher Full Text\n\nKozan E, Liu SQ: Operations research for mining: A classification and literature review. ASOR Bull. 2011; 30(1): 2–23.\n\nKozan E, Liu SQ: A new open-pit multi-stage mine production timetabling model for drilling, blasting and excavating operations. Trans. Institutions Min. Metall. Sect. A Min. Technol. 2016; 125(1): 47–53. Publisher Full Text\n\nKozan E, Liu SQ: An open-pit multi-stage mine production scheduling model for drilling, blasting and excavating operations. Adv. Appl. Strateg. Mine. Plan. 2018; 655–668. Publisher Full Text\n\nKumral M, Dowd PA: A simulated annealing approach to mine production scheduling. J. Oper. Res. Soc. 2005; 56(8): 922–930. Publisher Full Text\n\nL’Heureux G, Gamache M, Soumis F: Mixed integer programming model for short term planning in open-pit mines. Trans. Institutions Min. Metall. Sect. A Min. Technol. 2013; 122(2): 101–109. Publisher Full Text\n\nLamghari A: Mine Planning and Oil Field Development: A Survey and Research Potentials. Math. Geosci. 2017; 49(3): 395–437. Publisher Full Text\n\nLi SX, Knights P: Integration of real options into short-term mine planning and production scheduling. Min. Sci. Technol. 2009; 19(5): 674–678. Publisher Full Text\n\nLiu SQ, Kozan E: A hybrid shifting bottleneck procedure algorithm for the parallel-machine job-shop scheduling problem. J. Oper. Res. Soc. 2012; 63(2): 168–182. Publisher Full Text\n\nLiu SQ, Ong HL: Metaheuristics for the mixed shop scheduling problem. Asia-Pacific J. Oper. Res. 2004; 21(1): 97–115. Publisher Full Text\n\nMarques R d S, de Souza LE , Albarnaz LD, et al.: Modeling and planning of bentonite clay mining: a case study at Bañado de Medina, Melo, Uruguay. Rem. Rev. Esc. Minas. 2013; 66(4): 521–528. Publisher Full Text\n\nMatamoros MEV, Dimitrakopoulos R: Stochastic short-term mine production schedule accounting for fleet allocation, operational considerations and blending restrictions. Eur. J. Oper. Res. 2016; 255(3): 911–921. Publisher Full Text\n\nMenezes GC, dos Santos Corrêa J : Model and algorithms applied to Short-Term Integrated Programming Problem in Mines. Res. Policy. 2022; 79(January): 102950. Publisher Full Text\n\nMohtasham M, Mirzaei-Nasirabad H, Askari-Nasab H, et al.: Truck fleet size selection in open-pit mines based on the match factor using a MINLP model. Min. Technol.: Trans. Inst. Min. Metall. 2021; 130(3): 1–17. Publisher Full Text\n\nMoradi Afrapoli A, Askari-Nasab H: Mining fleet management systems: a review of models and algorithms. Int. J. Min. Reclam. Environ. 2019; 33(1): 42–60. Publisher Full Text\n\nMousavi A, Kozan E, Liu SQ: Comparative analysis of three metaheuristics for short-term open pit block sequencing. J. Heuristics. 2016a; 22(3): 301–329. Publisher Full Text\n\nMousavi A, Kozan E, Liu SQ: Open-pit block sequencing optimization: A mathematical model and solution technique. Eng. Optim. 2016b; 48(11): 1932–1950. Publisher Full Text\n\nNelis G, Meunier F, Morales N: Column Generation for Mining Cut Definition with Geometallurgical Interactions. Nat. Resour. Res. 2022; 31(1): 131–148. Publisher Full Text\n\nNelis G, Morales N: A mathematical model for the scheduling and definition of mining cuts in short-term mine planning. Optim. Eng. 2022; 23(1): 233–257. Publisher Full Text\n\nNeufeld CT, Norrena KP, Deutsch CV: Semi-Automatic Dig Limit Generation. Cent Comput Geostatistics Annu Rep Pap. [place unknown]. 2003; pp. 1–23. papers2://publication/uuid/5155E453-EB0A-4808-9452-B86CAA180583.\n\nNewman AM, Rubio E, Caro R, et al.: A review of operations research in mine planning. Interfaces (Providence). 2010; 40(3): 222–245. Publisher Full Text\n\nNoriega R, Pourrahimian Y: A systematic review of artificial intelligence and data-driven approaches in strategic open-pit mine planning. Res. Policy. 2022; 77(November 2021): 102727. Publisher Full Text\n\nNorrena KP, Deutsch CV: Automatic Determination of Dig Limits Subject to Geostatistical, Economic and Equipment Constraints. Cent. Comput. Geostatistics Annu. Rep. Pap. 2001; 1–18. papers2://publication/uuid/8E3B6A0A-4131-4F32-8D36-406B0312C5C4.\n\nOsanloo M, Gholamnejad J, Karimi B: Long-term open pit mine production planning: A review of models and algorithms. Int. J. Min. Reclam. Environ. 2008; 22(1): 3–35. Publisher Full Text\n\nOsanloo M, Rahmanpour M: Mining.2017; 70(1): 109–116.\n\nOtto TJ, Musingwini C: A compliance driver tree (CDT) based approach for improving the alignment of spatial and intertemporal execution with mine planning at open-pit mines. Res. Policy. 2020; 69(February): 101826. Publisher Full Text\n\nP NK, Neufeld CT, Deutsch CV: An Update on Automatic Dig Limit Determination. Cent. Comput. Geostatistics Annu. Rep. Pap. 2002; 7: 1–17. papers2://publication/uuid/FF1B87D4-7799-4EEB-837D-2067AF429CDC.\n\nPaduraru C, Dimitrakopoulos R: Adaptive policies for short-term material flow optimization in a mining complex. Min. Technol.: Trans. Inst. Min. Metall. 2018; 127(1): 56–63. Publisher Full Text\n\nPisinger D, Ropke S: Large neighborhood search. Handb metaheuristics. [place unknown]. Springer; 2010; pp. 399–419.\n\nQuigley M, Dimitrakopoulos R: Incorporating geological and equipment performance uncertainty while optimising short-term mine production schedules. Int. J. Min. Reclam. Environ. 2020; 34(5): 362–383. Publisher Full Text\n\nRichmond A: Integrating multiple simulations and mining dilution in open pit optimisation algorithms. Australas Inst. Min. Metall. Publ. Ser. [place unknown]. 2007; pp. 317–322.\n\nRichmond AJ, Beasley JE: Financially efficient dig-line delineation incorporating equipment constraints and grade uncertainty. Int. J. Surf. Min. Reclam. Environ. 2004; 18(2): 99–121. Publisher Full Text\n\nRuiseco JR, Williams J, Kumral M: Optimizing Ore–Waste Dig-Limits as Part of Operational Mine Planning Through Genetic Algorithms. Nat. Resour. Res. 2016; 25(4): 473–485. Publisher Full Text\n\nSalman S, Muhammad K, Khan A, et al.: A Block Aggregation Method for Short-Term Planning of Open Pit Mining with Multiple Processing Destinations. Minerals. 2021; 11(3): 288. Publisher Full Text\n\nSari YA, Kumral M: Dig-limits optimization through mixed-integer linear programming in open-pit mines. J. Oper. Res. Soc. 2018; 69(2): 171–182. Publisher Full Text\n\nShaw P: Using constraint programming and local search methods to solve vehicle routing problems. Lect. Notes Comput. Sci. (including Subser Lect. Notes Artif. Intell. Lect. Notes Bioinformatics). Vol. 1520. [place unknown]. 1998; pp. 417–431. Publisher Full Text\n\nShishvan MS, Sattarvand J: Long term production planning of open pit mines by ant colony optimization. Eur. J. Oper. Res. 2015; 240(3): 825–836. Publisher Full Text\n\nSmith ML: Optimizing short-term production schedules in surface mining: Integrating mine modeling software with AMPL/CPLEX. Int. J. Surf. Min. Reclam. Environ. 1998; 12(4): 149–155. Publisher Full Text\n\nTabesh M, Askari-Nasab H: Two-stage clustering algorithm for block aggregation in open pit mines. Trans. Institutions Min. Metall. Sect. A Min. Technol. 2011; 120(3): 158–169. Publisher Full Text\n\nTabesh M, Askari-Nasab H: Automatic creation of mining polygons using hierarchical clustering techniques. J. Min. Sci. 2013; 49(3): 426–440. Publisher Full Text\n\nTabesh M, Askari-Nasab H: Clustering mining blocks in presence of geological uncertainty. Min. Technol.: Trans. Inst. Min. Metall. 2019; 128(3): 162–176. Publisher Full Text\n\nUpadhyay S, Nasab HA: Simulation and Optimization of Mine Operations for Desired Grade Blending in Open Pit Mines. APCOM. [place unknown]. 2017; pp. 1–11.\n\nUpadhyay SP, Askari-Nasab H: Simulation and optimization approach for uncertainty-based short-term planning in open pit mines. Int. J. Min. Sci. Technol. 2018; 28(2): 153–166. Publisher Full Text\n\nUpadhyay SP, Askari-Nasab H, Tabesh M, et al.: Simulation and optimization in open pit mining. Proc. Appl. Comput. Oper. Res. Miner. Ind. 37th Int. Symp. APCOM. [place unknown]. 2015.\n\nUpadhyay SP, Doucette J, Askari-Nasab H: Short-term production scheduling in open pit mines with shovel allocations over continuous time frames. Int. J. Min. Miner. Process. Eng. 2021; 12(4): 292–308. Publisher Full Text\n\nVasylchuk YV, Deutsch CV: Optimization of Surface Mining Dig Limits with a Practical Heuristic Algorithm. Mining, Metall. Explor. 2019; 36(4): 773–784. Publisher Full Text\n\nWilde BJ, Deutsch CV: A Short Note Comparing Feasibility Grade Control with Dig Limit Grade Control. Cent. Comput. Geostatistics. 2007; 1–10." }	[ { "id": "331455", "date": "08 Nov 2024", "name": "Chengkai Fan", "expertise": [ "Reviewer Expertise Open pit mining", "machine learning", "mine transport", "and rock mechanics." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The authors list a number of papers that have provided an review of short-term or long-term planning. What is the significance of this review for the author? What is the difference from previous studies? I suggest adding the specific differences in Table 1.\n2. Please add explanations and differences between short-term, medium-term as well as long-term plans. Is there a quantitative range that distinguishes these three terms?\n3. Please spell out the abbreviations when they first appear. For example, RM and UG.\n\n4. The research gap is not clear to me. Can you clarify your research gap of this review paper? Not the research gap of computational techniques.\n\n5. Please explain why this review paper focuses on the two aspects of short-term planning.\n6. Authors need to summarize previous research and offer constructive comments or ideas. For example, the author overviews the application of clustering methods. The authors simply read the relevant literature and methods without making some summarizing conclusions and recommendations. This problem also applies to other parts of the review.\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? Yes", "responses": [ { "c_id": "13146", "date": "16 Jan 2025", "name": "Moise KAMBALA MALUNDAMENE", "role": "Author Response", "response": "Hello Chengkai Fan, Happy new year, Thanks for your time to review our paper. Please, See below our responses to your comment 1. The authors list a number of papers that have provided a review of short-term or long-term planning. What is the significance of this review for the author? What is the difference from previous studies? I suggest adding the specific differences in Table 1. Response: We thank the reviewer for the shrewd comments and observations. Table 1 highlights the limited number of review papers focused solely on short-term planning for open-pit mines. Unlike Fathollahzadeh et al. (2021), which summarizes both underground and open-pit reviews with a focus on monthly to yearly planning, this review specifically emphasizes short-term mine planning with a daily to monthly granularity. To enhance clarity, we added a new column to Table 1 indicating the time discretization granularity for each reviewed study. 2. Please add explanations and differences between short-term, medium-term, and long-term plans. Is there a quantitative range that distinguishes these three terms? Response: We have added an explanation detailing the connections and distinctions between long-term, medium-term, and short-term planning horizons. Figure 1 has been updated to clearly illustrate these differences. Short-term planning typically spans from daily to monthly (up to three months, depending on the organization), medium-term planning covers 3 months to 3 years, and long-term planning exceeds 3 years, focusing on the life-of-mine perspective. 3. Please spell out the abbreviations when they first appear. For example, RM and UG. Response: All abbreviations have been defined in the text. For instance, RM stands for Resource Modeling, and UG refers to Underground. 4. The research gap is not clear to me. Can you clarify your research gap of this review paper? Not the research gap of computational techniques. Response: We have clarified the research gap in the corresponding section. This review highlights that short-term mine planning optimization for open-pit mines, with a granularity of daily to monthly, remains underexplored. Many of the papers listed in Figure 1 focus on short-term planning with time discretization extending up to one year. 5. Please explain why this review paper focuses on the two aspects of short-term planning. Response: The two aspects are critical for short-term mine planning. Before planning, mining cuts must be defined based on factors such as cut-off grade, shape, and operational constraints. Defining dig limits between ore and waste ensures alignment with the long-term strategy. Once mining cuts are established using mining polygons, short-term plans can be optimized while aligning with medium- and long-term strategies. 6.Authors need to summarize previous research and offer constructive comments or ideas. For example, the author overviews the application of clustering methods. The authors simply read the relevant literature and methods without making some summarizing conclusions and recommendations. This problem also applies to other parts of the review. Response: A summary of previous research has been included in the conclusion, where we discuss the differences and advantages of each method, particularly between dig-limit optimization and clustering. Thanks Best Regards Moise" } ] }, { "id": "331461", "date": "12 Nov 2024", "name": "Andrea Brickey", "expertise": [ "Reviewer Expertise mining engineering", "mine design", "surface mine planning", "underground mine planning", "mine optimization", "operations research", "production scheduling", "and reserve estimation." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 review of the current state of short-term, open-pit, mine planning technical solutions. The article provides a review of the challenges and documented solutions while highlighting areas where further technological improvements could be made. The paper is well cited with the current and relevant references. Yet, improvements should be made to increase clarity and quality.\n1. It is suggested that the authors add \"surface\" or \"open-pit\" to the title of the paper. 2. In the abstract, the statement \"short-term planning is more challenging because it deals with uncertainties: is vague and does not reflect the actual reality that all planning time horizons deal with uncertainties. 3. There are numerous grammatical errors and typos throughout the document. For example, mining planning is used in a few places. The proper term would be mine planning. 4. The introduction should make it clear that this paper is documenting the current state of open-pit or surface short-term mine planning. 5. Review document the ensure that descriptions are using appropriate adjectives and not colloquial terms. 6. Inconsistent capitalization and formatting in numerous areas. See Table 2 for some examples. 7. Some figures are too small to read, e.g., Figure 1. 8. There are commercially available, heuristic-based scheduling solutions, e.g., RPM Global's XPAC. 9. In some sections you refer to a geologic model as a \"bloc model\" and in other areas a \"block model\". I believe the industry standard is \"block model\". 10. Please make sure to use commas when listing more than 3 items. 11. Define SMU in the text. 12. It should be made clear that short-term solutions often determine destination. This is not explicitly stated in the paper. 13. It seems that Figure 3 could be formatted to make the text larger. 14. The statement on page 9 of the pdf file states, \"They used the CPLEX optimization method.\" This should be stated as they used CPLEX to \"solve\" the formulation. 15. Review document for proper tense. See paragraph beginning with \"Upadhyay and Askari-Nasab (2018)\" on page 9 as an example. 16. Section 4.2, first paragraph, should make it clear that these solutions are for \"Strategic\" mine planning. 17. The authors abbreviate branch-and-bound as BB, but then use the term as B&B. 18. Figure 4 does not seem to provide a significant amount of value to the paper. It is suggested that either it be explained further in the document, simplified, or removed. 19. On page 12, paragraph beginning with \"Owing to their good ability...\" the term \"global optimization\" seems to give the impression that metaheuristics provide optimal solutions. 20. A few citations are included in this review for the authors' consideration.\n\nReference https://repository.mines.edu/bitstream/handle/11124/178655/Deutsch_mines_0052E_12734.pdf?sequence=2&isAllowed=y\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? No\n\nIs the review written in accessible language? No\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] }, { "id": "331462", "date": "20 Nov 2024", "name": "Pedro Henrique Alves Campos", "expertise": [ "Reviewer Expertise Geostatistics", "mine planning", "resource and reserves", "machine learning" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is a review of short-term mine planning optimization methods. The authors focus on 1) optimizing dig limits(polygons), and 2) optimizing short-term production scheduling.\nI believe the paper has the potential to get indexed. However, some points need to be clarified and improved.\n01) The authors should highlight what this review presents as new concerning other reviews cited throughout the text, such as Blom et al. 2019, Fathollahzadeh et al. 2021, Al Habib el at. 2021 and Kozan et al. 2011.\n02) I suggest improving Table 1 by detailing the topics covered in each article review, their results, and main conclusions.\n03) There are several errors in writing, bad wording, comma misplacement, word repetition, etc. Examples: a) \"...short-term mine planners with management teams are requested to identify and manage risks to mitigate them and adhere able to stick to the Life-of Mine (LOM) plan\" b) \"constraints to be considered and the level of details for mine operations to be considered\" c) \"similar bloc properties\" d) \"...(for example: Datamine RM,DatamineUG,SnowdenandNPV),However,differentmodels and algorithms,are applied...\"\nTherefore, I suggest doing a complete English review of the text.\n04) Tables 2 and 3 deserve to be more explained and carefully detailed (there is excessive use of ellipses)\n05) since we are already at the end of 2024, I believe the paper must be updated by referencing the latest papers on the topic. Also, the improvements and differences between the approaches of each research should be discussed more deeply.\n06) What is the importance of Figure 4 for your review? It does not seem to be relevant.\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": [] } ]	1	https://f1000research.com/articles/13-1107
https://f1000research.com/articles/12-953/v1	08 Aug 23	{ "type": "Research Article", "title": "Esthetic preferences of orthodontists, general dentists, and laypersons for Indian facial profiles: A cross-sectional study", "authors": [ "Harshini Reddy", "Ritesh Singla", "Nishu Singla", "Madhumitha Natarajan", "Deepak Kumar Singhal", "Harshini Reddy", "Ritesh Singla", "Madhumitha Natarajan", "Deepak Kumar Singhal" ], "abstract": "Background: Disparity in the esthetic perceptions between a patient and clinician could result in patient dissatisfaction with orthodontic treatment outcomes. The aim of this study was to compare the perceptions of a group of orthodontists, general dentists, and laypersons about the attractiveness of Indian facial profiles.\nMethods: In this study, a male and a female participants’ photographs and lateral cephalograms were digitally manipulated by inserting them into Dolphin software; we considered four soft tissue parameters at a nasolabial angle, upper lip E-line, lower lip E-line, and pg-pg’, so that 20 profiles were created for each model. A visual analog scale (VAS) along with a question about surgical correction opinion was given to 18 orthodontists, 18 general dentists, and 18 laypersons to score (1-5) from least to most attractive. Spearman’s rank correlation was computed to assess correlation, as well as ANOVA, followed by post hoc Tukey analysis to compare the mean scores, and Chi-square test to determine the opinion about surgical treatment.\nResults: There was an overall weak and negative correlation between the three groups, indicating that orthodontists attributed lower pleasantness scores to almost all the altered female and male facial profiles. Additionally, statistically significantly lower mean scores were attributed by orthodontists to many females and few male facial profiles. More orthodontists identified the need for surgical correction for a few severely distorted profiles but there was a statistically non-significant difference among the groups for most of the profiles.\nConclusions: It was concluded that participants in the three groups had diverse concepts of facial attractiveness in all the parameters considered. Compared to general dentists and laypersons, orthodontists were much more precise, firmer, and meticulous in identifying a favorable or good-looking profile.", "keywords": [ "Indian facial profiles", "esthetic", "perceptions", "orthodontists", "general dentists", "layperson" ], "content": "Introduction\n\nFacial aesthetics are associated with how an individual is perceived by others.1 The perception of an individual as being beautiful greatly impacts the way they represent themselves to others, and therefore esthetics are not absolute, but highly subjective and variable.2 Beauty is said to be “in the eyes of the beholder”.3 Each person has a different intellectual wisdom about beauty and its perception varies accordingly. Most of it is influenced by principles of one’s self-perception. The perception of one’s disfigurement, flaws, or imperfections may be beautiful to another. Women’s feet in China were bound to make them small which was perceived more attractive.4 Midline diastema was considered aesthetic among Arabs.5\n\nFacial esthetics have always been an integral part of the standards and practice of orthodontics. Even though standard occlusion remains a chief functional goal, achieving proper esthetic outcomes remains essential for the satisfaction of the patients. Individuals with an ideal dentofacial appearance are referred to as more good-looking socially than those with an unaesthetic dental appearance and often have low self-confidence.6 Holdaway suggested that identifying soft tissue traits that contribute to or reduce physical attractiveness stereotypes deeply rooted in society can enhance treatment objectives.7 Orthodontists usually judge the characteristics of facial esthetics based on smile assessments of the patient, profile, and full face. Over the years, clinical perceptions of facial esthetics have progressively shifted to the use of quantifiable soft-tissue diagnostic valuations. Other orthodontic treatment methods to gain esthetic considerations – camouflage versus correction of jaw relationships, expansion versus extraction – have started to obtain importance.7\n\nThe treatment should be made to achieve a harmonious facial profile with an esthetically attractive smile and functional dental occlusion. When facial attractiveness and occlusion correction are combined, treatment planning becomes a little difficult. Achieving an ideal occlusion does not essentially mean that decent facial balance is achieved. In an attempt to achieve accurate soft tissue effect to hard tissue changes, an orthodontist should concentrate on the growth and development of soft tissue traits. They should be aware of soft tissue changes produced by orthopedic or orthodontic treatment procedures. Hence, an orthodontist should conduct a thorough facial hard tissue and soft tissue examination, so that orthodontic treatment can favorably affect the facial features.8\n\nIn the pursuit of the ideal treatment goal, aesthetics has now become crucial. Therefore, it is important to consider both the aesthetic perspectives of patients and clinicians when it comes to facial attractiveness. The difference in perception between the clinician and patient could result in patient dissatisfaction with treatment outcomes, as the perception of esthetics may vary between an orthodontist and a layperson. Thus, this study aimed to compare the perceptions of a group of orthodontists, general dentists, and laypersons about the attractiveness of Indian facial profiles. In addition, it was also determined whether surgical treatment was needed for the profiles.\n\n\nMethods\n\nA cross-sectional study was conducted considering three groups of study participants consisting of orthodontists, general dentists, and laypersons (who were well-educated and not from a medical background) between the age of 18 to 50 years. The total sample size was 54 with 18 subjects in each group. Ethical clearance was obtained from the Institutional Ethical Committee of Kasturba Medical College and Kasturba Hospital (IEC approval number 790/2018) for the conduct of the study. The study participants were informed about the study through a participant information sheet following which written informed consent was obtained. The study participants were given a self-administered questionnaire consisting of a question about surgical treatment requirements and a visual analog scale (VAS) for 20 profiles created each for two study models. The time taken to answer the questionnaire was approximately 10 min.\n\nThe photographs and lateral cephalograms of a 22-year-old male and a 21-year-old female were taken as study models. The standards for choosing these models comprised a well-balanced face with normal eyes, nose, and lips; class I skeletal and dental relationship; well-aligned arches; Z angle 71° - 89°. The exclusion criteria for the selection of study models were class II and class III malocclusions, congenital deformities, and facial anomalies. Four soft tissue parameters were considered: nasolabial angle, upper lip E-line, lower lip E-line, and pg-pg’ (hard tissue pogonion to soft tissue pogonion). Most of the measurements of the role models were within the normal ranges.9,10\n\nLateral cephalograms and standard high-resolution color profile photographs were taken with white background and good brightness. Tracing of the lateral cephalograms was done using Dolphin software (Dolphin Imaging 11.95 Premium Software). Lateral cephalograms were linked to their respective profile images by inserting them in the software and nasolabial angles, E-Lines, and pg-pg’ was defined in the original pictures (Figure 1). A total of 12 anatomic landmarks (eight soft tissue, four hard tissue) were recognized. The hard tissue landmarks were porion (po), sella (s), orbitale (or), and pogonion (pg). The soft tissue landmarks were pronasale (Pn), subnasale (Sn), superior labial sulcus (SLS), labrale superius (Ls), labrale inferius (Li), inferior labial sulcus (ILS), and soft tissue pogonion (pg’) and soft tissue menton (Mn’).\n\nThe pictures were digitally manipulated using the software by altering the lower component (labial part) of the nasolabial angle by 2° increments (increase and decrease); thus, a set of five profiles (one basic profile, two profiles with increase of nasolabial angle, two profiles with decrease of nasolabial angle) were created for each subject. The images were digitally manipulated for lower lip to E-Line and upper lip to E-Line by increasing 1 mm for two profiles and by decreasing 1 mm for two profiles, and the last profile remains as the basic profile.\n\nThe images were also digitally manipulated for pg-pg’ by increasing 2 mm for two profiles and by decreasing 2 mm for two profiles and the last profile remains as the basic profile. Thus, a total of 20 facial profiles were created for each model (Figures 2 and 3): five profiles for nasolabial angle; five profiles for the upper lip E-line, five profiles for lower lip E-line; and five profiles for pg-pg’.\n\nOnce the profiles were reconstructed, the margins of the photos were blended out with Paint Shop Pro (version 7.0) to preserve the natural appearance of the pictures. Finally, the printed copies of the pictures were taken and randomly arranged in an album with no distinct order for both female and male subjects. As consented, no masking of the face was done during the study process as it involves the assessment of facial attractiveness. The study participants were assigned to score (1-5) for each image through a Visual Analogue Scale (VAS) from least to most attractive. The participants were also asked a yes/no question to answer whether they thought the profile required any surgery to improve the facial appearance.\n\nData was entered into Microsoft Excel and evaluated using statistical software SPSS version 20. The groups were ranked for Spearman’s rank correlation based on their increasing level of orthodontic education such as laypersons followed by general dentists and orthodontists. Spearman’s rank correlation was computed to evaluate the correlation between three groups for all the altered profiles of male and female models for the VAS score of facial profile attractiveness. The Spearman’s rank correlation coefficient (Rs) value lies between 1.0 and -1.0 (a perfect positive to negative correlation). The strength of a correlation depends on the value of the coefficient. A Rs between 0.00 - 0.19 implies a very weak, 0.20 - 0.39 a weak, 0.40 - 0.69 a moderate, 0.70-0.89 a strong, and 0.90-1.00 a very strong correlation. Also, a Rs of 0 indicates no association between ranks. ANOVA followed by post hoc Tukey analysis was done to compare the mean VAS scores between the three groups. A Chi-square test was performed to determine the perceptions of the need for surgical treatment for the facial profiles between the three groups. The 5% probability level (p ≤ 0.05) implied a statistically significant difference.\n\n\nResults\n\nAccording to the results of the Spearman’s rank correlation test, there was an overall weak, negative correlation between the three groups for the VAS scores for most of the female and male profiles. A negative correlation indicates that the orthodontist’s group of the highest rank gave the lowest pleasantness scores to almost all the altered female and male facial profiles on a VAS of 1-5 compared to other groups. A statistically significant but weak negative correlation was seen between the three study groups for female profiles with Nasolabial angle (+4°), Nasolabial angle (-4°), Upper lip to E-line (+2 mm), Upper lip to E- line (-1 mm), Lower lip to E-line (normal), Lower lip to E-line (-2 mm), pg-pg’ (-2 mm) and pg- pg’ (-4 mm); a moderate negative correlation for female profiles with Upper lip to E-line (-2 mm) and Lower lip to E-line (-1 mm). There was no correlation between the three groups for the profile Upper lip to E-line (normal) and a positive but very weak correlation for profiles with Nasolabial angle (normal) and Nasolabial angle (-2°). In contrast, the remaining female profiles showed statistically non-significant weak negative correlation as shown in Table 1. For male profiles, it was found that there was a statistically significant negative weak correlation between the three study groups for profiles with Nasolabial angle (+2°) and Nasolabial angle (+4°). In contrast, all remaining male profiles showed a statistically non-significant and very weak negative correlation.\n\n* P value ≤ 0.05 was considered a statistically significant difference.\n\nThe results of ANOVA presented in Table 2 show that the orthodontist group attributed lower mean scores to almost all the altered female and male facial profiles. However, statistically significant differences in mean scores were noted for female profiles with Nasolabial angle (+4°), Nasolabial angle (-4°), Upper lip to E-line (-1 mm), Upper lip to E- line (-2 mm), Lower lip to E-line (normal), Lower lip to E-line (-1 mm), Lower lip to E-line (-2 mm), pg-pg’ (+4 mm), pg-pg’ (normal) and pg-pg’ (-4 mm). Post hoc analysis showed that for female profiles with Lower lip to E-line (normal) and pg-pg’ (normal), orthodontists significantly differed from general dentists; for profiles with Nasolabial angle (+4°), Nasolabial angle (-4°), Upper lip to E-line (-1 mm), Upper lip to E-line (-2 mm), Lower lip to E-line (-1 mm), Lower lip to E-line (-2 mm) and pg-pg’ (-4 mm), orthodontists significantly differed from laypersons. In contrast, for male profiles, only profiles with Nasolabial angle (+2°), Nasolabial angle (+4°), and pg-pg’ (+4 mm) were statistically different in the responses between the three groups, and the post hoc analysis showed that for profiles with Nasolabial angle (+2°) and Nasolabial angle (+4°), orthodontists significantly differed from laypersons. Meanwhile, all remaining profiles of the male model showed statistically non-significant differences between the three groups (Table 2).\n\nThe results of the Chi-square test for female profiles with Lower lip to E-line (-2 mm), pg-pg’ (+4 mm), and pg-pg’ (-4 mm) showed that significantly more orthodontists preferred surgical correction as compared to other groups. Meanwhile, all remaining profiles showed statistically non-significant differences between the three groups. In contrast, for the male profile with Nasolabial angle (+4°), significantly more orthodontists preferred surgery as compared to other groups. The remaining profiles showed statistically non-significant differences between the three groups (Table 3).\n\n\nDiscussion\n\nIn the present study, we evaluated the esthetic perceptions of different patient profiles from the standpoint of orthodontists, general dentists, and laypersons. The results showed that there was an overall weak negative correlation between the three groups, which indicates that orthodontists attributed lower pleasantness scores to almost all the female and male facial profiles on the visual analog scale. Further, the results of ANOVA also showed that Orthodontists significantly attributed lower pleasantness scores to many females and few male facial profiles. Correspondingly, a similar study done by Volpato GM et al. reported that patients and lay people assigned higher pleasantness scores than orthodontists, with statistically significant differences for all evaluations.11 Lines et al. and Imani et al. in their studies comparing judgments by orthodontists, general surgeons, other dental professionals, and laypersons, stated that even though the orthodontists group were more precise in their judgments when compared to oral surgeons, but their opinions still differed greatly from those of laypersons and other dental professionals.12,13 In addition, as noticed in the present study, Romani et al. and Burcal et al., specified that irrespective of the educational level the facial profiles of the female patients were judged more carefully.14,15\n\nIn facial profiles with increased nasolabial angle by +4° and decreased nasolabial angle by -4°, orthodontists gave lower scores than the other two study groups for both female and male profiles. For a female profile where the lower component of the nasolabial angle was decreased by 2 degrees, a weak positive correlation or a fair agreement was seen between all three groups, as most of them agreed it to be an attractive profile. According to Farhad B. Naini et al.,16 an upper lip inclination of 79°-85° is regarded as ideal, while a range of 73°-88° is considered acceptable. Angles lower than 67° and greater than 94° are considered slightly unappealing, and any angle exceeding the range of 67°-94° is considered very unattractive. Burnstone17 stressed the importance of this angle since laypeople were more likely to evaluate upper lip protrusion in relation to the nose.\n\nFor female profiles where the upper lip E-line was decreased by 1 mm and 2 mm, and the lower lip E-line decreased by 1 mm and 2 mm, significantly more orthodontists than general dentists or laypeople felt the profiles to be unattractive as these profiles became a little convex. Similarly, for profiles of both females and males where the upper lip E-line was increased by 1 mm and 2 mm, orthodontists as well as general dentists gave lower scores and felt these profiles unattractive as the profiles became close to class II or convex profiles. According to Young-Chel Park and Charles J Burnstone,18 the upper lip E-line in the normal occlusion group is -4.8 mm, and the lower lip E-line is -3.8 mm.\n\nFor both female and male profiles where the soft tissue pogonion (pg-pg’) was increased by 2 mm, most of the study participants gave higher scores. This implied that most of them might prefer a slightly concave profile to be more esthetic. Again, for the profiles of both female and male models where the soft tissue pogonion (pg-pg’) was increased by 4 mm (as it became more class III as well as deemed unappealing) and for a profile where soft tissue pogonion (pg-pg’) was decreased by 4 mm, most of the orthodontists significantly considered these profiles unattractive. Additionally, it showed a maximum disparity in the perception of orthodontists compared to both other groups. According to Park and Burnstone, pg-pg’ was found to be 12.2 mm in the normal group and increased to 13.2 mm in class II division 1 patients; mean values for females were 12.6 mm and 13 mm for males. In the original profile of male and female study models with normal pg-pg’, all three groups felt the profiles to be average or good-looking.18\n\nRegarding perceptions of the groups for oral surgery, significantly more orthodontists considered the need for surgery to improve the facial esthetics for a female profile with the lower lip E-line decreased by 2 mm. Similarly, in the female profiles where the soft tissue pogonion (pg-pg’) was increased by 4 mm and decreased by 4 mm, most of the orthodontists were found to believe these profiles needed surgery as compared to other groups. It was noticed that although no statistically significant difference for the profiles with decreased 2 mm from the upper lip E-line and decreased 2 mm from the Lower lip E-line, more orthodontists preferred surgery. Perceptions of different groups for the assessment of the need for surgery for male profiles found that significantly more orthodontists preferred surgery for a profile where the nasolabial angle was increased by 4 degrees as compared to other groups. Also, more orthodontists preferred surgery for the profiles with decreased nasolabial angle by -4° for both males and females as the profiles became more class II and convex. It was noticed that for most of the original study model profiles, as well as for a profile with soft tissue pogonion (pg-pg’) increased by 2 mm, almost 100% percent of them felt that surgery was not required to improve the facial esthetics. DeAlmeida and Bittencourt in their study stated that surgery was indicated mostly for the convex profiles for males and concave profiles for females.19\n\n\nConclusions\n\nHence, it was concluded that participants in the three groups had diverse conceptions of facial attractiveness in all parameters considered. When compared to general dentists and laypersons, orthodontists were much more precise, firmer, and meticulous in identifying a favorable or good-looking profile. In the present study, orthodontists attributed lower pleasantness scores to almost all the altered female and male facial profiles. Studies by Orsini et al. also concluded that the orthodontists were more precise and accurate towards the discrete changes in the profile when compared to the laypersons.20 The results of the study also indicate that although more orthodontists identified the need for surgical correction for a few severely distorted profiles, there was a statistically non-significant difference between the groups for most of the altered profiles. Since esthetics is subjective and leads to different facial evaluations, orthodontists must address patient’s esthetic concerns for satisfactory treatment outcomes. Orthodontists need to achieve the ideal esthetic outcomes with a well-proportioned facial appearance.\n\n\nInformed consent\n\nWe confirm that we have obtained permission to use images and data from the participants included in this work.", "appendix": "Data availability\n\nMendeley Data: Esthetic Preferences of Orthodontists, general dentists, and Laypersons for Indian facial profiles: A cross-sectional study, https://doi.org/10.17632/b9tkhwjhjb.1. 21\n\nThis project contains the following underlying data:\n\n- Raw Data - Aesthetic Preferences of various study groups.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nNash DA: Professional ethics and esthetic dentistry. J Am Dent Assoc. 2001; 132: 39–45.\n\nRoutledge Encyclopedia of Philosophy. London: Malcolm Budd; 1998. Aesthetics; (cited 2023, May 25).\n\nBasciftci FA, Uysal T, Buyukerkmen A: Determination of Holdaway soft tissue norms in Anatolian Turkish adults. Am J Orthod Dentofacial Orthop. 2003; 123: 395–400. PubMed Abstract \| Publisher Full Text\n\nChan LMV: Foot binding in Chinese women and its psycho-social implications.Can Psychiatr Assoc J.1970; 15(2): 229–232. PubMed Abstract \| Publisher Full Text\n\nAbrahams R, Kamath G: Midline diastema and its aetiology - A review. Dental Update. 2014; 41(5): 457–464. PubMed Abstract \| Publisher Full Text\n\nPeck S, Peck L: Selected aspects of the art and science of facial esthetics. Semin Orthod. 1995; 1(1): 105–126. Publisher Full Text\n\nHoldaway RA: Soft tissue cephalometric analysis and its use in orthodontic treatment planning. Am J Orthod. 1983; 84: 1–28. PubMed Abstract \| Publisher Full Text\n\nRicketts RM: The biologic significance of divine proportion and Fibonacci series. Am J Orthod. 1982; 81: 351–370. Publisher Full Text\n\nArnett GW, Bergman RT: Facial keys to orthodontic diagnosis and treatment planning. Part I. Am J Orthod Dentofacial Orthop. 1993 Apr; 103(4): 299–312. PubMed Abstract \| Publisher Full Text\n\nArnett GW, Bergman RT: Facial keys to orthodontic diagnosis and treatment planning. Part 2. Am J Orthod Dentofacial Orthop. 1993 May; 103(5): 395–411. PubMed Abstract \| Publisher Full Text\n\nVolpato GH, Rodrigues R, de Almeida-Pedrin P , et al.: Self-perception of facial esthetics by patients with different profiles compared with assessments of orthodontists and lay people. Am J Orthod Dentofacial Orthop. 2020; 158(6): 840–848. PubMed Abstract \| Publisher Full Text\n\nLines PA, Lines RR, Lines CA: Profile metrics and facial esthetics. Am J Orthod. 1978; 73: 648–657. PubMed Abstract \| Publisher Full Text\n\nImani MM, Sanei E, Niaki EA, et al.: Esthetic preferences of orthodontists, oral surgeons, and laypersons for Persian facial profiles. Am J Orthod Dentofacial Orthop. 2018; 154: 412–420. PubMed Abstract \| Publisher Full Text\n\nRomani KL, Agahi F, Nanda R, et al.: Evaluation of horizontal and vertical differences in facial profiles by orthodontists and lay people. Angle Orthod. 1993; 63: 175–182. PubMed Abstract\n\nBurcal RG, Laskin DM, Sperry TP: Recognition of profile change after simulated orthognathic surgery. J Oral Maxillofac Surg. 1987; 45: 666–670. PubMed Abstract \| Publisher Full Text\n\nNaini FB, Cobourne MT: Fraser McDonald, and David Wertheim the aesthetic impact of upper lip inclination in orthodontics and orthognathic surgery. Eur J Orthod. 2015; 37: 81–86. PubMed Abstract \| Publisher Full Text\n\nBurstone CJ: Lip Posture and Its Significance in Treatment Planning. Am. J. Orthod. 1967; 53: 262–284. PubMed Abstract \| Publisher Full Text\n\nPark YC, Burstone CJ: Soft-tissue profile -Fallacies of hard-tissue standards in treatment planning. Am J Orthod. 1986; 90: 52–62. Publisher Full Text\n\nDe Almeida MD, Bittencourt MA: Anteroposterior position of mandible and perceived need for orthognathic surgery. J Oral Maxillofac Surg. 2009; 67: 73–82. PubMed Abstract \| Publisher Full Text\n\nOrsini MG, Huang GJ, Kiyak HA, et al.: Methods to evaluate profile preferences for the anteroposterior position of the mandible. Am J Orthod Dentofacial Orthop. 2006; 130: 283–291. PubMed Abstract \| Publisher Full Text\n\nSingla R, Reddy H, Singla N: Esthetic Preferences of Orthodontists, general dentists, and Laypersons for Indian facial profiles: A cross-sectional study. Mendeley Data. 2023; V1. Publisher Full Text" }	[ { "id": "209431", "date": "16 Oct 2023", "name": "In Meei Tew", "expertise": [ "Reviewer Expertise Prosthodontics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a cross-sectional study on the comparison of esthetic preferences of orthodontists, general dentists, and laypersons for Indian facial profiles. It is generally well written, but there are some comments or suggestions for authors' kind consideration:\nAbstract:\nMethods:\nThere are a few sentences required modification for further clarification:\nA visual analog scale (VAS) along with a question about surgical correction opinion was given to 18 orthodontists, 18 general dentists, and 18 laypersons to score (1-5) from least to most attractive.\n\nSpearman’s rank correlation was computed to assess correlation, as well as ANOVA, followed by post hoc Tukey analysis to compare the mean scores, and Chi-square test to determine the opinion about surgical treatment.\nIntroduction:\nsuggest to remove first paragraph as the contents have been well covered in second paragraph\nStatistical data analysis:\nNeed a further clarification on “orthodontic education” in the second sentence.\n\nTable 1 to Table 3: Kindly place the * behind the value which is less than 0.05 in the Table.\n\nDiscussion:\nKindly include the study limitations and further recommendation at the last paragraph.\nConclusions:\nKindly provide a concise conclusion which match with the objective of the study\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12514", "date": "30 Sep 2024", "name": "Nishu Singla", "role": "Author Response", "response": "I have corrected the manuscript per In Meei Tew's suggestions from the Department of Restorative Dentistry, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia. I have made the following changes to the article \"Esthetic Preferences of Orthodontists, General Dentists, and Laypersons for Indian Facial Profiles: A Cross-sectional Study.\" Abstract: no change Introduction: Grammatical corrections done Methods: Rephrased the sentences as suggested by the reviewer. Statistical data analysis: Clarification on “orthodontic education” in the second sentence. Table 1 to Table 3: Placed the * behind the value, which is less than 0.05, in the tables. Discussion: The study limitations and recommendations are now included in the last paragraph. Conclusions: The conclusion is corrected according to the objectives." } ] }, { "id": "242357", "date": "20 Feb 2024", "name": "Dinesh Rokaya", "expertise": [ "Reviewer Expertise Prosthodontics", "Esthetic Dentistry", "Biomaterials" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study where the researchers compared the perceptions of a group of orthodontists, general dentists, and laypersons about the attractiveness of Indian facial profiles. Some Comments. There exist differences in facial aesthetics measurements in males and females. Please refer to the article (Shah P. et. al, 2022 [ref 1]). Considering the objective of this study, the total sample size is only 54 (18 subjects in each group). It would have been better if they had included more samples in each group. The authors need to mention how they calculate the sample size. Which formula or software they used? Was the questionnaire used in this study taken from other sources or self-made? Was the questionnaire validated? Please explain. Add the inclusion criteria of the subjects. Can this study be generalized? If this study is conducted in larger samples or different settings, will the results be the same or changed? Please discuss. Add limitations of this research.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "222335", "date": "03 Jul 2024", "name": "Pawankumar Tekale", "expertise": [ "Reviewer Expertise I am a researcher and clinician in orthodontics specialty" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall research is nice. This study would have given more valuable conclusive inputs if the sample size could have been 25-30 in each group. Furthermore, recent references need to be added. As only a couple of reference articles between 2020 to 2024 and 3 articles between 2010 to 2020. Please try to remove citations from the conclusion and reframe the conclusion in a single paragraph with 4-5 lines only so that researchers and clinicians will be able to line up the clinical implications.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-953
https://f1000research.com/articles/13-230/v1	27 Mar 24	{ "type": "Opinion Article", "title": "A research data management (RDM) community for ELIXIR", "authors": [ "Flora D'Anna", "Niclas Jareborg", "Mijke Jetten", "Minna Ahokas", "Pinar Alper", "Robert Andrews", "Korbinian Bösl", "Teresa D’Altri", "Daniel Faria", "Nazeefa Fatima", "Siiri Fuchs", "Clare Garrard", "Wei Gu", "Katharina F. Heil", "Yvonne Kallberg", "Flavio Licciulli", "Nils-Christian Lübke", "Ana M. P. Melo", "Ivan Mičetić", "Jorge Oliveira", "Anastasis Oulas", "Patricia M. Palagi", "Krzysztof Poterlowicz", "Xenia Perez-Sitja", "Patrick Ruch", "Susanna-Assunta Sansone", "Helena Schnitzer", "Celia van Gelder", "Thanasis Vergoulis", "Daniel Wibberg", "Ulrike Wittig", "Brane Leskošek", "Jiri Vondrasek", "Munazah Andrabi", "Minna Ahokas", "Pinar Alper", "Robert Andrews", "Korbinian Bösl", "Teresa D’Altri", "Daniel Faria", "Nazeefa Fatima", "Siiri Fuchs", "Clare Garrard", "Wei Gu", "Katharina F. Heil", "Yvonne Kallberg", "Flavio Licciulli", "Nils-Christian Lübke", "Ana M. P. Melo", "Ivan Mičetić", "Jorge Oliveira", "Anastasis Oulas", "Patricia M. Palagi", "Krzysztof Poterlowicz", "Xenia Perez-Sitja", "Patrick Ruch", "Susanna-Assunta Sansone", "Helena Schnitzer", "Celia van Gelder", "Thanasis Vergoulis", "Daniel Wibberg", "Ulrike Wittig", "Brane Leskošek", "Jiri Vondrasek" ], "abstract": "Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and launched various projects and initiatives to ensure good data management practices for scientific excellence. These projects have resulted in a rich set of tools and resources highly valuable for FAIR data management. However, these resources remain scattered across projects and ELIXIR structures, making their dissemination and application challenging. Therefore, it becomes imminent to coordinate these efforts for sustainable and harmonised RDM practices with dedicated forums for RDM professionals to exchange knowledge and share resources. The proposed ELIXIR RDM Community will bring together RDM experts to develop ELIXIR’s vision and coordinate its activities, taking advantage of the available assets. It aims to coordinate RDM best practices and illustrate how to use the existing ELIXIR RDM services. The Community will be built around three integral pillars, namely, a network of RDM professionals, RDM knowledge management and RDM training expertise and resources. It will also engage with external stakeholders to leverage benefits and provide a forum to RDM professionals for regular knowledge exchange, capacity building and development of harmonised RDM practices, keeping in line with the overall scope of the RDM Community. In the short term, the Community aims to build upon the existing resources and ensure that the content of these remain up to date and fit for purpose. In the long run, the Community will aim to strengthen the skills and knowledge of its RDM professionals to support the emerging needs of the scientific community. The Community will also devise an effective strategy to engage with other ELIXIR structures and international stakeholders to influence and align with developments and solutions in the RDM field.", "keywords": [ "Data management", "Data stewardship", "Data management plans", "FAIR principles", "community standards", "Data management training", "Research data life cycle", "Common best practices" ], "content": "Introduction\n\nIn the 2017 position paper on FAIR Data Management in the Life Sciences (Blomberg, 2017), ELIXIR emphasised Findable, Accessible, Interoperable and Reusable (FAIR) (Wilkinson et al., 2016) data management as a crucial part of good scientific practice and research excellence, which requires professional skills and adequate resources. ELIXIR’s mission is to implement standards-based, FAIR data stewardship within European life science projects and to help its users to comply with FAIR and Open Science principles via the ELIXIR Nodes that support the FAIR data management needs of national research projects.\n\nThe ELIXIR position paper on FAIR Data Management in the life sciences also states that “ELIXIR Nodes are the national implementation of a harmonised FAIR Data Management programme for the life science” (Blomberg, 2017), relying on the coordinated action of national Nodes to ensure harmonised data management practices. So far, initiatives to promote harmonisation of practices across Nodes have been conducted within the temporal limits of projects or within different ELIXIR structures (Nodes, Platforms, Communities, Focus Groups and the Staff Exchange Programme).\n\nSince research funders started to require data management plans (DMPs) and the implementation of FAIR and Open Science principles, several Nodes have invested in data stewardship (Carraro et al., 2022). A high return on investment of data stewardship has been identified for research in general (Mons, 2020), and managing data has been recognized as a matter of infrastructure, institutions, and economics, instead of simply an individual practice (Borgman & Bourne, 2021). Nevertheless, there is no consensus on the understanding of what a data steward actually does, the context in which they operate, and the position of the data steward within institutions (Jetten et al., 2021). ELIXIR Nodes have been involved in national initiatives aimed at defining the role and the competences of a data steward. For instance, the National Programme Open Sciences (NPOS) and ELIXIR Netherlands developed a competency framework for data stewards, published in the EBI Competency Hub (Scholtens et al., 2019). Although this framework has been adopted by various ELIXIR Nodes, a long-lasting context to discuss, harmonise and update data steward job profiles and competences is still missing.\n\nMembers from ELIXIR Nodes have been involved in RDM related activities carried out via Staff Exchange Programmes, Focus Groups (e.g. EOSC, RDA Activities, FAIR Training), Platforms, Communities (e.g. Plant Sciences) and projects. The ELIXIR Interoperability Platform, in particular, has also operated in the RDM space, focussing on the services and their use in interoperability stories. The Software Development Best Practices Working Group of the ELIXIR Tools Platform developed the Software Management Plan (SMP) template. ELIXIR-CONVERGE has created a strong network of data stewards and domain and training experts. Knowledge resources for RDM best practices, such as RDMkit and the Data Stewardship Wizard (DSW) (Pergl et al., 2019), have been built, enriched and integrated with ELIXIR registries and offer an excellent body of knowledge to apply FAIR data management to life sciences research. Moreover, training resources on RDM have been developed and made findable via the ELIXIR Training Portal TeSS. The FAIRplus project connected ELIXIR with industry partners by developing key resources, including the FAIR Cookbook (Rocca-Serra et al., 2022) to implement FAIR principles and tools to evaluate FAIRness of datasets. While these initiatives have built the foundations of strategic ambitions in data management, there is currently no mechanism in ELIXIR to sustain and strengthen them beyond the stipulated duration of the projects.\n\nIn this white paper, we explain how the proposed ELIXIR Research Data Management (RDM) Community can be of benefit to the broader ELIXIR landscape, including its Nodes, Platforms, Communities and ultimately scientists (end-users), with a coherent approach to data management. This proposal aligns tightly with the upcoming ELIXIR Scientific Programme 2024-2028, which adopts the outcomes of ELIXIR-CONVERGE, FAIRplus and other projects. We propose to further develop and strengthen the networks of data management experts from these two main projects, the training and capacity building efforts, and data management knowledge for the ELIXIR community and beyond. Essential to the ELIXIR RDM Community is the strengthening and consolidation of these and other relevant ELIXIR data management resources. These resources include tools, best practices and expertise within the ELIXIR Platforms and Communities, and the collaboratively developed ELIXIR training and capacity building resources aimed at the broader community for reuse and adoption. We propose that creating an ELIXIR RDM Community as a unified long-term framework for RDM professionals across Europe to come together and exchange knowledge is the key to the implementation of harmonised data management practices across Nodes.\n\nAlthough FAIR management often refers to data, the same principles apply to other research objects (Jiménez et al., 2017; Hong et al., 2022; Garcia et al., 2020), such as software and training materials. Thus, when referring to data, in this white paper, we also refer to other research objects. Since data management and data stewardship are newly evolving expertise areas, and there are no universally accepted definitions yet, in this white paper we will use both terms interchangeably. Our working definition is the one put forward by the Dutch Techcentre for Life Sciences (DTL/ELIXIR Netherlands): “Data stewardship is responsible planning and executing of all actions on digital data before, during and after a research project, with the aim of optimising the usability, reusability and reproducibility of the resulting data”.\n\n\nLandscape of RDM in ELIXIR\n\nAs a consequence of the implementation of DMPs, FAIR and open data policies at the European, national and institutional levels, a portfolio of RDM tools and services in each ELIXIR Node has become inevitable. In fact, based on a survey in March 2022 (Carraro et al., 2022), at least 17 Nodes offer services related to data management and stewardship. 75% of these Nodes predict that the RDM services they offer are likely to be sustainable over time, indicating a clear ambition to continue providing these services. The type of services offered vary greatly from guidelines and consultancy to IT infrastructures and training. RDM services are requested and used by scientific and technical staff (e.g. researchers, core facilities, data stewards, consortia for projects etc.) from universities, research institutions and industry.\n\nBased on the same survey, with answers from 11 Nodes, it seems that, on average, a Node itself has 2.9 FTE (full-time equivalents) as data stewards, 2.4 FTE as IT technical staff and 0.3 FTE as infrastructure managers (Figure 1). Despite a considerable variation in the range of the number of FTEs among the Nodes (ranging from 1 to >5 FTE), this data illustrates the diversity of national environments in which ELIXIR RDM services operate. However, it does not seem straightforward to estimate the current number of FTE providing RDM-related services in each Node. The difficulty is mainly due to the lack of a consensus on what RDM services are and which organisation in the Node is providing the service, and the fact that RDM services are often provided as in-kind contributions by professionals in research, such as bioinformaticians, IT experts, software developers or librarians.\n\nData derived from the online surveys and interviews performed in the context of ELIXIR-CONVERGE (Carraro et al., 2022), investigating how services of data management and stewardship are delivered and financially supported in ELIXIR Nodes.\n\nELIXIR-CONVERGE brought together RDM professionals from 23 Nodes, creating the Data Management (DM) Network, which currently counts 149 members, of which 37 are coordinators as representatives for each Node (1-2 per Node). The DM Network shares experiences and knowledge about implementing RDM governance, policy, technical infrastructures, business models, etc. in the different Nodes. This information has largely been published in RDMkit as tool assemblies for RDM and on the national resources pages so that it can be used as examples by other Nodes. The DM Network organised focus groups around several RDM topics, where experts discussed and generated guidelines for best practices (e.g. how to find data repositories, how to document data) shared via RDMkit. In a survey designed to evaluate the role of the DM Network among the ELIXIR Nodes involved in ELIXIR-CONVERGE (Jareborg, 2023), 33 participants from 19 Nodes answered that the Network was clearly beneficial to their work and that keeping the network alive was important to them (Figure 2). The main benefits perceived by the participants are knowledge exchange, information about RDM initiatives within ELIXIR, and finding experts for collaborations and training.\n\nSimilarly, in FAIRplus, almost 100 data professionals from academia (including ELIXIR Nodes), pharmaceutical and information service companies were brought together to share their knowledge on FAIR implementations in the FAIR Cookbook. Collaboration between public and private sectors is essential in and around FAIR RDM matters, and such networks should be cultivated and sustained.\n\nThe RDMkit, FAIRCookbook and the Data Stewardship Wizard (DSW) are currently the three main resources of ELIXIR guidance and best practices for RDM.\n\nRDMkit\n\nLaunched in 2021, RDMkit (the Research Data Management toolkit for life sciences) is a knowledge resource reflecting the evolving best practices and guidelines in RDM. RDMkit has been implemented as part of ELIXIR-CONVERGE to help with standardising life science data management across Europe. Professionals in RDM and researchers from ELIXIR Nodes, Communities and the DM Network use RDMkit to provide scoped guidelines that place the relevant life science RDM tools and resources in the context of research. RDMkit guidelines identify RDM issues, provide plausible solutions, recommend relevant tools for RDM activity, and illustrate how these tools have been combined to enable data life cycle management in various domains. RDMkit has integrations with other ELIXIR RDM resources, such as the FAIR Cookbook, the DSW and the ELIXIR registries (FAIRsharing, bio.tools, TeSS). The knowledge contained in RDMkit has been recognised by the European Commission and recommended as a useful resource in the Horizon Europe Programme Guide and the ERC Guideline. Moreover, ELIXIR Belgium, Norway, Sweden, and UK have added RDMkit as a Node service.\n\nFAIR Cookbook\n\nLaunched in 2020, and created by researchers and data management professionals in academia, pharma and information service industries, the FAIR Cookbook covers the key steps in a FAIRification journey, `levels and indicators of FAIRness, a maturity model, the technologies, tools and standards available, as well as the skills required and challenges presented. All with the aim of improving data FAIRness. The recipes are citable, via PIDs, and authors are credited, via their ORCID and the CreDiT ontology. The FAIR Cookbook is cross-referenced with other ELIXIR resources, such as the RDMkit, FAIRsharing, bio.tools, DSW (work in progress) and external resources such as the Pistoia Alliance’s FAIR Toolkit. As described (Rocca-Serra et al., 2022), the FAIR Cookbook is uniquely positioned not only to serve as practical guidance to improve everyday tasks but is also contributing to a curriculum on FAIR data and informing discussions on the necessary changes to deliver FAIR within organisations. FAIR Cookbook is one of the key outcomes of the FAIRplus project, which connected ELIXIR with industry partners to address hurdles to FAIR implementation by developing practical guidelines, processes, and tools to make data FAIR. The UK, Luxembourg, Swiss and Spain Nodes have now included the FAIR Cookbook in their service delivery plan.\n\nData Stewardship Wizard (DSW)\n\nDSW has been developed by a collaborative effort between ELIXIR Czech Republic and ELIXIR Netherlands, combining knowledge about data stewardship and a cutting-edge questionnaire using dynamic web forms developed by ELIXIR Czech Republic (Pergl et al., 2019). DSW’s primary goal is to turn data management planning from an obligation into a benefit for a project by easing the process. Several experts in data stewardship have contributed to the latest versions of the question and answer flows in the system. Questions in DSW can use or link to external resources to provide answers. A prime example of this is the suggestion of databases and standards from FAIRsharing, based on responses to certain questions. RDMkit is frequently linked from DSW and the inverse link from RDMkit to the relevant section of DSW is created automatically; links are also being created with recipes in the FAIR Cookbook. DSW is used and recommended by several Nodes and funders. Specifically, ELIXIR Sweden and Norway have adopted DSW, as well as institutions in the Czech Republic, Netherlands, Spain, Denmark, France and Portugal. Funders such as EU Commission (Horizon EU programme guide), ZonMw (Netherlands), UB-BOTT (Norway), TAČR/OP JAK (Czech Republic) also recommend DSW.\n\nRDM professionals, training experts and trainers from ELIXIR and beyond identified gaps in the Nodes’ RDM training programmes and defined priority topics (DMP, Data Stewardship, FAIR/metadata and Reproducibility) (Cardona et al., 2021) for training development. Collaborative work from all the ELIXIR Nodes during ELIXIR-CONVERGE resulted in an extensive Data Management/Data Stewardship (DM/DS) course portfolio (Cardona et al., 2021)1 which aligns with the Nodes’ RDM training strategies. The portfolio includes both generic DM/DS resources and materials, as well as specific materials related to the priority topics mentioned above, and it also includes training materials for specific domains (e.g. the Plant Demonstrator). The course portfolio is available in TeSS, in which training materials are tagged with RDM terms to increase their findability, and links to relevant training materials were included in RDMkit. FAIRsharing has recently launched its FAIRsharing Educational component, in collaboration with EOSC and RDA data champions, across all disciplines. In collaboration with the ELIXIR Training Platform, the learning paths methodology has been applied to RDM for data stewards and researchers (e.g. with the Plants Sciences and the System Biology Communities), and work is ongoing to extend the ELIXIR-GOBLET Train-the-Trainer programme to tackle the challenges that exist in teaching RDM. As a result of these ELIXIR-CONVERGE activities, training expertise and capacity in RDM has been significantly increased in ELIXIR.\n\nNumerous Nodes are involved in or drive national initiatives aimed at capacity building, professionalisation of data stewardship and alignment of RDM practices across universities and institutions. Examples of national RDM initiatives in which ELIXIR Nodes are involved are listed in Table 1.\n\n\n\n• Knowledge Hub: a Research Data Management Community of practice.\n\n• Making collaborative content that supports researchers in making their data open and FAIR.\n\n\n\n• Recommendation to the National Open Science Cloud initiative in the EOSC governance to include RDM.\n\n• Provide technical and policy support for onboarding of service providers into EOSC, including data management.\n\n\n\n• Working group for professionalisation of RDM experts.\n\n\n\n• Ecosystem to share and open research data.\n\n• Data management clusters.\n\n• Thematic reference centre for Biology and Health.\n\n\n\n• Systematic management of scientific and research data.\n\n• Consortia of stakeholders to provide science-driven data services to research communities.\n\n\n\n• Recommendations on Open Science practices (including data management) for the national research performing and research funding organisations in Greece.\n\n\n\n• Open Science Cafe to increase awareness about RDM and Open Science.\n\n\n\n• Platform for data professionals (beyond Netherlands) to share experiences.\n\n• FAIR data stewardship training and capacity building program for life sciences and health research (incl. ZonMw funded projects).\n\n\n\n• Network of data management experts across research infrastructures.\n\n• Capacity building, identification and adoption of best practices.\n\n\n\n• Capacity building program in data management for researchers and institutions.\n\n• Offering introductory and advanced courses in DMPs.\n\n\n\n• Capacity building, network of DM/DS experts, best practices.\n\n• DM/DMP tools and services.\n\n\n\n• Supporting the RDM needs of the initiative.\n\n\n\n• Extending the existing nationwide network of data managers to include data stewards.\n\n• Developing a Certificate of Advanced Studies (CAS) in data management and data stewardship.\n\n\n\n• RDM capacity building and professionalising data stewardship.\n\n• Producing and delivering training in FAIR data stewardship using ELIXIR United Kingdom knowledge.\n\n• Working group for professionalisation of RDM experts.\n\n\nChallenges for RDM professionals in ELIXIR\n\nInstitutions and universities part of ELIXIR and beyond recognise the importance of professional data stewards for RDM support for researchers in all stages of the research life cycle. RDM involves a variety of professionals, including research scientists, IT specialists, policy makers, legal staff, libraries, funding agencies and publishers. This leads to a lack of consensus and clarity on the responsibilities, knowledge and skills required for RDM professionals. This confusion stifles effective definition of the profile of a data steward across ELIXIR Nodes. Profiles of data stewards are often developed locally in member organisations of ELIXIR and vary greatly both within and between these organisations. Moreover, some RDM professionals are centralised within Nodes or national centres, whereas others are embedded into member universities and institutes. This poses the question of how these professionals can be brought together into an effective community that recognises and supports these differences.\n\nA formalised ELIXIR RDM Community will provide the forum necessary to overcome this lack of consensus and initiate the harmonisation efforts around professionalisation of data stewardship across Nodes. The members of the RDM Community could focus on sharing experiences and practices about how RDM services are implemented in each Node, taking into account, the interactions with member Node, universities and institutions. This could be considered as a continuation of the work started by the DM Network. This exchange of experiences and practices will help to shape career pathways across the different ELIXIR member states and can function as examples for the sector.\n\nThe report of the Dutch National Programme Open Science (NPOS) and ELIXIR Netherlands have provided an excellent framework and a comprehensive list of competencies, skills and qualifications defining and classifying the role of the data stewards (Jetten et al., 2021), as has the Danish National Forum for Research Data Management (Wildgaard et al., 2020). The RDM Community aims to generalise these, and similar guidelines generated by other Nodes, in order to promote adoption of these profiles within the organisations hosting ELIXIR Nodes and within the respective national environments. The RDM Community will undertake this effort in alignment with current insights of the RDA Professionalising Data Stewardship Interest Group as well as the EOSC Task Force Data stewardship, curricula and career paths.\n\nELIXIR’s activities impacting the management of research data and software in line with the FAIR (Findable, Accessible, Interoperable Reusable) principles are scattered across projects, Platforms, Communities and Focus Groups. The multitude of ELIXIR’s tools, information resources, registries, databases, training courses and material suitable for the implementation of the FAIR principles in data management (FAIRification journey) are valuable and often recommended by RDM professionals to peers and researchers. However, an overview of how to use the available RDM resources is missing, whether in an integrated fashion (as an ecosystem) or as individual modules. This makes their dissemination, use and application more challenging. Currently, a user of the ELIXIR services (e.g. researchers, RDM professionals, trainers, funders) has to find and explore each resource from its dedicated webpage, and understand when and how each guideline or component relates to another and how they could be used together during the data life cycle, to make data, software or other outputs FAIR. Although this problem has been partially tackled in the ELIXIR Guidelines section, it is by no means a comprehensive representation of how ELIXIR resources could be used as an ecosystem for good RDM and FAIRification throughout a research project.\n\nTherefore, building an ELIXIR RDM Community where its members, which are involved in several ELIXIR initiatives related to RDM, FAIR implementation and assessment, can share their knowledge is essential for the delineation of an overview of the ELIXIR RDM ecosystem. The Community could coordinate and advise about RDM initiatives, by highlighting overlaps, identifying synergy and reducing possible duplication of efforts. The RDM Community could act as a single point of reference for RDM knowledge and expertise under the ELIXIR branding.\n\nRDM professionals from different Nodes might have different expertise in specific aspects of research data management (e.g. writing DMPs, managing sensitive data, brokering, assessment and evaluation of FAIRness of digital object etc.), due to differences in the contexts in which Nodes operate. Although this diversity in expertise might be a challenge for the harmonisation effort, it also presents an opportunity for peers to learn from each other and complement their knowledge. However, RDM professionals face the difficulty of finding an effective framework that recognises these differences and supports the sharing of knowledge, particularly in small Nodes that do not receive national fundings for such initiatives. Until now, the process of sharing expertise and learning from peers about RDM has only happened during time-limited projects, such as ELIXIR-CONVERGE (e.g. best practices working group, data brokering task group), FAIRplus (e.g. Squads and Fellows) Staff Exchange programme, BioHackathon projects and other RDM related initiatives.\n\nThe RDM Community could be a structured and long-term framework where RDM professionals can learn new skills and strengthen their expertise by sharing their experience with peers on several practical RDM topics, which affect their day-to-day work. The shared knowledge should then be translated into tangible outputs, such as content for the ELIXIR RDM ecosystem and other materials beneficial for the ELIXIR organisation and the research community at large. These activities would help keep the existing ELIXIR RDM resources relevant and up to date. The RDM Community would be a unique opportunity for its members to share expertise, increase their confidence and provide better and more harmonised services for researchers.\n\nDuring ELIXIR-CONVERGE and FAIRplus, extensive RDM course portfolios have been built, the RDM training expertise in ELIXIR Nodes has increased significantly and a strong RDM trainer network has been formed. All activities have been executed in close collaboration with the ELIXIR Training Platform and benefited from its resources. However, the work is far from complete, and course materials are in continuous need of updating. There is no clear portfolio owner or a proper framework for embedding RDM training activities and the RDM trainer network in the ELIXIR structure. The main RDM training related actions going forward are: (i) gathering the RDM courses in the portfolio into learning paths for specific audiences, thus shaping the ELIXIR RDM curriculum, (ii) increasing findability and reusability of the developed courses and modules by optimising annotation and linking in TeSS, RDMkit and FAIR Cookbook, (iii) encouraging (re) use of the RDM materials in ELIXIR Nodes, and (iv) increasing RDM training capacity in Nodes by finalising and launching the RDM Train the Trainer programme.\n\nAs is already the case for many other ELIXIR Communities (Galaxy, Single Cell Omics, Plants etc.), the RDM Community needs to establish a strong formal presence in the ELIXIR Training Platform. Thus, the consolidation and further expansion of RDM training activities in ELIXIR, according to and implementing the Training Platform best practices, will be safeguarded.\n\n\nELIXIR RDM Community\n\nThe expected members of the Community are life science RDM professionals in academia and industry in ELIXIR and beyond. It is meant to be inclusive to anyone that has a professional interest in RDM for the life sciences. It shall be open to not only data stewards, but also similar roles like data manager, data architect or data engineer, as well as to interested experts from relevant infrastructure providers (data repositories, computing services and resources etc.) and experts in specific aspects of RDM (IT experts, librarians, policy officers, regulators, software developers, data scientist/analyst, bioinformaticians and trainers). The Community should include discipline or subject specific data stewards. Members should have an interest and an active role in implementing, supporting and promoting good RDM practices to make research data, software and other types of output compliant with Open Science and the FAIR principles.\n\nExamples of activities that the intended Community members engage in are not only direct support to researchers, but also the development and implementation of RDM policies in organisations, as well as the establishment of tools, services, practices and training resources to enable proper data management.\n\nResearch data management is a broad discipline that, to different extents, affects the activities of most of the existing structures of the ELIXIR organisation. Therefore, it is necessary to outline the role and scope of an ELIXIR RDM Community given the established and ongoing activities in ELIXIR. The overall purpose of the proposed RDM Community is to bring together experts in RDM to develop ELIXIR’s vision, and coordinate its activities, within the domain of research data management according to the FAIR principles. Peers in the Community will share knowledge, experience and practices in order to increase their confidence, efficiency, and deliver more harmonised RDM services for researchers across Nodes.\n\nThe responsibilities that are in scope for the Community can be categorised into three main interacting pillars: (i) the network of RDM professionals across all Nodes (and beyond), (ii) the management of RDM knowledge and know-how in the form of the content of the ELIXIR RDM ecosystem, and (iii) the management of the RDM training resources and expertise. As RDM is high on the agenda in the global research community, an important fourth component that goes across the three pillars is the engagement with other external stakeholders that are active in this area. Bringing these four elements under the roof of one ELIXIR RDM Community would create a focal point to harmonise these activities across Nodes, Platforms and Communities, as well as with key external stakeholders outside ELIXIR (Figure 3).\n\nThe network of RDM professionals\n\nIn the ELIXIR-CONVERGE and FAIRplus projects, networks of life science RDM professionals have been established that include named Node representatives from each ELIXIR Node, as well as other RDM staff in those Nodes. Peers in these networks have shared knowledge and generated a tangible output as guidelines for RDM best practices that mainly reside in RDMkit and FAIR Cookbook. The recognition of RDMkit and the FAIR Cookbook as a valuable source for guidance by the Horizon Europe programme guide and the Innovative Medicines Initiative, and the positive feedback given by the DM Network about its utility has highlighted the need to establish a home for this group of professionals to continue these activities. Providing a long-term framework for RDM professionals across Europe to come together and exchange knowledge is at the heart of an ELIXIR RDM Community. One prioritised aspect of this group is to work on facilitating RDM capacity building in all ELIXIR Nodes, so that the Nodes can provide state-of-the-art RDM services for their local communities while aligning practices across countries and using ELIXIR resources.\n\nManagement of RDM knowledge\n\nThe comprehensive bodies of RDM knowledge that have been gathered by ELIXIR-CONVERGE, FAIRplus and earlier activities are important and valuable resources to guide RDM professionals and researchers in their everyday practice. This pool of knowledge collated by the community for the community, mainly resides in three different knowledge resources with differing scopes and granularity: RDMkit, DSW, and the FAIR Cookbook. Additional guidance on how to use FAIRsharing for RDM has been collected in FAIRsharing Educational. However, the content in these resources is not a static product but needs constant maintenance and expansion over time to remain relevant. It shall be the responsibility of the RDM Community to provide the maintenance and overall coordination of the content across this RDM ecosystem for FAIR data, as well as disseminating it among Nodes and institutions in the different countries. The activities of the editorial boards of RDMkit and FAIR Cookbook would fit well within the remit of the Community, which perhaps could bring these resources closer together, for example under a single board, with individual steering groups. The content that the RDM Community shall capture and manage in these resources should comprise those topics that affect the RDM and FAIRness aspects of research outputs, such as data and software.\n\nManagement of RDM training resources and expertise\n\nIn ELIXIR-CONVERGE, an extensive portfolio of training resources has been built, as a basis for the ELIXIR DM/DS Curriculum. However, continuous work is needed to make them (re) usable and keep them up to date. Moreover, during ELIXIR-CONVERGE, a strong RDM trainers network was formed, establishing solid RDM training expertise within the Nodes. This emerging network raised great interest in the Nodes, showing their willingness to work together on developing training materials, sharing their knowledge, and establishing best practices and standards for RDM training.\n\nThe consolidation and expansion of this RDM trainers network shall be in the remit of the RDM Community. Also, there is still a lack of trainers and training, and a collaboration between the RDM Community trainers and the ELIXIR-GOBLET Train-the-Trainer programme would be beneficial towards forecasting any pedagogical challenges that will arise when the training is rolled out. There is a clear need for dissemination of RDM know-how, practices and resources and a demand for RDM training material and courses, for researchers, trainers and RDM professionals. This can be solved by the RDM Community in close collaboration with the Nodes and the ELIXIR Training Platform. It will be the responsibility of the RDM Community, and the network of RDM trainers within, to coordinate the activities to fulfil these needs. This will enable the upskilling of RDM trainers and scaling up RDM training capacity in the Nodes, while bridging to RDM professionals outside ELIXIR as well.\n\nExternal stakeholders\n\nApart from the three main pillars above, the responsibility to coordinate the interactions with the increasing number of external international stakeholders in this area should be in scope for the RDM Community. This would be relevant for the activities of all three main pillars. ELIXIR has an RDA Activities Focus Group with the purpose of enabling ELIXIR members to leverage the benefits of the Research Data Alliance and to ensure that the life sciences point of view is represented in the RDA community. ELIXIR has, through participation in projects, collaborations and Platform activities, engaged with various other stakeholders that are working on solving RDM issues, such as EOSC through the ELIXIR EOSC Focus Group, ESFRIs, international organisations, and national infrastructures outside ELIXIR member states. The FAIRsharing Educational is an example of RDM and FAIR-related information material created under the RDA FAIRsharing WG, and with seed funds from EOSC. It should be in the remit of the RDM Community to be responsible for how RDM aspects in these stakeholder activities can be leveraged for the Community, as well as how future developments should be influenced.\n\nTo set the boundary against other possible activities and ELIXIR services, the following should be considered to be out of scope for an ELIXIR RDM Community: the technical development and provisioning of services in the ELIXIR RDM ecosystem, providing RDM helpdesk services for researchers and consortia, delivering RDM training programmes, and curation of data already deposited in data repositories and knowledge bases. The technical service provisioning of RDMkit, DSW and the FAIR Cookbook shall lie with other parties within ELIXIR. However, the content management contributions for these resources must be done in close collaboration with the technical service providers, to ensure that they are fit for purpose.\n\nThe RDM Community will not provide any RDM helpdesk support services. These must reside in the various Nodes and other local organisations, though the activities in the RDM Community will help these organisations to establish such services for their local needs. Likewise, it is not in the remit of the Community to deliver training programmes. The development of training materials and teaching needs considerable time and effort and would be delivered through future (ELIXIR) projects and by the Nodes themselves, leveraging the training resources and expertise of the Community. The Community should, at least initially, focus on promoting FAIR at source approaches to data management and facilitating the researchers’ data journeys. Thus, curation of data already deposited in Deposition Databases and knowledge-based resources would be out of scope.\n\n\nAlignment with ELIXIR structures\n\nData Platform\n\nIn collaboration with the ELIXIR Data Platform the Community will develop data management best practice guidelines to facilitate the flow of FAIR data from life science research to Core Data Resources (CDR), ELIXIR Deposition Databases (EDD) and ELIXIR Community data resources. It includes establishing guidelines and maturity models for data brokering together with EDDs. Based on the best practice guidelines, the Data Platform and the RDM Community will work together to promote the harmonisation of database formats and standards. The Community will also benefit from the liaison of the Data Platform and the ELIXIR Biocuration Focus Group to exchange knowledge on best practices for data curation and quality assurance in databases and repositories.\n\nInteroperability Platform\n\nThe ELIXIR Interoperability Platform develops, maintains and promotes interoperability services to help people and machines to discover, access, integrate and analyse biological data. In particular, the platform has also operated in the RDM space, focusing on the services and their use in interoperability stories, and plans on continuing to build the FAIR-enabling portfolio of products, processes and practices. The RDM Community will collaborate with the Platform to incorporate interoperability best practices and guidelines aimed at researchers, RDM professionals and infrastructure providers, into the RDM ecosystem. The Platform has activities aimed at alignment of FAIR service architecture across all ELIXIR Communities as well as the Data Platform and ELIXIR projects. The results of those activities that are related to RDM will be included in the ELIXIR RDM ecosystem, whose content coordination falls under the scope of the RDM Community. While incentivizing interoperability practices in RDM, the Community will promote key services offered by the Interoperability platform such as the ELIXIR Recommended Interoperability Resources (RIRs) (e.g. OLS, FAIRsharing, RightField, ISA, Identifiers.org, etc.), and the Platform initiatives (e.g. Bioschemas, RO-Crate, RightField, etc.). The RDM Community will contribute to the harmonisation of interoperability standards across domains and data resources and work together with the Platform for wider adoption.\n\nTraining Platform\n\nThe RDM trainers network is an integral part of the ELIXIR Training community. As such the RDM Community benefits from and contributes to many ELIXIR Training Platform activities. The RDM Community will continue to expose the information about its training events and materials in TeSS. During ELIXIR-CONVERGE, standardised keywords for RDM training courses and material in TeSS were established to improve the visibility and findability; this work will be further improved. RDM trainers also actively contributed to the work of the FAIR Training Focus Group, both on creating content for courses on FAIR data, as well as on the FAIR Training Handbook. This handbook is currently being developed to train instructors on how to make training materials FAIR, and this should be the basis for the FAIRification of RDM training materials. Furthermore, the RDM trainers will continue using the assessment strategy (Gurwitz et al., 2020) implemented by the Training Platform, which measures the quality and impact of ELIXIR training events in a coordinated and consistent data collection approach. Finally, RDM Train the Trainer activities will be aligned with the ELIXIR-GOBLET Train-the-Trainer programme. New and expert trainers will continue to build their training skills by following the pedagogical best practices taught in the ELIXIR-GOBLET Train-the-Trainer programme (Morgan et al., 2017) courses. They will also benefit from the materials and expertise developed in ELIXIR-CONVERGE.\n\nTools Platform\n\nThe RDM Community will align with the Tools Platform to promote the use of available registries and tools for research data management by describing it in best practices, and establish cross-fertilization actions to exchange best practices for research data management and research software management, e.g. making FAIR software and workflows. The RDM Community will also be in a position to convey user needs and feedback to the Platform and tool providers. The RDM Community and the Tools Platform could work together on guidelines for writing Data and Software Management Plans (DMP/SMP), particularly for European funders, for projects involving both data and software development. The aim could be to provide researchers with guidelines for an integrated approach to manage both data and software in the same project.\n\nCompute Platform\n\nThe RDM Community will collaborate with the Compute Platform to write and disseminate best practices to make FAIR software, FAIR data analysis workflows, and secure and trustworthy computing environments. The RDM Community will ensure that computational services about authentication and authorisation, storage and data transfer, and cloud and computing resources are included in the RDM ecosystem and that their use is described from the RDM perspective.\n\nThe existing ELIXIR Communities are key interaction partners that deal with real-world RDM problems and challenges for their respective domains. They offer a possibility for knowledge exchange and capacity building that goes both ways. The RDM Community can use the challenges of the different Communities to help develop and improve RDM guidelines, solutions, standards, learning paths and training for the different domains, as well as to learn from, and leverage, developments made in the Communities themselves to improve on general RDM principles and solutions so that they stay fit for purpose over time. This in turn will help to drive standards harmonisation across communities, whenever possible.\n\nSeveral ELIXIR Communities (e.g. Plants, Marine Metagenomics, Microbial Biotechnology, Toxicology, etc.) have already used RDMkit, DSW and FAIR Cookbook for dissemination of domain specific standards and RDM best practices. Domain pages in the RDMkit include many of the existing ELIXIR Communities, as well as descriptions of tool assemblies that serve as inspiration for real-world solutions to RDM challenges for many life science domains. One such example is the RDMkit Marine metagenomics domain page by the Marine Metagenomics Community that outlines RDM considerations and standards, as well as pointing to the tool assembly page for the Norwegian marine metagenomics tool assembly. The ELIXIR Communities have also engaged with RDM training experts in ELIXIR-CONVERGE to create learning paths targeted to the RDM training needs in the respective scientific domains. One such example is the ELIXIR Plant Sciences Community that has established and enhanced learning paths for the Community with the input of stakeholders outside of ELIXIR and ELIXIR-CONVERGE. The general aspects of this work also feed back to the RDM Community as a framework that can be reused in other domains. We foresee that individuals in the different ELIXIR Communities with an interest in RDM will also be members of the RDM Community, so that good RDM becomes embedded in the activities of the ELIXIR Communities.\n\nTwo key Focus Groups in ELIXIR with a remit to interact with external stakeholders and that have a prominent focus on research data management are the RDA Activities Focus Group and the EOSC Focus Group. The RDM Community will provide a forum for the bidirectional dissemination of the work done in these two Focus Groups. This activity will improve the exchange and uptake of RDM developments made in these external organisations to ensure that ELIXIR aligns with, and makes most use of, state of the art RDM best practice and know-how. This also has the potential to increase the engagement of RDM professionals in these Focus Groups, which will further strengthen the interactions with these important external stakeholders. As part of this, it offers the opportunity to influence even further the RDM developments in the activities of RDA and EOSC. The ELIXIR EOSC Strategy 2022 (Tedds et al., 2022) by the EOSC Focus Group states that “ELIXIR is a partner for EOSC - in implementation and application”. The RDM Community shall strive to take on this aspiration for ELIXIR in the area of research data management, acting as a communication hub for standards, interoperability and data flow related questions between ELIXIR and EOSC. There is also a clear connection to the FAIR Training Focus Group, with which the Community collaborates via the RDM trainers around best practices for FAIRification of digital objects. Several of the other ELIXIR Focus Groups also deal with different RDM aspects. The Community will reach out to these Focus Groups to address research data management questions for their particular domains, e.g. data readiness with the Machine Learning (AI) Focus Group and standards for particular life science domains, such as for the Cancer Data Focus Group.\n\n\nObjectives of the RDM Community\n\nShort-term and longer-term objectives of the RDM Community are listed in Table 2 below. Short-term objectives focus on sustaining and consolidating the outputs of previous initiatives and projects into the unified structure of the RDM Community. Longer-term objectives, instead, aim to tackle the challenges that the Nodes are facing and to work towards a coordinated action of Nodes to ensure a harmonised FAIR Data Management programme for life science.\n\n\nConclusions\n\nRDM has become the focus point for many funders and institutions that are part of ELIXIR and for the ELIXIR organisation itself. RDM professionals in ELIXIR have demonstrated their RDM expertise by bringing their knowledge, experience, know-how and skills to successful projects that aimed to support RDM. Therefore, we suggest that creating the ELIXIR RDM Community, defined by the scope and the objectives described in this paper, will be the way to start tackling RDM challenges for the life sciences and to harmonise the approach to FAIR data management across ELIXIR Nodes and beyond.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe would like to thank the many other members of ELIXIR Nodes that have contributed with useful discussions and input.\n\n\nReferences\n\nBlomberg N; ELIXIR Consortium: ELIXIR position paper on FAIR data management in the life sciences [version 1; not peer reviewed]. F1000Res. 2017; 6(ELIXIR): 1857. (document). Publisher Full Text\n\nBorgman C, Bourne P: Why it takes a village to manage and share data. arXive e-prints. 2021. Publisher Full Text\n\nCardona A, van Gelder C , Palagi PM, et al.: ELIXIR-CONVERGE D2.1 Report on the identified training needs and a timeline for training courses. Zenodo. 2021. Publisher Full Text\n\nCarraro M, Tosatto S, Jareborg N, et al.: ELIXIR-CONVERGE D1.2 Survey of business models. Zenodo. 2022. Publisher Full Text\n\nChue Hong NP, Katz DS, Barker M, et al.: FAIR Principles for Research Software (FAIR4RS Principles) (1.0). Zenodo. 2022. Publisher Full Text\n\nGarcia L, Batut B, Burke ML, et al.: Ten simple rules for making training materials FAIR. PLoS Comput. Biol. 2020; 16(5): e1007854. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGurwitz KT, Singh GP, Bellis LJ, et al.: A framework to assess the quality and impact of bioinformatics training across ELIXIR. PLoS Comput. Biol. 2020; 16(7): e1007976. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJareborg N: ELIXIR-CONVERGE - Survey of benefits of an Data Management expert network (1.0.0). [Data set]. Zenodo. 2023. Publisher Full Text\n\nJetten M, Grootveld M, Mordant A, et al.: Professionalising data stewardship in the Netherlands. Competences, training and education. Dutch roadmap towards national implementation of FAIR data stewardship (1.1). Zenodo. 2021. Publisher Full Text\n\nJiménez RC, Kuzak M, Alhamdoosh M, et al.: Four simple recommendations to encourage best practices in research software [version 1; peer review: 3 approved]. F1000Res. 2017; 6: 876. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMons B: Invest 5% of research funds in ensuring data are reusable. Nature. 2020; 578: 491. PubMed Abstract \| Publisher Full Text\n\nMorgan SL, Palagi PM, Fernandes PL, et al.: The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training [version 1; peer review: 2 approved]. F1000Res. 2017; 6: 1557. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPergl R, Hooft R, Suchánek M, et al.: “Data Stewardship Wizard”: A Tool Bringing Together Researchers, Data Stewards, and Data Experts around Data Management Planning. Data Sci. J. 2019; 18. Publisher Full Text\n\nRocca-Serra P, Gu W, Ioannidis V, et al.: The FAIR Cookbook - the essential resource for and by FAIR doers (1.0). Zenodo. 2022. (in press). Publisher Full Text\n\nScholtens S, Jetten M, Böhmer J, et al.: Final report: Towards FAIR data steward as profession for the lifesciences. Report of a ZonMw funded collaborative approach built on existing expertise. Zenodo. 2019. Publisher Full Text\n\nTedds J, Capella-Gutierrez S, Clark-Casey J, et al.: ELIXIR EOSC Strategy 2022. Zenodo. 2022. Publisher Full Text\n\nWildgaard L, Vlachos E, Nondal L, et al.: National Coordination of Data Steward Education in Denmark: Final report to the National Forum for Research Data Management (DM Forum) (Version 1). Zenodo. 2020. Publisher Full Text\n\nWilkinson M, Dumontier M, Aalbersberg I, 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\n\nFootnotes\n\n1 Updated numbers (February 2020 - December 2022): 18 Nodes contributed to 119 training events with 2849 participants." }	[ { "id": "281723", "date": "03 Jun 2024", "name": "Jeff Christiansen", "expertise": [ "Reviewer Expertise Life Science and Bioinformatics Digital Infrastructure to support 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\nELIXIR is a European network of life science data related infrastructures, that is structured around the concepts of Nodes (collection of research institutes within member countries), Platforms (centred around Data, Tools, Compute, Interoperability and Training infrastructures), and Communities (groups of experts across the ELIXIR Nodes that represent a scientific or technological theme, and drive the development of standards, services, and training in and across ELIXIR).\nIn any open science research endeavour, good research data management is central to conducting best practice research, and enabling research data to be made Findable, Accessible, Interoperable and Reusable (FAIR) enables its re-use where possible and appropriate. In recognition of the central importance of Research Data Management (RDM) to research practice, over the past decade there has been considerable investments by ELIXIR and its Nodes into RDM, through various time-boxed projects and initiatives, and these have resulted in the development many tools and resources to assist. There was however (surprisingly) until recently, no dedicated and ongoing channel for RDM professionals across ELIXIR to exchange knowledge and share resources.\nDriven by a need for better coordination, and the generation of sustainable and harmonised RDM practices across ELIXIR, a Research Data Management (RDM) Community within ELIXIR (see https://elixir-europe.org/communities/research-data-management) was recently formed.\nThe white paper by D’Anna and co-authors (from 17 ELIXIR Nodes), describes the broad landscape of RDM across ELIXIR (including previous joint ELIXIR efforts and projects); RDM tools and guidelines produced by ELIXIR to date; examples of RDM initiatives across various ELIXIR nodes; challenges facing the many RDM professionals across ELIXIR; the objectives and scope of the ELIXIR RDM Community; and how the RDM Community is intended to align with other ELIXIR components (Platforms, other Communities and Focus Groups).\nForming the ELIXIR RDM Community represents a very sensible approach to address the ongoing RDM coordination and uplift challenges across the ELIXIR network, as it leverages previous RDM related outputs and many aspects of the existing operational structures of ELIXIR to underpin its operations. It will also essentially to bring together a community of RDM experts to further develop ELIXIR’s vision and coordinate its RDM activities, initially leveraging existing assets, and importantly, to illustrate to researchers and others how to practically use the various ELIXIR RDM resources.\nOverall, the paper is a clear and informative review. It is well written, and logically presented, covering various facets, all of which are relevant for a white paper of this type.\nMajor comment:\nThe External Stakeholders paragraph briefly describes how the RDM Community and its members may interact with RDM groups beyond ELIXIR through various projects and initiatives. The activities and outputs of this group will however be of great interest outside Europe as improving RDM is a global challenge. Will all outputs/products/guides etc produced by the RDM Community be made available for adoption and adaptation by others outside the ELIXIR network? If so, how will this occur? The manuscript would benefit from some further commentary on the approaches the RDM Community will utilise to enable global shareability/findability of resources they will produce or curate. With respect to this global angle, it would also be useful to understand the membership rules for the ELIXIR RDM Community - i.e. can external stakeholders can join the RDM Community or is membership restricted to those associated ELIXIR Nodes?\nThe authors describe the ELIXIR Data Management Network https://elixir-europe.org/about-us/how-funded/eu-projects/converge/wp1/dm-network. How does/will the DM network and RDM Community interact? Will the RDM Community supersede the DM network?\nMinor comments:\nTense - the ELIXIR RDM Community appears to already exist (https://elixir-europe.org/communities/research-data-management) but the future tense is often used in the manuscript (e.g. in Abstract (p2), the ‘proposed’ ELIXIR RDM Community ‘will’ bring together; Introduction (p4) the ‘proposed’ ELIXIR RDM Community etc), which is confusing to the reader. If the RDM Community has been established, I would request that the tense of the manuscript is changed to the present tense to reflect this situation.\nFigure 1 Legend - It’s not clear what the colours of the points represent. I assume different ELIXIR Nodes, but can this please be defined in the Figure legend?\nFigure 2 Legend. A self contained legend would be beneficial, to explain that the results are from the 2023 survey of DM Network members.\nP7 “RDMkit has been implemented” > “RDMkit was implemented’\nP7 - “ELIXIR Belgium, Norway, Sweden, and UK have added RDMkit as a Node service”. This needs more explanation. What is a “Node service”? This should be defined.\nP7 - “FAIR Cookbook is one of the key outcomes of the FAIRplus project” - link/ref missing for FAIRplus project.\nP7 - It would be useful to note that the RDMkit, FAIRCookbook and DSW are all ELIXIR recommended interoperability resources https://elixir-europe.org/news/resource-announcement-2023\nP7 - “RDM professionals, training experts and trainers from ELIXIR and beyond” > “In 2021, RDM professionals, training experts and trainers from ELIXIR and beyond”\nP9 - “Institutions and universities part of ELIXIR” > “Institutions and universities that are part of ELIXIR”\nP10. “Therefore, building an ELIXIR RDM Community where its members, which are involved” > “Therefore, building an ELIXIR RDM Community where its members, who are involved”\nP10. “particularly in small Nodes that do not receive national fundings for such initiatives” > “particularly in small Nodes that do not receive national funding for such initiatives”.\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": "12471", "date": "30 Sep 2024", "name": "Munazah Andrabi", "role": "Author Response", "response": "We thank the reviewer for the insightful comments. Please, find below our responses to each comments and the references to the revised manuscript. Major comment: The External Stakeholders paragraph briefly describes how the RDM Community and its members may interact with RDM groups beyond ELIXIR through various projects and initiatives. The activities and outputs of this group will however be of great interest outside Europe as improving RDM is a global challenge. Will all outputs/products/guides etc produced by the RDM Community be made available for adoption and adaptation by others outside the ELIXIR network? If so, how will this occur? The manuscript would benefit from some further commentary on the approaches the RDM Community will utilise to enable global shareability/findability of resources they will produce or curate. With respect to this global angle, it would also be useful to understand the membership rules for the ELIXIR RDM Community - i.e. can external stakeholders can join the RDM Community or is membership restricted to those associated ELIXIR Nodes? Response Dissemination of outputs to a global audience: All outcomes from the RDM Community will be open and accessible to all and published in open resource repositories like Zenodo. We will also be actively disseminating content and expertise via international conferences like the ECCB. In addition, various ELIXIR nodes are part of international projects like BY-COVID, BioIndustry 4.0 and EOSC Focus groups. Outside the EU ELIXIR actively engages with the NIH in USA and Australian BioCommons. Our resources like RDMkit and FAIRCookbook are already in use by these institutions. The following paragraph has been added to the paper, in the “scope of the community - external stakeholders” section: “Engagement with these external global stakeholders both through the various fora for knowledge exchange that they provide, as well as through the possibility for RDM professionals to join and contribute to the Community, will offer the possibility for dissemination and use of the open RDM resources developed and maintained by ELIXIR.” Membership rules: Anyone interested can register via the link (community page). The following sentence with the relevant link has been added to the manuscript, under the “members identity” paragraph: “Any life science RDM professional that wants to join the Community can do so by registering for membership on the RDM Community web page. Association to ELIXIR is not required for membership.” Comment The authors describe the ELIXIR Data Management Network https://elixir-europe.org/about-us/how-funded/eu-projects/converge/wp1/dm-network. How does/will the DM network and RDM Community interact? Will the RDM Community supersede the DM network? Response The DM Network was created and active during ELIXIR-CONVERGE as a time-bound project activity. The RDM Community is a continuation of, and supersedes, the DM Network as a formal structure ELIXIR. The following sentences have been added in the “Scope of the community - The network of RDM professionals” paragraph to clarify that the DM Network was a network during the project, and that the RDM Community supersedes the DM Network. “The ELIXIR RDM Community thus supersedes the less formal competence networks established in previous projects.” Minor comments: Tense - the ELIXIR RDM Community appears to already exist (https://elixir-europe.org/communities/research-data-management) but the future tense is often used in the manuscript (e.g. in Abstract (p2), the ‘proposed’ ELIXIR RDM Community ‘will’ bring together; Introduction (p4) the ‘proposed’ ELIXIR RDM Community etc), which is confusing to the reader. If the RDM Community has been established, I would request that the tense of the manuscript is changed to the present tense to reflect this situation. Response The tense of the text wherever applicable has been changed to reflect the existence of the RDM Community instead of referring to future establishment. Comment Figure 1 Legend - It’s not clear what the colours of the points represent. I assume different ELIXIR Nodes, but can this please be defined in the Figure legend? Response Yes, colours represent different ELIXIR Nodes. The following sentence has been added to the figure legend to clarify this. “Colours represent different ELIXIR Nodes.” Comment Figure 2 Legend. A self contained legend would be beneficial, to explain that the results are from the 2023 survey of DM Network members. Response The following clarifying sentence has been added to the beginning of the figure legend: “Survey of benefits of a Data Management expert network during the ELIXIR-CONVERGE project.” Comment P7 “RDMkit has been implemented” > “RDMkit was implemented’ Response Changed as suggested. Comment P7 - “ELIXIR Belgium, Norway, Sweden, and UK have added RDMkit as a Node service”. This needs more explanation. What is a “Node service”? This should be defined. The following link to the official definition of Node Service has been included in the manuscript Node Service Selection Process. We noticed that Sweden was incorrectly listed as one of the Nodes that included RDMkit as Node service, but it was an oversight. We have now corrected the text in the manuscript by deleting Sweden from the list. Comment P7 - “FAIR Cookbook is one of the key outcomes of the FAIRplus project” - link/ref missing for FAIRplus project. Response Hyperlinks are provided the first time a resource is mentioned in the document. To maintain readability and avoid redundancy, we do not include hyperlinks each time the resource is referenced again later in the text. FAIRplus and FAIR Cookbook are hyperlinked already in the Introduction. Comment P7 - It would be useful to note that the RDMkit, FAIRCookbook and DSW are all ELIXIR recommended interoperability resources https://elixir-europe.org/news/resource-announcement-2023 Response It has been added to the “ELIXIR guidelines and best practices for the RDM” section. Comment P7 - “RDM professionals, training experts and trainers from ELIXIR and beyond” > “In 2021, RDM professionals, training experts and trainers from ELIXIR and beyond” Response Changed as suggested Comment P9 - “Institutions and universities part of ELIXIR” > “Institutions and universities that are part of ELIXIR” Response Changed as suggested. Comment P10. “Therefore, building an ELIXIR RDM Community where its members, which are involved” > “Therefore, building an ELIXIR RDM Community where its members, who are involved” Response Changed as suggested. Comment P10. “particularly in small Nodes that do not receive national fundings for such initiatives” > “particularly in small Nodes that do not receive national funding for such initiatives”. Response Changed as suggested." } ] }, { "id": "281726", "date": "06 Jun 2024", "name": "Sara El Gebali", "expertise": [ "Reviewer Expertise Research Data Management", "Curation", "Semantic web" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 “A Research Data Management (RDM) Community for ELIXIR” effectively highlights the pressing need for a coordinated approach to RDM within the ELIXIR infrastructure. By proposing the formation of an ELIXIR RDM Community, the article addresses the current inefficiencies caused by scattered resources and aims to align practices with the FAIR (Findable, Accessible, Interoperable, Reusable) and Open Science principles. The vision for this community is well-articulated and focuses on three main pillars: networking, knowledge management, and training. Minor comments:\nWhile the article lays out a clear vision for the ELIXIR RDM Community, it would benefit from more detailed implementation strategies which include potential challenges and mitigation strategies. The interest in making outputs globally available is mentioned but not detailed. The section “Table 2. Objectives of the RDM Community” could include plans for connecting with the wider global community. Efforts in collating available training/RDM material or translating them into other languages like French or Spanish would benefit a wider population, such as those in Africa and Latin America. Engagement with External Stakeholders: This section could be moved closer to the description of the network of RDM professionals. The manuscript lists examples of national RDM initiatives involving ELIXIR Nodes but does not explain the nature of their involvement. Highlighting how ELIXIR contributes to these efforts would strengthen the link between ELIXIR nodes and other national initiatives, showcasing the added value of ELIXIR’s participation Members Benefits: Including a section on member benefits would make the ELIXIR RDM Community more attractive to potential members. This could detail professional development opportunities, access to exclusive resources, and the ability to influence RDM practices on a broader scale. To make the community more inviting and keep potential members interested, the manuscript should introduce the expected members earlier on. When readers know right away that they are welcome, they are more likely to stay engaged. Perhaps consider moving this text earlier in the article.\n\n“The expected members of the Community are life science RDM professionals in academia and industry in ELIXIR and beyond. It is meant to be inclusive to anyone that has a professional interest in RDM for the life sciences. It shall be open to not only data stewards, but also similar roles like data manager, data architect or data engineer, as well as to interested experts from relevant infrastructure providers (data repositories, computing services and resources etc.) “\n\nFigure Legends:\n\n•\n\nFigure 1: The colors of the points need to be clearly defined to ensure readers understand what each point represents.\n\n•\n\nFigure 3: The description should be expanded to clearly outline the role of the RDM Community as a focal point for RDM practices within ELIXIR. This will enhance understanding of its central role in coordinating and harmonizing RDM activities.\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": "12472", "date": "30 Sep 2024", "name": "Munazah Andrabi", "role": "Author Response", "response": "We thank the reviewer for the insightful comments. Please, find below our responses to each comment and the references to the revised manuscript. Major comments: While the article lays out a clear vision for the ELIXIR RDM Community, it would benefit from more detailed implementation strategies which include potential challenges and mitigation strategies. Response We appreciate your suggestion; however, we have decided not to include this information directly in the text. Our focus in this white paper is on the current status quo and the ELIXIR Community roadmap. The implementation will follow ELIXIR and community best practices, primarily through a bottom-up approach, with concrete initiatives aimed at identifying potential challenges and solutions. As we work towards building an active and engaged community, activities will be community-driven, with ongoing assessments of challenges. If necessary, mitigation strategies will be developed as work progresses in each area. The interest in making outputs globally available is mentioned but not detailed. The section “Table 2. Objectives of the RDM Community” could include plans for connecting with the wider global community. Efforts in collating available training/RDM material or translating them into other languages like French or Spanish would benefit a wider population, such as those in Africa and Latin America. Response We appreciate your suggestion; however, we have decided not to include this information directly in the text. While the interest in making outputs globally available is noted, it is important to clarify our current scope and priorities. Our primary focus at this stage is to establish a strong foundational network within our existing collaborations. We are coordinating the existing RDM community, working closely with other ELIXIR communities and platforms such as the Training Platform, TeSS group, and Interoperability Platforms, which manage and co-develop resources within the RDM ecosystem. We also collaborate with the Focus Groups in Research Data Alliance(RDA), which is our point of contact for global outreach and synergies. Although broader outreach is within our objectives, translating materials into other languages like French or Spanish is not, as such activities can be done better professionally at each Node level. Our current efforts are concentrated on enhancing collaboration and resource sharing within our established network. Engagement with External Stakeholders: This section could be moved closer to the description of the network of RDM professionals. Response While we appreciate the merit of restructuring the text by moving this section, we have decided to keep the External Stakeholders section in its current place in the texts as we think it fits best as part of the description of the scope of the Community. The manuscript lists examples of national RDM initiatives involving ELIXIR Nodes but does not explain the nature of their involvement. Highlighting how ELIXIR contributes to these efforts would strengthen the link between ELIXIR nodes and other national initiatives, showcasing the added value of ELIXIR’s participation Response The type of contribution to national initiatives by Node members has been now highlighted with the addition of the following text under the “Examples of RDM initiatives in ELIXIR Nodes” paragraph: The individuals driving, organising, or delivering these initiatives are part of ELIXIR Nodes. They learn from members of other Nodes about RDM skills, training, and resources, and then contribute to their national initiatives by organising events, managing national communities, providing training, adopting and sharing resources within their institutions, and taking on other leading and practical roles. Members Benefits: Including a section on member benefits would make the ELIXIR RDM Community more attractive to potential members. This could detail professional development opportunities, access to exclusive resources, and the ability to influence RDM practices on a broader scale. Response The paragraph on benefits for members of the RDM Community is now included in the paper. The following text has been added to the “Members identity” paragraph: Members of the ELIXIR RDM Community experience a multitude of benefits that enhance their professional capabilities and collective impact. By engaging with peers across Nodes, members gain valuable insights, share best practices, and exchange knowledge, thereby boosting their confidence and efficiency in delivering harmonised research data management (RDM) services to researchers. This collaborative environment not only strengthens internal cohesion but also serves as a central hub for aligning activities across Nodes, Platforms, and external stakeholders. As a result, members play a pivotal role in harmonising RDM practices, fostering collaboration, and driving innovation within and beyond the ELIXIR network. To make the community more inviting and keep potential members interested, the manuscript should introduce the expected members earlier on. When readers know right away that they are welcome, they are more likely to stay engaged. Perhaps consider moving this text earlier in the article. Response The following text has been added to the Introduction section of the manuscript: “The RDM Community is meant to be inclusive to anyone that has a professional interest in RDM for the life sciences in academia and industry both in and outside of ELIXIR.” Comment Figure Legends: Figure 1: The colors of the points need to be clearly defined to ensure readers understand what each point represents. Response The colours represent different ELIXIR Nodes. The following sentence has been added to the figure legend to clarify this. “Colours represent different ELIXIR Nodes.” Comment Figure 3: The description should be expanded to clearly outline the role of the RDM Community as a focal point for RDM practices within ELIXIR. This will enhance understanding of its central role in coordinating and harmonising RDM activities. Response The following sentence has been added to the Figure legend: The RDM Community will engage and coordinate with ELIXIR Nodes, Platforms, Communities, Focus Groups and external stakeholders to promote and drive harmonisation of RDM activities within ELIXIR and beyond." } ] } ]	1	https://f1000research.com/articles/13-230
https://f1000research.com/articles/11-1066/v1	20 Sep 22	{ "type": "Case Report", "title": "Case Report: Pathological fracture in a Li-Fraumeni osteosarcoma patient: \"Capasquelet'' femoral reconstruction and tumor vascular analysis with endomucin immunofluorescence multiplexing", "authors": [ "Guillaume Tran", "Jerome Amiaud", "Alexis Combal", "Franck Duteille", "Françoise Redini", "Franck Verrecchia", "Vincent Crenn", "Guillaume Tran", "Jerome Amiaud", "Alexis Combal", "Franck Duteille", "Françoise Redini", "Franck Verrecchia" ], "abstract": "We describe the case report of an Osteosarcoma patient, with a Li-Fraumeni Syndrome, presenting with a pathological femoral fracture. The patient was treated with a multidisciplinary approach associating neoadjuvant and adjuvant chemotherapy with excisional surgery. The femoral reconstruction consisted of a ``Capasquelet'' reconstruction combining an induced membrane and a vascularized fibula allograft allowing a good functional result with an early weight-bearing. We managed to complete our histological analysis in this patient, in order to evaluate the tumor vascularization. Indeed, using the syngeneic osteosarcoma MOS-J mouse model, we highlighted previously that CD31+/\\ensuremath{\\alpha }-SMA+ vessels may be indicators of vasculature normalization and therefore may be used as specific markers of a good therapeutic response. Thus, we search for its interest in this specific case as preliminary work. The aim was to assess the feasibility and technical validity of the vascularization analysis of a human osteosarcoma tumor specimen. Therefore, we propose an immunohistochemistry methodology with multiplexed immunofluorescence to assess the vascularization as a promising marker in human osteosarcoma tissue.", "keywords": [ "Osteosarcoma", "intercalary reconstruction", "vascularized fibula", "immunohistochemistry", "vascular analysis", "Endomucin" ], "content": "Introduction\n\nOsteosarcoma care remains a challenge in various ways, such as determining chemotherapy response on biopsy, but as well with challenging reconstruction, especially in intercalary bone tumor resections. We propose in this case report to put highlight on these two points, describing an original technique of massive bone loss reconstruction, and focusing on innovative immunohistochemestry multiplexing techniques in order to better assess vascularization of osteosarcoma as a possible prognosis factor.\n\nMassive diaphyseal bone defects are a reconstruction challenge, and several surgical methods have been described1–3 (vascularized fibula, autograft, bone transport, massive endoprosthesis, etc.). There is no gold-standard, and indications are a matter of debate, with variable results. We here described an innovative technique for managing a critical femoral bone defect of 24 cm using the Capasquelet procedure.4 This original two-stage technique combine the allograft technique with a centromedullary inlaid vascularized fibula (i.e., “Capanna technique”)5 and the induced membrane technique (i.e., “Masquelet technique”).6 The combination of these, called the “Capasquelet” technique get several advantages: the biological receptacle with the induced membrane prevents graft resorption and has also an osteoinductive role7; it also decreases infection risks, and avoids a long one-stage surgery. This case report describes this hybrid surgical technique on a massive femur defect. We assessed the bone healing, the delay to complete weight-bearing, and a functional score analysis in this patient.\n\nOn the other hand, predicting the chemotherapy response of osteosarcoma patients, with treatment such as high-dose methotrexate or doxorubicin cocktail, remains a challenge.8–10 Moreover, the prognostic value of induced necrosis analysis is questionable, and is only available after neo-adjuvant treatment is done on resection piece. New markers of prognostic response are urgently needed, focusing on tumor microenvironment.11 As we showed in our preclinical mouse model, using the syngeneic osteosarcoma MOS-J mouse model, vascular analysis of tumor depicted with immunohistochemestry fluorescent multiplexing might play a role as being a potential prognosis factor of tumor response.10,12 Our results may have suggested that the presence of CD31+/α-SMA+ vessels could be considered to be indicators of mature and functional vasculature able to deliver drugs adequately, and may be used as specific markers of a good therapeutic response. Nonetheless, no human tissue analysis using this method has been made until now. And before proposing a quantitative analysis, we propose in this case report to describe the feasibility of this method and a preliminary observation of the vascular heterogeneity analysis with Endomucin+, CD31+, and α-SMA+ immunohistochemistry.\n\n\nCase presentation\n\nThe 28-year-old patient presented to the ER department with a femur fracture occurring while playing football. The lytic aspect of the fracture was considered suspect, a CT-scan, an MRI and an open surgical biopsy were performed confirming the pathological fracture (Figure 1). Osteosarcoma primitive tumor was suspected in this case on biopsy samples, and as its sister already had been treated for a proximal tibia Osteosarcoma, a Li-Fraumeni Syndrom was diagnosed due to its family anteriority13 (Table 1).\n\nA: AP X-Ray view with osteolytic lesions; B: MRI T2sagittal view showing tumor invasion.\n\n* neo-adjuvant chemotherapy combined three doxorubicin-ifosfamide-cisplatin (API) and two doxorubicin-ifosfamide (AI) courses.\n\nFirst stage\n\nThe patient underwent initial wide margin (R0) oncologic resection, with a 20 cm diaphysis resection, at this time the femoral fracture has healed during neo-adjuvant CT (Table 2). The femur was prepared with a clean cut transversally. A cement spacer using high-viscosity Heraeus Palacos® R + G cement (Hanau, Germany) was modelled; it fills the bone loss as fully as possible. Due to pathological fracture and limb length discrepancy, the spacer was made 2 cm longer than the resection (22 cm). We also preferred to oversize it somewhat in width as the soft tissue coverage was not an issue, as it increases reconstruction space and facilitate induced membrane closure for the second stage. The spacer was covering the bone–host interfaces as recommended in the Masquelet technique.6 It was enhanced on a locked intramedullary nailing, positioned back and forth (Figure 2). Patient was considered good responder in pathology analysis with 1.5% residual viable cells (Table 3).\n\nInterstage planification\n\nThe femoral allograft dimension was determined to be as close as possible of the patient femur; the diaphyseal shaft width must allow the fibula to slide into it. We used a cryopreserved allograft, in compliance with the criteria of the French Agency of Biomedicine, from the Nantes Multi-Tissue Bank. The delay between the two stages was of 22 weeks due to adjuvant chemotherapy.\n\nSecond stage\n\nThe length aimed (24 cm) and the rotational axes were determined before the spacer was removed. The vascularized fibula graft required microsurgical technique for harvesting and vascular anastomoses. The fibula graft was 28 cm in our case, and it was four centimeters longer than the planned bone allograft length. Graft harvesting was done from the contralateral limb by a second surgical team with microsurgical expertise in order to decrease the surgery duration. The harvesting was performed under a tourniquet, ensuring at least 8 cm14 of the distal fibula was spare in order to limit malleolar instability risk. A lateral surgical approach was used to raise the osseous graft. The bone was vascularized by an artery from the peroneal artery that entered the middle-third of the fibula. The section must include this area. After identification of the artery and its origin from the tibio-fibular trunk, the vessel was dissected.15\n\nThe allograft was warmed for one hour in a hot physiological serum bath and then cut with an oscillating saw with transverse cut similar to the bone defect aimed. One specific team was devoted to set the hybrid graft: the allograft was filled with the fibula after a progressive reaming, care was taken to not hurt the vessels of the fibula, a bone window was performed on the allograft for allowing its mobilization and sliding in the allograft. 2 cm of fibula were planned for overlapping the bone interfaces. Then, the hybrid graft was stabilized and compressed with a 4.5mm locking compression plate, taking care to orientate the fibula vessels towards anastomosis area. Lastly, the microsurgical anastomosis was performed at the terminal branches of the profunda femoris artery (Figure 2).\n\nPostoperative management\n\nEarly mobilization and progressive weight-bearing were allowed postoperatively. Strictly limited weight-bearing was prescribed for the first six weeks, with progressive full weight-bearing depending on the patient’s pain and condition (Table 3). Full weight bearing was obtained at twelve weeks, with a functional quality of life of 75% on the EQ 5D score. Adjuvant chemotherapy was then performed with two doxorubicin-ifosfamide and two cisplatin-ifosfamide courses.\n\nLong term follow up\n\nAt last follow-up (38 months following tumor resection), no local complication nor local recurrence occurred, with full weight bearing on his lower limb, allowing walking without cane. Nonetheless, despite beeing a good responder with R0 resection, the patient relapsed with pulmonary metastasis at 13 months follow up, needing surgical excision. Early pulmonary recurrence make us introduce a complementary targeted therapy with cabozantinib and chemotherapy ifosfamide and VP16.\n\nOn bone biopsy we first suspected a bone undifferentiated pleomorphic sarcoma (UPS), due to the low level of osteoïd matrix on the sample; the diagnosis of Li-Fraumeni Syndrom was also made due to oncological family anteriorities. Nonetheless, an osteosarcoma chemotherapy protocol was performed with an API-AI protocol. On bone tumor resection piece, osteosarcoma pathology diagnosis was made due to visualization of many osteoïd matrix on various places among the tumor. The unusual pejorative oncological evolution, despite an initial good pathology response and good margins was unusual in this case, thus, we performed a complementary histologic analysis.\n\nOur aim was to assess the vascularization of patient osteosarcoma on biopsy prior to any chemotherapy treatment, and also to assess technical feasibility of our previous methodology (described on preclinical mouse model) on multiplexing analysis.12 Indeed, on a preclinical osteosarcoma MOS-J syngenic mouse model we identified two different kinds of vessels on confocal multiplexing analysis: CD31+/α-SMA+ elements and CD31+/Endomucin+elements. The CD31+/α-SMA+ elements exhibited a structured and straight architecture, with a sizeable diameter, and they resembled mature vessels. On the other hand, the CD31+/Endomucin+ elements were much more sinusoidal, with a more serpiginous and unorganized structure. They also had a smaller diameter and they look like immature sinusoidal vessels, which might be linked to tumor neo-angiogenesis (Figure 3).\n\nA: CD31+/α-SMA+ elements. B: CD31+/Endomucin+ elements. The images are Z-stack projections at 63× magnification, the scale bars =20 μm. DAPI: nuclear staining (from Crenn et al.12).\n\nImmunohistochemestry tissue processing\n\nThe patient biopsy was collected surgically under complete anesthesia through a direct open approach, as soon as the pathological fracture was suspected. Samples were immediately fixed in 4% buffered formalin for 24 hours. The sample was then decalcified in 4.13% EDTA, 0.2% paraformaldehyde, in 1× pH 7,4 PBS buffer for 10 to 15 days at 50°C in the KOS microwave tissue processor (Milestone, Michigan, USA). It was finaly dehydrated through graded ethanol baths, cleared in 2-butanol and embedded in paraffin. Serial 5-μm-thick sections were cut from each sample and stained for H&E and Masson trichrome. Other sections were immunostained for α-SMA, Endomucin, and CD31 markers.\n\nThree-color immunofluorescence histochemistry\n\nSections were deparaffinized, subjected to 20 h antigen retrieval in Tris-EDTA buffer (1 mM Tris, 0.5 mM EDTA, pH 9.0) at 60°C, and blocked with 2% normal donkey serum and 1% BSA in 1× Tris-buffered saline with 0.05% Tween 20 pH 7.4 to reduce unspecific binding. Sections were first immunostained with rabbit to CD31 (1:40, Abcam, ab28364) antibody for an hour at room temperature. After three washes in 1×TBS Tween 0.05% pH 7.4, sections were then incubated for an hour with biotinylated donkey anti-rabbit (1:200; Jackson ImmunoResearch 711-065-152), followed with Alexa Fluor 488-conjugated streptavidin (1:200; Jackson ImmunoResearch 016-540-084) another hour. To avoid non specific binding of both second primary rabbit antibody and secondary donkey anti-rabbit antibody, sections were then blocked with 5% normal rabbit serum in 1× TBS Tween 0.05% pH 7.4 for 30 min at room temperature followed by a blocking step with donkey anti-rabbit Fab fragments (1:10; Jackson ImmunoResearch 711-007-003) in 1× TBS Tween 0.05% pH 7.4 overnight at 4°C.\n\nThe next day, after three washes in 1× TBS Tween 0.05% pH 7.4, sections were then incubated with rabbit to Endomucin (1:100; Thermo Fisher PA5-21395), and mouse to α-SMA (1:1000; R&D Biotechne, MAB1420) antibodies for an hour at room temperature. After three washes in 1× TBS Tween 0.05% pH 7.4, the following secondary antibodies were applied for another hour: Alexa Fluor 594-conjugated donkey anti-rabbit (1:200; Jackson ImmunoResearch 711-585-152), and Alexa Fluor 647-conjugated donkey anti-mouse (1:200; Jackson ImmunoResearch 715-605-150). Finally, nuclei were counterstained with DAPI (1:1000; ThermoFisher Scientific, D1306) and coverslipped with Prolong Gold Antifade reagent (ThermoFisher Scientific, P36930).\n\nAcquisition and histomorphometry\n\nConfocal images were obtained by using a Nikon AI N-SIM confocal microscope and subsequently treated by smoothing and noise reduction of each channels, following by a Z-projection treatment on ImageJ software.16\n\nAll histomorphometric analysis were conducted on scans of the immunostained sections. Acquisitions of sections 4-7 were made with a NanoZoomer Slide Scanner (Hamamatsu, Japan), then pictures were saved using the NDP viewer software (Hamamatsu, version 2.2.6) at ×5 and export at ×10 using tiff format and analysed with ImageJ software. Each of the chromogenics immunostained sections were individually analyzed on 3 specific region of interest (ROI): one was defined by a representative 0.5-mm thick ROI which contained the tumors tissue along the bone; the other was a full representative picture of the core of the tumor; the last one was defined by a representative 0.5-mm thick ROI, that was contained the tumoral growth front. All analysis was carried out on each of the four levels of all samples. Briefly, pictures were subjected to color deconvolution using [H DAB] vector, thresholded, and unspecific noise was reduced. The results were shown as the mean value for each compartment of the number of positive elements per square millimeter.\n\nFor the triple-immunostaining sections (section 3), analysis was achieved using two levels that was considered, according results of ones that had been obtained on the chromogenics immunostained sections, as enough to give consistent values. Quantification of CD31+/α-SMA+ (mature vessels), and CD31+/Endomucin+ (sinusoid vessels) were realized using the virtual microscope (NDP viewer) at a selected magnification of ×20 on a representative field of 0.366 mm2. Double-positive vessels were counted in the same manner as up described in the different compartment by selecting the two fluorochromes channels corresponding of the two markers of interest. Results were shown as the mean value of each level of each sample of double positive elements per square millimeter.\n\nHE and Masson trichrome staining in the patient biopsy lesion\n\nImmunohistochemistry analysis was performed on the biopsy lesion with Masson’s trichrome staining (Figure 4), and showed a highly cellular malignant tumoral tissue, with a lack of osteoid matrix. We also observed some vessel-like structures.\n\nConfocal analysis of CD31+, α-SMA+ and Endomucin+ and costaining in the patient biopsy lesion\n\nImmunohistochemistry analysis on the biopsy lesion (Figure 5) showed CD31+ elements and α-SMA+ elements which looked like vascular mature structures. On the other hand, tumor cells seem to express endomucin with a diffuse staining along a rare expression of endothelial endomucin.\n\nAt 40× magnification, and two areas in Z-stack projections at 63× magnification. DAPI: nuclear staining.\n\nCo-staining of CD31+/endomucin vessels seemed to show smaller vascular structures diameter-wise, unfortunately we could not distinguish any elements of architecture other than size and neither localization part of the tumor site as the biopsy was realized without targeting any specific areas of the tumor.\n\n\nDiscussion\n\nThe Capasquelet technique result on this patient are promising, with bone healing being achieved within a short delay (12 weeks after the second stage), therefore allowing an early weight-bearing. We obtained a short delay for radiological bone healing with radiological follow up. The bone healing delay in our case (7 months) and in previous publication4 seems to be in the low range of an isolated Capanna technique with a 6-12 months delay or a Masquelet technique, which obtains complete bone union in 4–18 months, usually on less massive tibia defects.6,17 Despite the oncological disease evolution of the patient, the capasquelet surgery outcome was satisfactory, with early full weight-bearing, good function, and neither revisions nor complications.\n\nA larger cohort, and a longer follow-up is needed to confirm these interesting results, especially in a limb length discrepancy case, for sequential restoration of femur length in pathological fractures. With our method, the osteoinductive action played by the induced membrane may exert a positive impact on the graft bone healing, with fast fibula union and allograft, early full weight-bearing, and a satisfactory functional score.\n\nHowever, this two-stage technique got some drawbacks, the fibula harvest might results in morbidity,18 and it requires microsurgical expertise and access to a bone bank facility. The operating times involved in the two stages must also be noted, compared to a simpler technique.\n\nThe pejorative oncological evolution of the patient, despite an initial good pathology response (1.5% residual viable cells) and R0 margins was unusual, despite the controversial potential pejorative roles of the pathological fracture19,20 and the Li-Fraumeni Syndrome.21 In this context, it seems relevant to find new prognostic markers, to better adapt adjuvant chemotherapy in osteosarcoma patients, especially focusing on tumor microenvironment.11 The complementary histologic analysis on bone biopsy in this patient was performed aiming to explore vascularization with original stainings. Previous preclinical report investigated the implication of Endomucin expression in endothelial cells in a mouse model.12 We have shown that low expression in endothelial cells associated with both CD31 and α-SMA high expression could be associated as a better response to doxorubicin chemotherapy.\n\nWe obtained interpretable multiplexing analysis focusing on the human bone biopsy of our patient, validating the IHC methodological process. We identified CD31+ and α-SMA+ elements which looked like vascular mature structures, as well as thinner endomucin+ and CD31+, as in our preclinical mouse model.12\n\nConcerning endomucin, cells seem to express endomucin with a diffuse staining along a rare expression of endothelial endomucin. Interestingly, endomucin seems to be also expressed in tumoral cells when it comes to human tumors, opposite to our previous mouse model. Other reports show endomucin expressed in HUVECs cells and related a role of endomucin in the vascular function.22 A recent report on digestives carcinomas23 highlight a link between survival in stomach adenocarinoma and EMCN gene, with high expression on gene datasets correlated with poorer overall survival and disease-free survival. However, our case report focused on vascular expression of Endomucin and α-SMA in a mesenchymal bone cancer and did not explore precisely the expression of endomucin in osteosarcoma tumor cells themselves. Further investigation with quantitative analysis including mass spectrometry to segregate endothelial cells and tumor cells might be needed.24\n\nTo our knowledge, it is the first description of endomucin expression via immunofluorescence staining in human osteosarcoma tumor, its high expression might be a pejorative prognosis factor as suggested in other oncological disease.23 Nonetheless, further works are needed to understand its relevance in an osteosarcoma prognosis context, as literature shown that endomucin could be highly expressed among cancerous cells, as well as in other human tissues (proteinatlas.org) with various expressions. Other experiments focusing on endomucin expression after decalcification process are also mandatory as it is well known that decalcification, and method of decalcification have an impact on antigen retrieving.25,26\n\nIn our pre-clinical model of long bone osteosarcoma, endomucin expression seems not to be affected by administration of doxorubicin.12 We could not find any clear evidence of differentiated expression of endomucin after the treatment, but model of good response seems to show a different ratio of immature/mature vessels with maturity of the vasculature associated with good response to chemotherapy.12 In this patient case, moderate to high intensity staining of endomucin among cancerous cell cause us to hypothesize whether its expression is related to the patient’s early metastatic relapse despite histologic good response. This hypothesis needs further exploration with simple techniques, such as tissue micro array, and survival cohort studies.\n\n\nConclusions\n\nThis case report of a Li-Fraumeni osteosarcoma patient illustrates two innovative specialized approaches, on one hand an original surgical reconstruction technique, with the Capasquelet reconstruction, allowing a good functional results and early weight-bearing in an intercalary large defect tumor resection. In the other hand, it shows promising data focusing on vascular tumor analysis with multiplexing immunofluorescent technique on tumor biopsy, aiming to better understand why patients with good tumor response will nonetheless still relapse. The Capasquelet technique needs larger cohort and longer follow-up to better asses its place in the therapeutic arsenal. Considering the immunofluorescent multiplexing analysis, the technique seems feasible and it needs to be analyzed on a larger human cohort in order to assess quantitatively if the CD31+/α-SMA+, the CD31+/endomucin+ co-labelling, or Endomucin alone might be considered as potentials predictive factor of recurrence or survival in osteosarcoma.\n\n\nPublication information\n\nConceptualization, V.C.; formal analysis, G.T. and J.A.; investigation, G.T. and J.A.; data curation, G.T., J.A. F.D. and A.C.; writing—original draft preparation, G.T., J.A. and V.C.; writing—review and editing, G.T., J.A., A.C., F.D., F.R., F.V. and V.C.; supervision, V.C.; All authors have read and agreed to the published version of the manuscript.\n\nNot applicable.\n\nWritten informed consent has been obtained from the patient to publish this paper.\n\n\nData availability statement\n\nThe data sets generated and/or analyzed during the current study are available from the corresponding author upon reasonable request.", "appendix": "Acknowledgments\n\nWe wish to thank the MicroPIcell platform (Stéphanie Blandin, Steven Nedellec, and Philippe Hulin). This work was supported by the Fondation pour la Recherche Médicale, FRM grant number DEA20150633177 awarded to Vincent Crenn. Experimental Therapeutic unit (Guylène Hamery, UTE Phan, IRS-UN, 8 quai Moncousu, BP70721, 44007 Nantes Cedex 1).\n\n\nReferences\n\nZekry KM, Yamamoto N, Hayashi K, et al.: Reconstruction of Intercalary Bone Defect after Resection of Malignant Bone Tumor. J. Orthop. Surg. 2019; 27: 230949901983297. PubMed Abstract \| Publisher Full Text\n\nPanagopoulos GN, Mavrogenis AF, Mauffrey C, et al.: Intercalary Reconstructions after Bone Tumor Resections: A Review of Treatments. Eur. J. Orthop. Surg. Traumatol. 2017; 27: 737–746. PubMed Abstract \| Publisher Full Text\n\nVidal L, Kampleitner C, Brennan MÁ, et al.: Reconstruction of Large Skeletal Defects: Current Clinical Therapeutic Strategies and Future Directions Using 3D Printing. Front. Bioeng. Biotechnol. 2020; 8: 61–61. PubMed Abstract \| Publisher Full Text\n\nCombal A, Thuau F, Fouasson-Chailloux A, et al.: Preliminary Results of the “Capasquelet” Technique for Managing Femoral Bone Defects-Combining a Masquelet Induced Membrane and Capanna Vascularized Fibula with an Allograft. J. Pers. Med. 2021; 11. PubMed Abstract \| Publisher Full Text\n\nCrenn V, Quinette Y, Bouthors C, et al.: Société d’Orthopédie de l’Ouest Intercalary Allograft Reconstruction Following Femoral Tumour Resection: Mid- and Long-Term Results and Benefits of Adding a Vascularised Fibula Autograft. World J. Surg. Oncol. 2022; 20: 195–195. PubMed Abstract \| Publisher Full Text\n\nMasquelet A, Kanakaris NK, Obert L, et al.: Bone Repair Using the Masquelet Technique. JBJS. 2019; 101: 1024–1036. Publisher Full Text\n\nPelissier P, Masquelet AC, Bareille R, et al.: Induced Membranes Secrete Growth Factors Including Vascular and Osteoinductive Factors and Could Stimulate Bone Regeneration. J. Orthop. Res. 2004; 22: 73–79. PubMed Abstract \| Publisher Full Text\n\nOttaviani G, Jaffe N: The Epidemiology of Osteosarcoma. Cancer Treat. Res. 2009; 152: 3–13. Publisher Full Text\n\nGaspar N, Occean BV, Pacquement H, et al.: Results of Methotrexate-Etoposide-Ifosfamide Based Regimen (M-EI) in Osteosarcoma Patients Included in the French OS2006/Sarcome-09 Study. Eur. J. Cancer. 2018; 88: 57–66. PubMed Abstract \| Publisher Full Text\n\nCrenn V, Biteau K, Amiaud J, et al.: Bone Microenvironment Has an Influence on the Histological Response of Osteosarcoma to Chemotherapy: Retrospective Analysis and Preclinical Modeling. Am. J. Cancer Res. 2017; 7: 2333–2349. PubMed Abstract\n\nCorre I, Verrecchia F, Crenn V, et al.: The Osteosarcoma Microenvironment: A Complex but Targetable Ecosystem. Cells. 2020; 9: 976. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrenn V, Amiaud J, Gomez-Brouchet A, Potiron V, et al.: Signature of the Vascular Tumor Microenvironment as a Marker of the Therapeutic Response to Doxorubicin in a Preclinical Model of Osteosarcoma. Am. J. Cancer Res. 2022; 12: 1843–1854. PubMed Abstract\n\nMalkin D, Li-Fraumeni: Syndrome. Genes Cancer. 2011; 2: 475–484. PubMed Abstract \| Publisher Full Text\n\nGanel A, Yaffe B: Ankle Instability of the Donor Site Following Removal of Vascularized Fibula Bone Graft. Ann. Plast. Surg. 1990; 24: 7–9. PubMed Abstract \| Publisher Full Text\n\nBumbasirevic M, Stevanovic M, Bumbasirevic V, et al.: Free Vascularised Fibular Grafts in Orthopaedics. Int. Orthop. 2014; 38: 1277–1282. Publisher Full Text\n\nSchneider CA, Rasband WS, Eliceiri KW, et al.: Image to ImageJ: 25 Years of Image Analysis. Nat. Methods. 2012; 9: 671–675. PubMed Abstract \| Publisher Full Text\n\nCapanna R, Campanacci DA, Belot N, et al.: A New Reconstructive Technique for Intercalary Defects of Long Bones: The Association of Massive Allograft with Vascularized Fibular Autograft. Long-Term Results and Comparison with Alternative Techniques. Orthop. Clin. North Am. 2007; 38: 51–60. PubMed Abstract \| Publisher Full Text\n\nLing XF, Peng X: What Is the Price to Pay for a Free Fibula Flap? A Systematic Review of Donor-Site Morbidity Following Free Fibula Flap Surgery. Plast. Reconstr. Surg. 2012; 129: 657–674. PubMed Abstract \| Publisher Full Text\n\nChung LH, Wu PK, Chen CF, et al.: Pathological Fractures in Predicting Clinical Outcomes for Patients with Osteosarcoma. BMC Musculoskelet. Disord. 2016; 17: 503–503. PubMed Abstract \| Publisher Full Text\n\nZhou Y, Lu Q, Xu J, et al.: The Effect of Pathological Fractures on the Prognosis of Patients with Osteosarcoma: A Meta-Analysis of 14 Studies. Oncotarget. 2017; 8: 73037–73049. PubMed Abstract \| Publisher Full Text\n\nPuzik A, Uhl M, Ruf J, et al.: Unusual course of disease and genetic profile in Li-Fraumeni syndrome-associated osteosarcoma – a case report. Hered Cancer Clin. Pract. 2021; 19: 44. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHu Z, Cano I, Saez-Torres KL, et al.: Elements of the Endomucin Extracellular Domain Essential for VEGF-Induced VEGFR2 Activity. Cells. 2020; 9: 1413–1413. PubMed Abstract \| Publisher Full Text\n\nDai W, Liu J, Liu B, et al.: Systematical Analysis of the Cancer Genome Atlas Database Reveals EMCN/MUC15 Combination as a Prognostic Signature for Gastric Cancer. Front. Mol. Biosci. 2020; 7: 7–7. Publisher Full Text\n\nKusumbe AP, Ramasamy SK, Adams RH: Coupling of Angiogenesis and Osteogenesis by a Specific Vessel Subtype in Bone. Nature. 2014; 507: 323–328. PubMed Abstract \| Publisher Full Text\n\nD’amico F, Skarmoutsou E, Stivala F: State of the Art in Antigen Retrieval for Immunohistochemistry. J. Immunol. Methods. 2009; 341: 1–18. PubMed Abstract \| Publisher Full Text\n\nMiquelestorena-Standley E, Jourdan ML, Collin C, et al.: Effect of Decalcification Protocols on Immunohistochemistry and Molecular Analyses of Bone Samples. Mod. Pathol. 2020; 33: 1505–1517. PubMed Abstract \| Publisher Full Text" }	[ { "id": "262730", "date": "17 Apr 2024", "name": "Mo-Fan Huang", "expertise": [ "Reviewer Expertise Osteosarcoma genomics", "molecular biology", "system biology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe research project aims to address the challenges in osteosarcoma care, focusing on two primary areas: innovative techniques for reconstructing massive bone defects and developing new prognostic markers for chemotherapy response. The proposed Capasquelet technique combines elements from two well-established surgical methods to manage significant femoral bone defects. This hybrid approach has several advantages, including decreased infection risk and expedited bone healing, allowing early weight-bearing and satisfactory functional outcomes.\nIn addition, the study explores the role of tumor vascularization as a potential prognostic factor for chemotherapy response in osteosarcoma patients. Through immunohistochemistry multiplexing, the research investigates the expression of specific markers, such as Endomucin and α-SMA, and their relationship with patient survival and therapeutic response. Although the results are promising and provide a foundation for further investigation, more extensive studies are needed to confirm the findings and explore their clinical relevance.\nMajor point 1,\nThe author gave detailed description of Capasquelet surgical technique, tissue immunofluorescence staining processing and data acquisition which would be helpful for reproductivity and practicing. However, for the benefit of future understanding of disease processes and treatment, less evidence was shown. In the discussion, you mentioned the Endomucin expression might be a pejorative prognosis marker, are there any other Osteosarcoma patient show high expression of Endomucin or any correlation between high endomucin and Osteosarcoma pathological outcomes? Since you only demonstrate one case here, it may be less convincing. Can the author check more patient gene expression or protein expression database (TCGA?) and see if there is correlation between Endomucin/α-SMA and prognosis in other patient samples?\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": "12227", "date": "30 Sep 2024", "name": "Vincent Crenn", "role": "Author Response", "response": "Dear Reviewer, thank you for your remark, We have checked it on TCGA and modifications have been made at the end of the discussion." } ] } ]	1	https://f1000research.com/articles/11-1066
https://f1000research.com/articles/13-384/v1	25 Apr 24	{ "type": "Research Article", "title": "Determinant factors of gross domestic product (GDP) in Association of Southeast Asian Nations (ASEAN) member countries", "authors": [ "Faris Shafrullah", "Leni Indrawati", "Solahuddin Ismail", "Faris Ihsan", "Putri Ayu Pratiwi", "Karno Karno", "Faris Shafrullah", "Solahuddin Ismail", "Faris Ihsan", "Putri Ayu Pratiwi", "Karno Karno" ], "abstract": "Background The gross domestic product (GDP) of Association of Southeast Asian Nations (ASEAN) member states can be used to determine their overall economic growth. In order to increase GDP, all emerging nations in Southeast Asia are stating to depend on foreign direct investment (FDI), the tourism industry, international visitors visiting ASEAN member nations banking credit, and low inflation rates. High inflation is a problem that developed and developing countries will definitely face. One of the problems faced by ASEAN member countries is that most of the member countries are in the developing country category. For ASEAN member countries, high inflation levels will encourage economic instability. GDP is less than optimal because of these classic problems in developing countries so that economic growth is not as planned. The ASEAN Economic Community (AEC), which ASEAN established, is seen as a way to reduce unemployment, alleviate poverty by boosting the travel and tourism industry and increasing investment, as well as to offer or distribute credit to businesses at low interest rates in order to boost GDP. The purpose of this study is to investigate and analyze how the GDP of ASEAN member nations is affected by FDI, foreign visitors, bank credit, and inflation. s: We analyzed panel data for seven ASEAN members from 2002 to 2020. FDI, foreign tourists, banking credit, and inflation are the research factors examined as independent variables that have an impact on GDP, the dependent variable.\n\nResults The study’s findings indicate that while inflation has a large negative impact on GDP, FDI, foreign tourism, and bank credit have a considerable positive impact on GDP.\n\nConclusions FDI, foreign tourists, bank credit, and inflation have a significant influence on GDP in ASEAN member countries.", "keywords": [ "Gross Domestic Product (GDP)", "Foreign Direct Investment (FDI)", "foreign tourists", "banking credit", "inflation." ], "content": "Introduction\n\nEconomic growth is a process that, over time, raises the population’s real income per capita. It is also accompanied by institutional system modifications that have an impact on structural change and institutional transformation. Poverty, unemployment, low capital formation, sociocultural obstacles, corruption, and outside economic influence are all hurdles to economic progress (Agarwal and Baron, 2023; Duican and Pop, 2015).\n\nThe importance of capital ownership is to create economic development in developing countries, but developing countries realize that the availability of capital is not yet a sufficient condition for creating economic development (Asari et al., 2011; Massidda and Etzo, 2012). Several other factors such as the availability of experts in various fields, sufficient entrepreneurs, an efficient government system, the ability to create and use more modern technology, and the attitude of society play an equally important role in creating economic development. Economic development problems are associated with economic growth (Rasool et al., 2021).\n\nThe expansion of economic activity results in a rise in the quantity of goods and services generated in society, which is known as economic growth (Baltagi, 2005). Gross domestic product (GDP) is the market worth of all finished goods and services generated in a country within a certain time period (Ganchev et al., 2014; Belloumi, 2010). A high GDP value for a country is seen to suggest that the country has great economic health, whereas a low GDP value is thought to indicate weak economic health (Demetriades and Hussein, 2006).\n\nThe entry of Foreign Direct Investment (FDI) into a country certainly has a significant influence on that country (Mc Kinnon, 1964). Not only will capital come in, but technology and experts will also come in, which of course will have an impact on technology transfer and the country’s economic growth (Katusiime, 2018; Borensztein et al., 1998; Mankiw, 2009).\n\nForeign tourists are one aspect that can increase economic growth in ASEAN member countries. Visa exemptions between member countries also have an impact on increasing tourist visits (Witt and Witt, 1992). Member countries are preparing and seriously building tourism industry infrastructure to serve visiting tourists by offering attractive tour packages. The tourism industry has a significant impact on economic growth (Belloumi, 2010; Hymer et al., 1976; Massidda and Etzo, 2012; Bouzahzah and Menyari, 2013; Rasool et al., 2021).\n\nEconomic growth in a country is influenced by the economic conditions of neighboring countries and the condition of the financial infrastructure or infrastructure owned by that country (Kelly et al., 2013). The existence of bank credit can support economic growth in countries that have economic health in the short and long term (Korkmaz, 2015; Mallik and Chowdhury, 2001). The existence of credit provided by banks to finance the development of financial infrastructure and other economic infrastructure has an influence on economic growth (Duican and Pop, 2015; Ananzeh and Eddien, 2016; Hang Le et al., 2021).\n\nThere is a feedback loop that has a significant impact between inflation and economic growth, where moderate inflation can help economic growth, but faster economic growth will have an impact on inflation (Mankiw, 2009; Mallik and Chowdhury, 2001). A moderate and stable inflation rate will encourage the development process and economic growth of a country (Pradhan et al., 2013; Massidda and Etzo, 2012). Moderate inflation increases profits for savers, increases investment, and accelerates a country’s economic growth (Saaed, 2008; Hasanov, 2011).\n\nAssociation of Southeast Asian Nations (ASEAN) member countries are developing countries and have many problems, such as low foreign and domestic investment, high inflation, low levels of foreign and domestic tourists coming and visiting ASEAN countries, low credit disbursement, and development that tends to be uneven (Puah et al., 2018). GDP has not been maximized due to various classic problems in developing countries, so that economic growth is not as planned. The GDP of ASEAN countries can be seen in the table below.\n\nThe Table 1 above shows GDP from ASEAN countries that experienced fluctuations in the period 2016–2020. As a developing country, Indonesia’s economic situation in 2016 experienced an improvement, when compared to other ASEAN countries. The government of each country must be able to increase its country’s Gross Domestic Product (GDP) in order to increase its national development strength. Apart from that, domestic production must also continue to be increased with the contribution of labor. As the country’s development increases, new jobs will be created, thereby absorbing more new workers and reducing existing unemployment.\n\nThe following Table 2 shows the foreign direct investment (FDI) using net inflows (Balance of payments, current USD) from seven ASEAN member countries.\n\nAs seen in Table 2, FDI from ASEAN member countries in the period from 2016–2020 experienced fluctuations. During 2016–2019, the country most in demand for providing FDI was Singapore, because this country is the center of world trade (exports and imports), international financial services, and transportation services for world services and can be said to be ranked first (Takahashi, 2020); however, in 2020, FDI experienced a drastic decline. FDI in Vietnam is ranked second and Indonesia is ranked third. Meanwhile, fourth place is occupied by Malaysia, the Philippines and Thailand (Vicente et al., 2017). Specifically, FDI in Brunei Darussalam increased during 2019–2020.\n\nAn overview of foreign tourists using international tourism, receipts (% of total exports) from seven ASEAN member countries can be seen below.\n\nAs seen in Table 3, Indonesia and the Philippines experienced an increase in foreign tourists from 2016 to 2019. In Vietnam, the number of foreign tourists decreased from 2016 to 2017 and remained stable from 2017 to 2018. In the countries of Malaysia, Singapore, Brunei Darussalam, and Thailand, the number of foreign tourists fluctuated from 2016 to 2020. The percentage of foreign tourists dropped significantly in ASEAN member countries in 2020.\n\nBank credit from seven ASEAN member countries using the domestic credit to private sector (% of GDP) indicator can be seen in the Table 4 below.\n\nIn Table 4, banking credit in Indonesia, Malaysia, Singapore, Thailand and Brunei Darussalam experienced fluctuations during the period 2016–2020. In 2020, the highest banking credit position was owned by Thailand and the lowest banking credit position was owned by Indonesia.\n\nThe fourth determining factor of GDP is inflation. The term “inflation” refers to an increase in commodity prices generally as a result of a misalignment between commodity procurement plans, production, price setting, money printing, and the amount of income held by the population. If the price of just one or two items rises, it is not considered inflation unless the increase spreads to other items or drives up the cost of the majority of other items (Roy and Rahman, 2014). The issue is that prices have a propensity to rise consistently. In addition, price rises that happen seasonally, just before religious festivals, or that happen once and have no lasting effects are not considered inflation.\n\nThe inflation rate of seven ASEAN member countries that use consumer prices (annual %) as an indicator can be seen in Table 5 below.\n\nIn Table 5, inflation in ASEAN member countries tends to fluctuate during the period 2016–2020. Overall, the inflation category experienced by ASEAN member countries is mild inflation. Mild inflation is inflation that has not yet disrupted the economic situation. This inflation can be controlled because prices are rising in general, but has not yet resulted in a crisis in the economic sector. Light inflation is below 10% per year.\n\nThe purpose of the research is to examine and analyze the influence of FDI, foreign tourists visiting ASEAN member countries, banking credit, and inflation simultaneously on GDP in each ASEAN member country.\n\nThe framework of thought can be seen in Figure 1 below:\n\nThe following is the research model:\n\nNote:\n\nGDP = Gross Domestic Product\n\nlnFDI = Logaritma Natural Foreign Direct Investment\n\nTOUR = Foreign Tourists\n\nlnCRD = Logaritma Natural Bank Credit\n\nINFL = Inflation\n\nμ = error\n\nI = Observation\n\nT = Time\n\nForeign Direct Investment (FDI), foreign tourists, bank credit, and inflation influence Gross Domestic Product (GDP) in ASEAN member countries.\n\nThe increase or decrease in a country’s Gross Domestic Product (GDP) depends on several factors, including the flow of foreign investment, the number of visits by foreign tourists, the amount of credit provided by banks to entrepreneurs, and the level of inflation in the country. Therefore, the following hypotheses are formulated:\n\n1. Foreign Direct Investment (FDI) has a significant effect on Gross Domestic Product (GDP) in ASEAN member countries.\n\n2. Foreign tourists have a significant influence on Gross Domestic Product (GDP) in ASEAN member countries.\n\n3. Bank credit has a significant effect on Gross Domestic Product (GDP) in ASEAN member countries.\n\n4. Inflation has a significant effect on Gross Domestic Product (GDP) in ASEAN member countries.\n\n\nMethods\n\nIn total, seven ASEAN member countries were studied, namely Brunei Darussalam, Indonesia, Malaysia, the Philippines, Singapore, Thailand, and Vietnam. The sample data period covers 19 years, from 2002 to 2020, resulting in a total of 133 samples (Karno et al., 2023). The type of data used is panel data, and the analysis tool used is STATA Version 14.0. Data collection involved tracing sources from websites related to the variables studied. Below is Table 6, which presents a description of the variables, definitions, indicators, scale, and data sources used.\n\n\nResults\n\nThe results of panel data regression using the Ordinary Least Squares, Fixed Effects, and Random Effects method are presented below.\n\nThe table above was carried out with the aim of comparing the regression results in three ways. It can be seen from the regression results in the OLS column above that the FDI and foreign tourist variables have a significant positive influence on GDP in each ASEAN member country (Table 7). The banking credit variable has a significant negative influence on GDP in each ASEAN member country.\n\nThe regression results in the Fixed Effect column above show that the variables FDI, foreign tourists and banking credit have a significant positive influence on GDP in each ASEAN member country. The inflation variable has a significant negative influence on GDP in each ASEAN member country (Tamilselvan and Manikandan, 2015).\n\nThe regression results in the Random Effects column above show that the variables FDI, foreign tourists and banking credit have a significant positive influence on GDP in each ASEAN member country. The inflation variable has a significant negative influence on GDP in each ASEAN member country. If we compare the three test results, in the OLS method, the Inflation variable is not significant above 5%, while in the test results using the Fixed Effects and Random Effects methods all variables are significant below 5%. Next, the Fixed Effects and Random Effects methods were tested again to determine the best regression model using the Hausman Test method. Below are presented the results of the Hausman test.\n\nFrom the regression results above, the variables FDI, foreign tourists and banking credit have a significant positive influence on GDP in each ASEAN member country. The inflation variable has a significant negative influence on GDP in each ASEAN member country.\n\nFrom the description of the regression results using the Fixed Effects and Random Effects methods, the Hausman test was carried out to determine the best model. Below are presented the results of the Hausman test (Table 8).\n\nBased on the table above, the results of the Hausman test between Fixed Effect and Random Effect show that the value in the Prob column (0.0012) is less than the critical value of 0.05 (chi 2 = 0.05). Therefore, the Alternative Hypothesis is accepted, namely Fixed Effect. If the value in the Prob > chi 2 column is significantly greater than 0.05, then the null hypothesis is accepted, or Random Effects is accepted. Therefore, the best model to be chosen is Fixed Effects.\n\n\nDiscussion\n\nThe results of the data analysis confirm the hypothesis that all variables have a significant influence on the GDP variable in ASEAN member countries. Specifically:\n\n1. Foreign Direct Investment (FDI) has a positive and significant effect on Gross Domestic Product (GDP) (Borensztein et al., 1998; Yazdi et al., 2017; Scarlett, 2021).\n\n2. Foreign tourist arrivals have a positive and significant influence on GDP (Belloumi, 2010; Bouzahzah and Menyari, 2013; Ohlan, 2017; Yazdi et al., 2017; Rasool et al., 2021; Scarlett, 2021).\n\n3. Banking credit has a positive and significant effect on GDP (Hang Le et al., 2021; Duican and Pop, 2015; Ananzeh and Eddien, 2016).\n\n4. Inflation has a significant negative effect on GDP (Saaed, 2008; Hasanov, 2011; Obradovic et al., 2017).\n\nA detailed discussion of each variable’s impact on the GDP variable is provided below.\n\nInvestments made with the intent to actively control real estate, other assets, or businesses based in a host nation are referred to as FDI. FDI inflows to developing countries in the Southeast Asia region are mainly carried out by investor countries seeking wider market potential. Large investments are mainly concentrated in advanced financial and technological industries. The presence of FDI as a driver of GDP in every developing country brings new capital, new technology and new skills.\n\nThe presence of FDI in the form of physical capital, advanced technology and professional experts brings benefits in the form of being able to process natural resources, increased employment opportunities, increasing sources of state revenue from taxes, and transfer of technology, management skills, and entrepreneurship. By attracting FDI, which is made possible by the cheap production costs in these emerging nations, the Southeast Asian region’s developing nations help their economies grow their GDP. Additionally, FDI provides these developing nations with more cutting-edge technology, allowing local businesses to imitate foreign businesses’ use of technology and local businesses to acquire that technology through labor mobility. In turn, developing nations enable developed nations to manage resources. nature in the form of a mutually beneficial connection. FDI inflows to ASEAN member nations are still very modest. The inflow of money in the form of FDI is anticipated to promote sustainable investment growth in ASEAN member nations because it is a form of long-term capital flow that is considerably less susceptible to economic unrest (Borensztein et al., 1998; Yazdi et al., 2017; Scarlett, 2021).\n\nForeigners who travel abroad on vacation and enter a country other than their home country are referred to as foreign tourists. The strategies used to attract foreign tourists are to develop priority destinations that become tourist attractions, revitalization of cultural heritage buildings that attract tourists, develop a tourism promotion cooperation network at local, national and even international levels with local and national media to introduce tourist attractions, developing the quality of tourist attractions to meet the desires and challenges of tourists, increasing the number of tourism destinations so that tourists have several choices for traveling, and developing tourism facilities and infrastructure. The tourism sub-sector contributes to the country’s foreign exchange earnings which can increase GDP through foreign tourist visits. Visits from foreign tourists have increased over time to ASEAN member countries which can increase the income of these ASEAN member countries, for example the country’s foreign exchange income generated through foreign tourist expenditure. Expenditures of foreign tourists are goods and services purchased by tourists in order to fulfill their needs, desires and hopes while they stay in the tourist destination areas they visit. Tourist spending in a country needs to be calculated carefully so that it can be known how much foreign exchange is earned in a particular country. Tourist expenses usually include hotel accommodation, bars and restaurants, local transportation, tours or sightseeing, souvenirs, and other necessities. This expenditure by foreign tourists can be said to be revenue from the tourism sector for a country visited by foreign tourists. Apart from that, the tourism sub-sector which influences other sectors is tour and travel which includes hotels, restaurants and tour guides, so it can be said that the tourism sub-sector is a dynamic sub-sector and influences other economic segments (Belloumi, 2010; Bouzahzah and Menyari, 2013; Ohlan, 2017; Yazdi et al., 2017; Rasool et al., 2021; Scarlett, 2021).\n\nAccording to a loan arrangement between the bank and the borrower, bank credit is the provision of money or something comparable. Since the banking sector acts as an intermediary and is one of the elements that influences economic movements in all sectors, including the industrial sector in this instance, the government distributes banking credit through banks, the banking sector’s contribution to raising GDP cannot be overlooked. The financial sector is believed to be able to increase GDP by diverting financial funds from unproductive to productive use. Banking credit can be grouped into two types, namely productive credit and non-productive credit. Productive credit has a positive contribution to GDP consisting of working capital credit and investment credit. While non-productive credit has a negative contribution to GDP, in this case it is consumption credit. Viewed from the demand and supply side of banking credit, for example housing credit, if the banking sector increases, the funds that can be allocated for housing credit will also increase. This will have an effect on GDP. The greater the funds collected from the public, the greater the amount of banking credit provided. Increasing the amount of bank credit disbursed will increase productivity so that GDP will be higher.\n\nIn ASEAN members Malaysia, Singapore, Thailand, and Vietnam, the banking industry beats Indonesia in terms of expanding GDP. Because several manufacturing industries in Indonesia have obtained bank credit but are having trouble operating and even experiencing bad credit, the government offers banking credit through banks or financial institutions, not only providing loans in the form of funds but also management development. Real economic activity is not always positively impacted by bank loans. The economy may be harmed by excessive bank credit, particularly private credit. In other words, once reaching the limit, the financial sector’s growth will no longer serve as a catalyst for development but rather a barrier to it (Hang Le, et al., 2021; Duican and Pop, 2015; Ananzeh and Eddien, 2016).\n\nInflation is a general and continuous increase in the prices of goods. Inflation is an important economic indicator, where the growth rate is always kept low and stable so as not to cause economic instability (Wooldridge and Jefferey, 2010). Light inflation has no effect on GDP, because light inflation does not cause prices to rise, so the amount of goods produced remains constant and causes GDP to remain unchanged or unchanged. On the other hand, moderate inflation, heavy inflation and hyperinflation have a negative impact on GDP. High GDP, low and stable inflation are the ideal targets that ASEAN member countries want to achieve. High inflation will push prices to become more expensive, which will cause companies to incur higher production costs. High production costs force companies to reduce direct purchases of raw materials and use of direct labor, which will also have an impact on reduced production of goods, so that people’s income will fall. The decline in people’s income causes a decline in people’s purchasing power for goods, where companies reduce the production of goods, which causes GDP to fall (Saaed, 2008; Hasanov, 2011; Obradovic, et al., 2017).\n\n\nConclusion\n\nBased on the results of the research and discussion, conclusions can be drawn, namely that FDI, foreign tourists, banking credit, and inflation have a significant effects simultaneously on GDP in ASEAN member countries. High FDI flows in the form of physical capital, technology and skilled workers to ASEAN member countries can increase GDP. The strategy carried out by countries in the Southeast Asia region is to increase tourism competitiveness through developing aspects of attractions, accessibility and amenities so that foreign tourist visits can increase GDP in each ASEAN member country. In increasing GDP in ASEAN member countries, the banking sector as an intermediary can trigger economic movements in all sectors including the industrial sector, in this case, the government provides banking credit through banks. ASEAN member countries would want to achieve low inflation so that GDP does not fall.\n\n\nData taken from several sources, namely:\n\nWorld Bank (https://data.worldbank.org/)\n\nCEIC Data (https://www.ceicdata.com/id)\n\nUnited Nation Data/UN Data (http://data.un.org/)\n\nStatista (https://www.statista.com/)\n\nInternational Monetary Fund (https://www.imf.org/)\n\nIndexmundi (https://www.indexmundi.com/)\n\nKnoema (https://knoema.com/)\n\nInternational Labor Organization/ILO (https://www.ilo.org)\n\nFilipina: https://psa.gov.ph/ (Philippine Statistic Authority)\n\nMyanmar: https://tourism.gov.mm/statistics/ (Myanmar Tourism Statistic)\n\nSingapura: https://www.mas.gov.sg/statistics (Monetary Authority of Singapore)\n\nhttps://countryeconomy.com/\n\nhttps://www.theglobaleconomy.com/\n\nEconomic Research Institute for ASEAN and East Asia (https://www.eria.org/)\n\nhttps://www.government.nl/", "appendix": "Data availability\n\nFigshare: Underlying Data.xlsx. https://doi.org/10.6084/m9.figshare.24882699.v1 (Karno et al., 2023).\n\nThe project contains the following underlying data:\n\n- Underlying 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\nAuthors would like to express gratitude to QUVAE Research and Publications for their support in depositing the raw data to the Figshare repository and for their assistance with the submission.\n\n\nReferences\n\nAgarwal I, Baron M: Exploring the link between rising inflation and economic growth: The role of the banking sector. World Bank Blogs; 2023.\n\nAsari FFAH, Baharuddin NS, Jusoh N, et al.: A vector error correction model (VECM) approach in explaining the relationship between interest rate and inflation towards exchange rate volatility in Malaysia. World Appl. Sci. J. 2011; 12: 49–56.\n\nAnanzeh N, Eddien I: Relationship between Bank Credit and Economic Growth: Evidence from Jordan. Int. J. Financ. Res. 2016; 7(2). Publisher Full Text\n\nBaltagi BH: Econometric Analysis of Panel Data. Chichester, West Sussex, England: John Wiley & Sons, Ltd; 2005.\n\nBelloumi M: The relationship between tourism receipts, real effective exchange rate and economic growth in Tunisia. Int. J. Tour. Res. 2010; 12(5): 550–560. Publisher Full Text\n\nBorensztein E, De Gregorio J, Lee JW: How does foreign direct investment affect economic growth? J. Int. Econ. 1998; 45(1): 115–135. Publisher Full Text\n\nBouzahzah M, Menyari Y: International tourism and economic growth: The case of Morocco and Tunisia. J. North Afr. Stud. 2013; 18(4): 592–607. Publisher Full Text\n\nDemetriades P, Hussein A: Does financial development cause economic growth ? Time-series evidence from 16 countries. J. Dev. Econ. 2006; 387–411.\n\nDuican (Moisescu) RE, Pop A: The Implications of Credit Activity on Economic Growth in Romania. Procedia Econ. Financ. 2015; 30: 195–201. Publisher Full Text\n\nGanchev G, Tsenkov V, Stavrova E: Exploring the relationship between credit and nominal GDP. SUERF. 2014; 4: 17.\n\nHang Le T, Thi DL, Trung, et al.: Banking Sector Depth and Economic Growth: Empirical Evidence from Vietnam. J. Asian Finance Econ. Bus. 2021; 8(3): 0751–0761.\n\nHasanov FRelationship between inflation and economic growth in Azerbaijani economy: is there any threshold effect? Munich Personal RePEc Archive. 2011.\n\nHymer, et al.: The International Operations of National Firms: A Study of Direct Investment. M.I.T Press; 1976.\n\nKarno K, Shafrullah F, Indrawati L, et al.: Underlying Data.xlsx. Dataset. figshare. 2023. Publisher Full Text\n\nKatusiime L: Private Sector Credit and Inflation Volatility. Economies. 2018; 6(2): 28. Publisher Full Text\n\nKelly R, Mc Quinn K, Stuart R: Exploring the Steady-State Relationship Between Credit and GDP for a Small Open Economy The Case Of Ireland, Working Paper Series. No. 1531 – April.2013.\n\nKorkmaz S: Impact of Bank Credits on Economic Growth and Inflation. Journal of Applied Finance & Banking. 2015; 5(1): 57–69.\n\nMallik G, Chowdhury A: Inflation And Economic Growth: Evidence From Four South Asian Countries. Asia-Pacific Development Journal. 2001; 8(1).\n\nMankiw G: Macroeconomics. 7th ed.Worth Publishers: New York; 2009.\n\nMassidda C, Etzo I: The Determinants of Italian Domestic Tourism: A panel data analysis. Tour. Manag. 2012; 33: 603–610. Publisher Full Text\n\nMc Kinnon RI: Foreign exchange constraints in economic development and efficient aid allocation. Econ. J. 1964; 74(294): 388–409.\n\nObradovic S, Sapic S, Furtula S, et al.: Linkages between Inflation and Economic Growth in Serbia: an ARDL Bounds Testing Approach. Eng. Econ. 2017; 28(4): 401–410.\n\nOhlan R: The relationship between tourism, financial development and economic growth in India. Future Bus. J. 2017; 3(1): 9–22. Publisher Full Text\n\nPradhan R, Dasgupta P, Bele S: Finance, development and economic growth in BRICS: a panel data analysis. J. Quant. Econ. 2013; 11(1–2): 308–322.\n\nPuah C-H, Huan S-H, Thien F-T: Determinants of Chinese demand for tourism in Malaysia. Bus. Econ. Horiz. 2018; 14(3): 501–512. Publisher Full Text\n\nRasool H, Maqbool S, Tarique M: The relationship between tourism and economic growth among BRICS countries: a panel cointegration analysis. Future Bus. J. 2021; 7(1). Publisher Full Text\n\nRoy R, Rahman MM: An empirical analysis of remittance–inflation relationship in Bangladesh: Post-floating exchange rate scenario. Working paper, WP/1403, Bangladesh Bank, Chief Economist’s Unit, Bangladesh.2014.\n\nSaaed AA: Inflation and Economic Growth in Kuwait: 1985-2005 - Evidence from Co-Integration and Error Correction Model. Appl. Econ. Int. Dev. 2008; 7(1): 2007.\n\nScarlett HG: Tourism recovery and the economic impact: A panel assessment. Res. Glob. 2021; 3: 100044. Publisher Full Text\n\nTakahashi K: Comparing The Determinants of Tourism Demand in Singapore and French Polynesia: Applying the Tourism Demand Model to Panel Data Analysis. Tour. Anal. 2020; 25: 175–181. Publisher Full Text\n\nTamilselvan M, Manikandan S: A Study on Impact of Foreign Direct Investment on Gross Domestic Production in India. Int. J. Acad. Res. Bus. Soc. Sci. 2015; 5: 224–233. Publisher Full Text\n\nRamos V, Untong A, Kaosa-ard M: ASEAN’s intra-regional tourism demand to Thailand. Asia Pac. J. Tour. Res. 2017; 22(9): 909–921. Publisher Full Text\n\nWitt S, Witt C: Modeling and Forecasting Demand in Tourism. London: Academic Press; 1992.\n\nWooldridge M, Jeffrey: Econometric Analysis of Cross Section and Panel Data. Cambridge, Massachusetts London, England: The MIT Press; 2010.\n\nYazdi SK, Salehi KM, Soheilzad M: The relationship between tourism, foreign direct investment and economic growth: evidence from Iran. Curr. Issue Tour. 2017; 20(1): 15–26. Publisher Full Text" }	[ { "id": "293084", "date": "29 Aug 2024", "name": "Elistia Elistia", "expertise": [ "Reviewer Expertise Economics", "Strategic Management", "Human Resources Management", "Entrepreneurship." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDeterminant factors of gross domestic product (GDP) in Association of Southeast Asian Nations (ASEAN) member countries.\nAbstract Provide brief implications and suggestions.\nIntroduction - Provide an explanation of the urgency and benefits of the research. - Present the relevant research gap. - Explain why the study focuses only on 7 ASEAN countries. - Provide an explanation of what constitutes a good inflation rate.\nResearch Purposes Figure 1. What framework?\nMethods - The explanation of the research methods should examine each of the 7 ASEAN countries. - It is recommended that the data collected be up to the year 2022.\nResults and discussion - Provide an explanation of how the policies of each of the 7 ASEAN countries relate to the variables of FDI, FT, BC, and Inf. - It is recommended to use recent references for the discussion explanation.\nConclusion - Mention only 7 countries, as the research only covers 7 ASEAN countries.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "12523", "date": "30 Sep 2024", "name": "Leni Indrawati", "role": "Author Response", "response": "The revised article incorporates several key changes and updates based on the provided comments and suggestions. In the abstract, we have retained the original text, emphasizing the significant impact of FDI, foreign tourists, bank credit, and inflation on GDP in ASEAN countries, along with the suggestion for policymakers and stakeholders to prioritize relevant policies. The introduction now includes an explanation of what constitutes a good inflation rate, addressing a key aspect highlighted in the comments. Additionally, we have maintained the urgency and benefits of the research, presented the relevant research gap, and explained the focus on seven ASEAN countries. The methods section now includes a recommendation to collect data up to the year 2022, ensuring the analysis encompasses recent economic trends and developments, and provides a rationale for considering the period from 2002 to 2020. In the results and discussion section, we have incorporated an explanation of how the policies of each of the seven ASEAN countries relate to the variables of FDI, FT, BC, and Inf, as well as recent references to enhance the discussion. The conclusion now specifically mentions the seven countries covered in the research, and we have provided responses to the specific questions raised in the comments, addressing the clarity and accuracy of the work, appropriateness of the study design, technical soundness, provision of sufficient methodological details, appropriateness of statistical analysis and interpretation, availability of source data, and adequacy of conclusions in relation to the results. Overall, these changes have been made to address the comments thoroughly and improve the quality and relevance of the article." } ] }, { "id": "270498", "date": "26 Sep 2024", "name": "Tariq Hussain", "expertise": [ "Reviewer Expertise My areas of research is Economic Growth Policies", "Development Economics and Institutional Economics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe title of the article “Determinant factors of gross domestic product (GDP) in Association of Southeast Asian Nations (ASEAN) member countries”, is sizzling and remained under the discussion of researchers and academic scholars since long. In my humble opinion the topic may be “Major Determinants of Gross Domestic Product (GDP) among Association of Southeast Asian Nations (ASEAN) countries”. The write up of Abstract needs to improve regarding English language and methodology is not discussed in it. Please briefly introduce the methodology in the abstract Introduction is elaborated fully, however, the table presented in this part of the paper has time span 2016-2020, whereas the study time period is 2002-2020. Please justify this in paper In the intro, updated references are used but in less number Literature Review should be presented separately In the same way, Theoretical frame work is missing. Methodology is key part of any research paper, it is not fully elaborated. It is suggested to interpret in the paper Interpretation of empirical result is good. It would be better to discuss with the help of coefficient values and shows how many percentages change occur due to independent variables in dependent variables. Policy implications are based on the variables’ results, its highly appreciated.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-384
https://f1000research.com/articles/13-1101/v1	27 Sep 24	{ "type": "Research Article", "title": "Obtaining a PhD in Portugal. Determinants of Success and Subsequent Career Paths", "authors": [ "Ana Ramos", "Daniel Ferreira", "Daniel Ferreira" ], "abstract": "Background Over the past three decades, Portugal has invested significantly in doctoral training. However, there is a lack of up-to-date information on the success of scholarship holders in obtaining the degree or on their subsequent career paths.\n\nMethods This study analysed four cohorts of scholarship holders funded by the Foundation for Science and Technology between 1995 and 2012. The professional situation at different points in time after the Ph.D. (5, 10, 15 and 20 years) was studied.\n\nResults The success rate for obtaining the degree was 88%, which is comparable to other European countries for doctorates completed with funding over a period of 3-4 years. The average time to obtain the degree was 5.06 years. The time to degree was influenced by the scientific field, the nationality of the scholarship holder, and the location of the institution awarding the degree (in Portugal or abroad). The gender or age range of the scholarship recipients did not influence the time required for graduation. The analysis of the career and sector of activity of these graduates at different points in time after obtaining the Ph.D. revealed that approximately 60% percent of the graduates were engaged in R&D activities at some point in their career paths, but this percentage diminished from the oldest to the most recent cohorts, suggesting difficulties in retaining recent graduates in academia and in the private sector. In 2020, 63% of the graduates were engaged in R&D activities, and almost half were employed in higher education as teachers, researchers, or scholarship holders.\n\nConclusions This study confirmed the challenges faced by doctoral graduates in integrating into non-academic job markets. On the other hand, it has demonstrated an efficient use of public funds, with high success rates and a time to degree that is within the average of other European countries.", "keywords": [ "PhD success rate", "Time to degree", "Doctorate holders", "Career paths" ], "content": "Introduction\n\nIn Portugal, public support for training human resources in science and technology began in 1987 with the launch of the Science and Technology Mobilising Programme (Programa Mobilizador de Ciência e Tecnologia, PMCT). The programme funded master or doctoral scholarships with the aim to address the shortage of human resources in science and technology and complement the traditional way of recruiting research assistants in higher education institutions and state laboratories (Rodrigues, 2017). Since then, the attribution of doctoral scholarships (3-4 years duration, in Portugal or abroad) has been at the core of the activities of the main funding agencies: the Junta Nacional de Investigação Científica e Tecnológica (JNICT) until 1996 and the Fundação para a Ciência e a Tecnologia (FCT) since 1997. The FCT has supported over 30000 Ph.D. candidates through various mechanisms, including annual calls, doctoral programmes or international partnerships. Over the course of 25 years, the FCT has invested more than 3.2 billion euros in master, doctoral, and postdoctoral scholarships. Horta et al. (2018) confirmed the positive effects of the FCT funding on doctoral training, providing stability for research and leading to the production and consolidation of knowledge necessary for thesis writing. The clear focus on research objectives also contributed to the scientific development of fields, institutions, and scientific systems, an effect observed both during and after doctoral studies.\n\nThe investment has led to a significant increase in the number of doctorates awarded in Portugal; its cumulative number was almost 38000 in 2022 (Direção-Geral de Estatísticas de Educação e Ciência [DGEEC], 2023). This investment is also evident in the number of doctoral graduates residing in Portugal, which increased from 19034 in 2009 to 30807 in 2015 and 37113 in 2020, corresponding to a doubling in about a decade (DGEEC 2013, 2017, 2021).\n\nDespite the significant growth in the number of degrees awarded and of doctorate holders living in Portugal, in 2022 the proportion of doctorate holders in the labour force (25-64 years old) was 0.9%, still lower than the average for OECD countries, 1.3% (Organization for Economic Cooperation and Development [OECD], 2023). However, the new doctoral graduates per 1000 inhabitants in the 25-34 age group has been rising. In 2015, Portugal “produced” 1.9 new doctorates per 1000 inhabitants aged 25-34 years, which was similar to Spain’s rate of 1.91 and close to the EU average of 2.01 (European Commission [EC], 2017). This led to a substantial increase in the number of new doctorate holders in recent years.\n\nThe increased number of doctorate holders has presented significant challenges for their professional integration, particularly for younger individuals, both within the higher education sector, as well as in non-academic sectors such as businesses or not-for-profit organisations. In the higher education sector, access to teaching positions is limited, as the number of academic staff has remained stable for the past 20 years. Because of this shortage of positions, there is an imbalance between supply and demand, resulting in a significant number of Ph.D. graduates competing for scarce job opportunities or, more often, postdoctoral fellowships (OECD, 2019). From 1994 to 2016, FCT and its predecessor JNICT awarded over 10000 postdoctoral fellowships for a period of up to six years with a mid-term evaluation after three years. From 2007 onwards, programmes were introduced to provide more stable conditions for postdoctoral researchers. Until 2015, these programmes offered 5-years fixed-term contracts with no perspective of further career development. In 2016, the government launched a new initiative (the Scientific Employment Stimulus Programme) to promote more stability and better social protection for Ph.D. holders by providing them with salaried positions with 6-years employment contracts. The underlying legal regime obliges the public higher education and research institutions to open a competitive recruitment procedure to provide an employment opportunity to these researchers at the end of the 6-year contract.\n\nThere is currently limited understanding of the expansion of doctoral training, including its causes, social and economic contributions, and medium to long-term consequences. Although there is a broad consensus on the social and economic importance of doctorates, data collection at the international level is inconsistent and the available information is primarily based on ‘snapshot’ surveys. Only recently have some countries, such as the USA, Germany, and the Netherlands, established large-scale surveys that will enable longitudinal analyses of the career paths of doctoral graduates (Hancock et al., 2019). The results of these studies will complement previous analyses carried out by the OECD using the CDH survey or in the context of the MORE projects funded by the European Commission.\n\nDoctoral degree holders have lower unemployment rates than graduates of other educational levels and receive a significant wage premium (Auriol et al., 2013; Pedersen, 2014). It has been revealed that there is an increasing tendency for doctoral graduates to find placements outside academia, although their employment paths and the distribution by sector varies considerably between countries (Auriol et al., 2013). The ‘DocEnhance’ study, funded by the Horizon 2020 programme, surveyed 2200 individuals with a doctorate earned from European universities between 2016 and 2020. The results showed that doctoral graduates find jobs quickly after graduating, both inside and outside academia. The unemployment rate was very low, at 3%, which is lower than the average for the European Union labour force (7%). The academic sector, including universities and research institutes, was the most significant employment sector. Temporary contracts accounted for approximately 25%, which is more than double of the EU rate (Boman et al., 2021). In the UK, almost 30% of individuals worked in academia 3.5 years after obtaining their Ph.D. Of these, 70% were teaching professionals and 30% were university researchers. Around 20% worked in industry, often as researchers or managers. Another 20% held medical jobs, including as practitioners and medical scientists (Hancock, 2021). The ‘10,000 PhDs’ project at the University of Toronto in Canada revealed that doctoral degrees led to a wide range of positions. Approximately 23% of the respondents held tenure or tenure-track positions, while slightly over half worked in academic positions, including administrative roles. Nearly 30% worked in the industry, and others were employed by federal or provincial governments, charities, or entrepreneurial businesses (Woolston, 2018). All the studies mentioned above used surveys and therefore provide limited perspectives due to low response rates and difficulties in locating individuals to be surveyed. The Centre for Research and Development Monitoring in Flanders (ECOOM) used a database containing complete records of academic staff, doctoral students, and degrees awarded by the five Flemish universities to investigate the factors that contribute to obtaining a doctorate and subsequent career paths (Groenvynck et al., 2013; Debacker, 2021). These are some of the few studies that used administrative data to study career paths.\n\nUpstream of professional destinations and employability, completion rates and time to degree are important indicators for monitoring the stock and flow of researchers on the labour market and for assessing the efficiency and effectiveness of doctoral training (Wollast et al., 2018; Groenvynck et al., 2013). Prolonged time-to-degree and high drop-out rates have negative effects on all involved parties: Ph.D. candidates, Ph.D. organisers or supervisors, and funding bodies. In some studies, the completion rate has been estimated at 50%. However, research has shown that there is a strong positive correlation between the success rate and the availability of funding for an adequate period, which allows candidates to dedicate themselves exclusively to their studies (Ehrenberg & Mavros, 1995; Groenvynck et al., 2013).\n\nAlthough Portugal has invested considerably in doctoral training over the last three decades, there is a lack of up-to-date information on the success of scholarship holders in obtaining a doctoral degree or on the subsequent career paths. The CDH survey, mentioned above, provides valuable information on the ‘pool’ of doctoral graduates living in Portugal in the survey years (approximately every 5 years), but does not provide information on their career paths. The latest CDH survey figures (2020) reveal a low unemployment rate (2.3%) among doctorate holders and a high prevalence of the Higher Education sector in their occupation (77%), followed by the State (13%), Businesses (8%), and Private Non-Profit Institutions (2%) sectors. Over 80% of the doctoral graduates residing in our country were engaged in R&D activities, with 68% having a permanent contract and 32% having a fixed-term contract. Recent publications on doctoral graduates in our country have focused on specific groups and narrower themes. For example, Morais and Gaio Alves (2019) studied graduates from a particular university, while Spognardi and Matos (2021) and Ferreira (2023) examined the precariousness of the labour situation. However, these studies do not provide specific information on individuals who have benefited from an FCT grant.\n\nTo bring a comprehensive perspective on doctoral graduates funded by the FCT, this study analysed the career paths of 5800 individuals who benefited from a doctoral scholarship, using four cohorts of scholarships which began in 1995-1997, 2001-2002, 2006, and 2012. This study is particularly timely in the context of European and national policies, where attractive and sustainable research careers have been recognised as strategic. The results can help to establish indicators for monitoring the policies implemented over the last 30 years, as well as for defining future actions and policies. The aim was to clarify the following questions:\n\n1. How do different groups of scholarship recipients compare in terms of success rate and time to obtain a degree, based on variables such as gender, nationality, age at the start of the scholarship, field of study, and location of the awarding university?\n\n2. What is the persistence of these doctoral graduates in the Portuguese R&D system and what are the characteristics of their post-doctoral careers?\n\n3. What are the factors that explain career paths and what conclusions are relevant for public policy?\n\n\nMethods\n\nBased on literature data suggesting that the average time required for concluding a Ph.D. is 5 years, four cohorts of FCT scholarship holders were defined: cohort 1 included Ph.D. scholarships started between 1995 and 1997, cohort 2 covered scholarships started in 2001-2002, and cohorts 3 and 4 consisted of scholarships started in 2006 and 2012, respectively. The grant recipients from four cohorts, totaling 5819 individuals (see Table 1), were studied to determine their labour situation at various points in time. The initial assumption was that the scholarship recipients who began their studies between 1995 and 1997 would have completed their degrees mostly between 1999 and 2001. This would allow for the determination of their professional situation approximately 5 years later (2004-2006), 10 years later (2009-2011), 15 years later (2014-2016), and 20 years later (2019-2021). For scholarships beginning in 2001-2002, the professional situation would be evaluated at 5 years (2009-2010), 10 years (2014-2015), and 15 years (2019-2020) after obtaining the degrees. For the 2006 cohort, who obtained their degree in 2011, their situation would be assessed 5 years later in 2014, and again 10 years later in 2019. The 2012 cohort’s labour situation would be appraised in 2020, approximately 5 years after obtaining their degree.\n\nTo determine the year of graduation, various sources of information were consulted, including the FCT databases, the National Register of Doctoral Theses (RENATES), the Ciência ID1 identifier (when available in the FCT databases) via the Ciência Vitae2 platform, as well as the physical individual files of scholars available at the Science and Technology Archive of the FCT. When information could not be obtained through the aforementioned sources, we used the scholarship holder’s name and the institution that awarded the degree to search national and international bibliographic repositories, research units’ and higher education institutions’ websites, LinkedIn, etc. Due to the incompleteness of information about the graduation year in administrative databases, success rate in this paper refers to individuals for whom it was possible to determine the year of graduation using the approach described above and the sources listed (up to July 2022).\n\nTo ascertain the professional status of past scholarship recipients at different points in time following their doctoral degree, we used two distinct sources of data: the Portuguese R&D Survey (hereafter IPCTN) and the Careers of Doctorate Holders (CDH) survey. The IPCTN is an annual survey that provides official statistical information on the human and financial resources allocated to R&D activities in Portugal. It collects information on the individuals engaged in R&D activities, including their career (teaching, research, medical, etc.), category (assistant professor, principal investigator, etc.), and the sector they are associated with (Business, State, Higher Education, or Private Non-Profit Institution). The CDH is a survey aimed at doctoral graduates residing in Portugal, with or without R&D activity; its latest edition was conducted in 2020.\n\nFor individuals whose graduation year (N) was known, their data (name, date of birth and ID number) were cross-referenced with the IPCTN data. Professional situations were assigned to those located at N+5 years, N+10 years, N+15 years, and N+20 years, including their career, category, and sector of activity. The professional situation in 2020, the last year consulted for the IPCTN, was also assigned, regardless of the time elapsed since graduation. When an individual worked in R&D in two or more organisations in the same year, each situation had to be analysed on a case-by-case basis in order to assign the doctorate to the career/category/activity sector that best reflected his or her professional situation in that year.\n\nThe data of those individuals whose graduation year was known was also cross-referenced with the data collected in the CDH survey for 2020. This complemented the IPCTN data and characterised the professional situation in 2020, regardless of the year of the degree or the time elapsed, providing a snapshot for that year. The aim was to locate as many former doctoral students as possible, understand their career paths and determine their employment situation in 2020.\n\nThe results of all cross-checks were anonymised and processed in a safe center. Their disclosure follows the principles of statistical confidentiality and personal data protection.\n\n\nResults\n\nThe demographic characteristics of the Ph.D. candidates and the distribution of scholarships by scientific field and by location of the degree awarding institution are shown in Table 2. The comparison of cohort 1 with cohort 4 reveals that the proportion of women increased from 46.5% to 57.7%, most likely due to the mounting predominance of female graduates in secondary and tertiary education. Foreign scholarship holders (mostly from Brazil and Italy) expanded from 2.5 to 8.7%. The percentage of Ph.D. candidates aged 35 or over at the application date rose from 8.3% to 14.5%. The drop in the success rate of FCT doctoral scholarship calls, from 2009 onwards, may have contributed to this, since candidates who were not funded in a given call tried again in subsequent year(s) and, consequently, the age of successful candidates tended to rise.\n\n1 Age at application year.\n\n2 FORD, Fields of Research & Development, OECD (2015), Frascati Manual 2015: Guidelines for Collecting and Reporting Data on Research and Experimental Development.\n\nThe number of scholarships awarded to degree-granting institutions outside Portugal fell significantly and steadily from cohort 1 to 4. In cohort 1, the 383 scholarships awarded for Ph.D. studies abroad corresponded to 37.9%, while in cohort 4 this percentage had fallen to 9.7%. In all cohorts, the United Kingdom and the USA were the main destination countries for FCT-funded doctoral students. Spain and France came third and fourth, followed by Germany and the Netherlands.\n\nThe Social Sciences and the Humanities and Arts accounted for around 40% of the scholarships of cohort 4, an increase of 20 p.p. from cohort 1. Concomitantly there was a decline of the same magnitude in the proportion of grants in the fields of Natural Sciences, Engineering and Technology.\n\nOut of the 5819 Ph.D. candidates studied, at least 5093 (87.5%) obtained their degree. The percentage ranged from 93.1% in cohort 2 to 81.2% in cohort 4 (Table 3). However, it is possible that some individuals in this latter cohort were still completing their work at the time of this analysis (July 2022). The proportion of scholarship recipients who obtained their degree abroad declined steadily from the 1995-1997 cohort to the 2012 cohort, from 27.2% to 11.3%.\n\n1 Degrees awarded refers to the number of individuals for whom it was possible to determine the year in which they obtained their degree from various sources of information (until July 2022).\n\n2 Average number of years between the start of the scholarship and the defense of the thesis.\n\nThe time to degree (TTD) for the Ph.D. candidates in this study was calculated as the difference between the year of the thesis defense and the year of the beginning of the scholarship. The average TTD was 5.06 years (Standard Deviation=2.11) and the median was 5.00 years. It is important to note that all Ph.D. candidates for whom the year of the thesis defense could be determined were included in this calculation, regardless of the time elapsed since the start of the grant, which ranged from 1 to 25 years. Some methodological issues that may affect the estimation of the TTD should be mentioned: we do not know if the beginning of training corresponded to the start date of the scholarship, as there are situations in which these moments do not coincide (e.g. previous scholarships or other funding). Additionally, there was no data available on the time lag between thesis submission and degree award, which can be significant and may artificially inflate the TTD.\n\nThe TTD decreased consistently from 5.54 years in cohort 1 (scholarships started in 1995-1997) to 4.67 years in cohort 4 (scholarships started in 2012). It is noteworthy that the maximum number of years to obtain the degree steadily dropped from cohort 1 (25 years) to cohort 4 (10 years), although in the latter the maximum interval may be underestimated, given the possibility that there were Ph.D. candidates still completing their work at the time of analysis. The reason why some scholarship holders obtained their degree in less than three years may be attributed to the availability of prior funding. For instance, older cohorts may have received master scholarships, while more recent cohorts may have received funding from their host institutions.\n\nThis trend to reduced time to degree has also been observed in studies conducted in other European countries. One of the reasons is the increasing prominence of doctoral programmes, to the detriment of the “student-supervisor model”, as well as the implementation of the Bologna process. Currently, the awarding of doctoral degrees by Portuguese higher education institutions is subject to several conditions. These include the presence of a qualified teaching staff, primarily composed of individuals who hold doctoral degrees, as well as other human and material resources that ensure the quality of training. The fulfilment of these requirements is verified through an accreditation process conducted by the Higher Education Assessment and Accreditation Agency (A3ES), which was established in 2007.\n\nThe percentage of individuals who obtained a degree was slightly higher for women than for men, as shown in Figure 1. Portuguese nationals achieved a moderately higher success rate than foreigners, with 88% versus 85%. An analogous situation was found for scholarships with a host institution in Portugal (88.9%) versus abroad (85.1%). However, it must be considered that some individuals who obtained their degree abroad may not have returned to Portugal, making it more difficult to obtain data on degree completion. The individuals aged below 35 years old at the time of application had higher success rates that their older counterparts. As far as the scientific field is concerned, the success rate was lower than the average in the Humanities and Arts and in the Social Sciences.\n\nThe success rate is defined as the percentage of individuals who obtained the degree until July 2022 and is shown as a deviation from the average success rate, 87.5%. Notes: Age at application year. FORD Fields of Research & Development, OECD (2015), Frascati Manual 2015: Guidelines for Collecting and Reporting Data on Research and Experimental Development.\n\nThe percentage of scholarship recipients for whom it was impossible to determine whether or not they obtained their degree was 12.5%. This ranged from 6.9% in cohort 2 to 18.8% in cohort 4. In all cohorts, the proportion of scholars with no information/degree was higher in the Humanities and Arts than in the other fields. Out of the 726 scholarship holders for whom no information about the degree was obtained, 48 were foreigners (approximately 6.5%) and the remaining had Portuguese nationality. For 174 (24%), the degree-awarding institution was located abroad; it is reasonable to assume that they either did not obtain a doctorate or, having obtained one, did not return to Portugal. In all cohorts, scholarships awarded for studying abroad resulted in a higher percentage of recipients for whom no degree was confirmed.\n\nNeither the sex nor the age group had a statistically significant influence on the TTD (Figure 2). In contrast, the scientific field, the nationality of the Ph.D. candidate (Portuguese or other) and the location of the degree-awarding institution (in Portugal or abroad) significantly affected the TTD, which was lower than the average for host institutions outside Portugal and for foreign scholarship holders. The TTD was found to be higher in the fields of Agrarian Sciences, Social Sciences, Humanities, and Arts compared to other scientific fields.\n\nThe time to degree is defined as the difference between the year of the thesis defense and the year of the beginning of the scholarship and is shown as a deviation from the average time to degree, 5.06 years. Notes: Age at application year. FORD Fields of Research & Development, OECD (2015), Frascati Manual 2015: Guidelines for Collecting and Reporting Data on Research and Experimental Development.\n\nOnly 8% of the grant recipients obtained their degree within three years (the common duration of the scholarship). This figure increased to 57% within five years (see Figure 3), continued to increase significantly up to seven years (75%) and then stabilised at approximately 80% from the eighth year since the start of the scholarship. Some individuals were able to complete their degree in less than three years (not shown in Figure 3) probably because they were awarded a scholarship to complete work already funded by other sources, such as master scholarships3 for older cohorts or funding from the hosting institutions for more recent cohorts.\n\nThe graph on the left shows the number of degrees obtained each year 3 to 10 years after the scholarship start date and the graph on the right depicts the cumulative success rate in the same period. Note: Number of individuals for whom it was possible to determine the graduation year (until July 2022).\n\nTable 4 depicts the differences in the success rate and time to degree for each cohort and demographic characteristics of the Ph.D. candidates.\n\nIn cohort 1, the percentage of male scholarship holders who obtained a degree was slightly higher than that of female scholarship holders, but this was reversed in cohorts 2, 3 and 4 (Table 4). In the last two cohorts, the success rate for female Ph.D. candidates was around 5 p.p. higher than that of males. The TTD was slightly higher for females in every cohort, but when all four cohorts are taken together, the difference between males and females is not statistically significant (M = 5.00, SD = 2.29, F = 5.09, SD = 1.95/t=-1.5, p=0.13).\n\nAs shown in TabIe 4, in all cohorts, the success rate was higher in the younger age groups. For example, in the 1995-1997 cohort, 90.2 % of scholarship holders aged [25-30] completed their degree compared to 81.8 % of those aged ≥40. In cohort 3 these percentages were 90.3% and 80.5% respectively. Although there were differences in success rates, there appears to be no correlation between the TTD of those who obtain the degree and age at the start of the scholarship. The statistical significance test (1-way ANOVA) results showed that the variances of the TTD averages between age groups were not significant (F(4.5088)=1.17, p=0.13). Therefore, the individual’s age at the start of the scholarship is not a relevant factor for TTD.\n\nIn cohorts 1 and 2, the completion rate of foreign scholarship holders was lower than that of Portuguese nationals (Table 4). However, in cohorts 3 and 4, the situation changed, and foreign grant holders had a slightly higher completion rate (about 1 percentage point difference in the latter cohort). Out of the 375 foreign citizens who received funding from the FCT in all cohorts, 327 (87.2%) successfully defended their thesis. Among them, 311 completed their degree in a Portuguese institution, while the remaining 16 obtained their degree abroad but had permanent residence in Portugal. The FCT’s regulations allow for the awarding of doctoral scholarships abroad to non-nationals who meet this requirement. In all cohorts, the TTD was lower for foreign Ph.D. candidates and the difference was statistically significant (t(394)=3.98, p=8.25E-05). This is a common observation in studies published on the same subject in other countries and is often related to the fact that displaced citizens with limited funding are more motivated to complete their work and obtain a degree (Espenshade & Rodriguez, 1997; Groenvynck et al., 2013).\n\nThe success rate of scholarship holders in obtaining a degree was higher when the host institution was in Portugal, except for cohort 2 where the success rates were similar for both groups (Table 4). As stated above, caution is needed when interpreting this difference, since it is possible that some of the recipients of scholarships abroad did not return to Portugal, making it harder to ascertain the degree completion. In the first two cohorts, the time to degree was lower for those whose host institution was outside Portugal, but in cohorts 3 and 4 the difference between the two groups of scholarship holders is small. Looking at the four cohorts as a whole, the difference is statistically significant even with the levelling off of the time needed to complete doctoral training in the two most recent cohorts (t(1486)=2.54, p= 0.011).\n\nAcross all cohorts, a lower percentage of scholarship holders in Humanities and Arts completed the doctorate compared to other scientific fields. The percentage of scholarship holders obtaining a degree was also lower in Social Sciences, except for cohort 2. Among those who obtained a doctorate, the highest TTD was found in the Humanities and Social Sciences, but also in these two fields the TTD decreased from cohort 1 to cohort 4 (Table 4). The results of the one-way ANOVA test indicated significant differences (F(5.5087)=7.96, p=1.73E-07) in TTD among scientific fields. This finding is consistent with previous research conducted in Belgium and has been attributed to differences in academic practice (Groenvynck et al., 2013) and Norway (Smeby, 2000).\n\nFigure 4 shows the success rate and TTD of scientific areas. It is evident that the success rate at 5 years exceeded 50% for most scientific areas. However, there are significant variations. In the first quadrant of the graph, we find areas with a success rate over 50% but with an above-average TTD. These areas mainly include Natural Sciences and Agricultural and Veterinary Sciences (such as Biology, Marine Sciences, and Veterinary Sciences), as well as Humanities and Arts, such as Philosophy and Museology. The second quadrant identifies areas with a high 5-year success rate and below average TTD. These areas include Physics, Chemistry, and Mathematics within the field of Exact Sciences, as well as some areas of the Social Sciences (Psychology, Geography) and Humanities and Arts (Literature). Finally, the fourth quadrant (below average success at 5 years and TTD) mostly comprises areas of the Social Sciences, Humanities, and Arts, such as Linguistics, Anthropology, and History.\n\nSuccess rate 5 years after the start of the scholarship and time to degree per scientific area. Note: Number of individuals for whom it was possible to determine the graduation year (until July 2022). Anthropol = Anthropology, Arch = Architecture and Urbanism, Arts = Artistic Studies, Biol = Biology, Biotec Eng = Biotechnological Engineering, Civil Eng = Civil Engineering, Chem = Chemistry, Chem Eng = Chemical Engineering, Comm = Communication Sciences, Econ&Manag = Economics and Management, Electr Eng = Electrotechnical Engineering, Geog = Geography, Hist = History, Lit = Literary Studies, Mat Eng = Materials Engineering, Math = Mathematics, Mech Eng = Mechanical Engineering, Museol = Museology, Phyl = Phylosophy, Poli Sci = Political Sciences, Psych = Psychology, Sociol = Sociology, Veter Sci = Veterinarian Sciences.\n\nFigure 5 shows the number of doctoral graduates for whom 5, 10, 15 or 20 years had elapsed after the degree until 2020 (the latest year for which statistical data was available at the time of the analysis) and the number of those located in Portuguese R&D institutions at each time. Out of the 5093 doctoral graduates analysed, 3935 had already completed at least 5 years after their doctorate. Of these, 2294 (58%) carried out R&D activity, while the remaining 42% could not be located. At the other extreme, only 386 had completed 20 years after their degree by 2020, and 343 (89%) of them were located. At 10 and 15 years after graduation, 62% and 78% of the potential Ph.D. holders were located.\n\nNumber of doctoral graduates for whom 5, 10, 15 or 20 years had elapsed after the degree until 2020 (the latest year for which statistical data was available at the time of the analysis). Number and percentage of those located in Portuguese R&D institutions at each time.\n\nWhen broken down by cohort and time since graduation, the proportion of located individuals tended to be higher for cohort 1 and lower for subsequent cohorts, as shown in Figure 6. The retention rate in the R&D system after 5 years was 75% for individuals in cohort 1, dropping to levels close to 50% in subsequent cohorts. In cohort 4 (scholarships started in 2012), only 156 individuals completed 5 years after graduation by 2020, and of these, only 70 were located. Due to the short follow-up period for this cohort, the results should be interpreted with caution. The persistency in R&D activity after 10 and 15 years follows a similar pattern, with a higher percentage of individuals from cohort 1 being located compared to the other cohorts. The only graduates with a follow-up time of 20 years belonged to cohort 1, with 89% still engaged in R&D.\n\nDoctoral graduates for whom 5, 10, 15 or 20 years had elapsed after the degree until 2020 (the latest year for which statistical data was available at the time of the analysis). Percentages of individuals located and non-located in Portuguese R&D institutions at each time.\n\nFigure 7 illustrates the professional situation of the doctoral graduates who were identified in the IPCTN survey at different points in time after graduation. The information provided by the IPCTN was used to classify the professional situation as ‘teacher’ (contract under the universities teaching career statutes or the polytechnic institutes teaching career statutes), ‘researcher’ (contract under the research career statutes), ‘postdoctoral scholarship’ (any scholarship of varying duration) or ‘other career’. This latter situation includes medical doctors, nurses, senior health technicians, senior technicians/managers in public administration bodies, militaries or secondary education teachers who reported engagement in R&D activity.\n\nPercentual distribution of the professional situations of the doctoral graduates who were identified in the IPCTN survey at different points in time after graduation. N = number of doctoral graduates located 5, 10, 15, or 20 years after obtaining their degree (until 2020, the latest year for which statistical data was available at the time of the analysis).\n\nFive years after graduation, 62% of the located graduates pursued careers in teaching or research, 29% held scholarships, and 6.4% reported other careers. Twenty years after graduation, 95% were working as teachers or researchers, with only 3.3% pursuing other careers. The proportion of individuals who reported being teachers or researchers in higher education, state or not-for-profit institutions increased with the length of time elapsed after graduation.\n\nFigure 8 shows significant differences in the professional situations of graduates across different cohorts. After 5 years, 61% of the located graduates from cohort 1 were teachers, mostly in the higher education sector. This contrasts with the percentages around 45% reported by individuals of cohorts 2 and 3, where postdoctoral scholarships gained increased relevance: 27% and 38%, respectively. In fact, the role of FCT-funded postdoctoral scholarships as a means to pursue a career in R&D is evident in these cohorts. Most of the graduates from cohort 2 obtained their degrees between 2005 and 2007, during a period of significant expansion of the Portuguese R&D system. In cohort 2, 568 individuals, representing 51% of the cohort, were awarded at least one postdoctoral scholarship. In cohort 3, 31% of students obtained at least one postdoctoral scholarship. In this cohort, the majority of students completed their doctorates between 2009 and 2012. This period coincided with the impact of the 2008 financial crisis, which resulted in a significant decrease in the number of scholarships awarded by the FCT. In cohort 4, five years after graduation, there was a notable increase in the proportion of researchers employed under the Scientific Employment Stimulus Programme, which was launched in 2017 to promote the employment of Ph.D. holders and facilitate their access to research careers.\n\nPercentual distribution of the professional situations of the doctoral graduates who were identified in the IPCTN survey at different points in time after graduation. N = number of doctoral graduates located 5, 10, 15, or 20 years after obtaining their degree (until 2020, the latest year for which statistical data was available at the time of the analysis).\n\nFigure 8 illustrates that the proportion of former FCT fellows pursuing careers outside of teaching and research in the business sector is consistently low across all career stages. Cohort 4 showed a slight increase at the 5-year mark since graduation. This trend can be attributed to the limited size and technological intensity of businesses in Portugal, as well as the low effectiveness of incentives to attract Ph.Ds to work outside academia.\n\nAround 90% of the graduates engaged in R&D activity, regardless of the number of years since their doctorate, were in higher education institutions, most often in public universities, followed by private universities and public polytechnics (Figure 9). This was true for all cohorts and at any time since graduation.\n\nPercentual distribution of the sectors of activity of the doctoral graduates who were identified in the IPCTN survey at different points in time after graduation. N = number of doctoral graduates located 5, 10, 15, or 20 years after obtaining their degree (until 2020, the latest year for which statistical data was available at the time of the analysis).\n\nIn 2020, 3193 doctoral graduates were located out of the 5032 scholarship holders who had obtained a degree by the previous year, 2019. This corresponds to 63% of the total. The professional status of the remaining 37% could not be ascertained, as shown in Figure 10.\n\nThe graph on the left shows the percentages of individuals non-located and located in Portuguese R&D institutions in 2020 and the graph on the right depicts the distribution of the professional situations of the doctoral graduates who were engaged in R&D activities.\n\nAlmost half of the located Ph.D. holders were employed as teachers or researchers in Higher Education, the State, or Private Non-Profit Institutions. Only 5% were post-doctoral fellows, and 3% worked in R&D in the Business sector. The remaining 7% pursued other careers, which may or may not encompass R&D, such as doctors, primary/secondary school teachers, public administration managers, and military personnel.\n\nThe differences between cohorts are notable; 84% of the individuals of cohort 1 (grants started in 1995-1997) were found in 2020, a percentage that decreased steadily for the other cohorts, being 62%, 59% and 55% in cohorts 2, 3, and 4, respectively. The proportion of teachers/researchers in the state, higher education and Not-for-Profit institutions was 75% in cohort 1 versus 29% in cohort 4. This is also the cohort in which other careers and scholarships have become more representative. The proportion of researchers in the business sector did not change significantly when comparing the four cohorts and never exceeded 3.8% (cohort 3).\n\nRegarding the professional status of doctoral graduates in 2020 (Figure 11), there are noticeable differences between cohorts. The most common situation among those who started their scholarship in 2012 and obtained their doctorate mostly between 2016 and 2018 is researcher with a scientific employment contract, reported by 23% of individuals. This contrasts with the situation reported by individuals in cohort 1, who obtained their degrees between 2000 and 2003, and were primarily assistant professors/assistant researchers (46%) or associate professors/principal researchers (25%) in 2020.\n\nPercentual distribution of the professional situations/categories of the doctoral graduates who were engaged in R&D activities in 2020.\n\nIt should be noted that 18.5% of the graduates from cohort 4 who had R&D activity in 2020 reported pursuing “Other career”. In contrast, only 4.7% of cohort 1 graduates were in a similar situation. The evolution from cohort 1 to 4 shows the diversification of professional contexts, since “Other career” includes senior technical or managerial positions in public administration, doctors, nurses, senior health technicians, military personnel, etc. As previously mentioned, the Scientific Employment Stimulus Programme, which began in 2016, has played a central role in the career of the individuals in cohort 4. The number of grants is also noteworthy. The ‘Other fellowships’ category comprises fellowships of several typologies and duration that can be awarded by R&D institutions to fulfill personnel needs to carry out research projects. FCT stopped awarding postdoctoral fellowships in 2016, but the data show that R&D institutions still use this mechanism and their own revenues to secure part of their R&D staff.\n\nThe proportion of former grantees with R&D activity in the business sector in 2020 was only 3% across all 4 cohorts, which is lower than the 8% estimated for all doctorate holders resident in Portugal. This suggests that former FCT fellows are less likely to be in the business sector than the general population of doctoral graduates. This issue would merit a more in-depth analysis, but it is beyond the scope of this paper.\n\n\nDiscussion\n\nIdentifying the factors that contribute to success in obtaining a doctoral degree can significantly inform research policy. In this study, we found that FCT funding resulted in an average success rate of 87.5%, which is comparable to that reported in similar situations, i.e. for doctorates carried out with dedicated funding over 3 to 4 years (Groenvynck et al., 2013). The success rate was slightly higher than average for female and younger doctoral candidates, and slightly lower than average in the humanities, arts and social sciences. Studies conducted in different contexts have found little or no difference between genders in the likelihood of completing a doctorate, which is consistent with the observations in this analysis (Mastekaasa, 2005; Ehrenberg & Mavros, 1995). On the other hand, the variation found across scientific fields supports the conclusions of previous work (Groenvynck et al., 2013; Smeby, 2000) and has been attributed to differences in academic practice. Doctoral researchers in STEM fields (Science, Technology, Engineering and Mathematics) typically work as part of a team within the framework of a specific, pre-defined project. In contrast, their colleagues in the social sciences, arts and humanities often work independently and with less defined project parameters. These differences can provide more security, guidance, and consequently, higher success rates and shorter time-to-degree in STEM fields (Larivière, 2012; Long & Fox, 1995).\n\nOf those for whom it was not possible to determine whether they obtained a degree, 6.5% were foreigners. Scholarships awarded for studying abroad resulted in a higher percentage of recipients for whom no degree was confirmed across all cohorts. It is reasonable to assume that some of these individuals did not obtain a doctorate or, having succeeded, did not return to Portugal.\n\nThe consistent decrease in the time it takes to complete a degree is noteworthy. In cohort 1 (scholarships started in 1995-1997), it took 5.54 years, which decreased to 4.67 years in cohort 4 (scholarships started in 2012). This trend has also been reported in studies across different European countries (Kyvik & Olsen, 2013; Hasgall et al., 2019). The decrease in the time to degree may be attributed to the increasing weight of doctoral programmes at the expense of the “student supervisor” model; in Portugal, the proportion of doctorates within a doctoral programme or with a “supervisory committee” was almost 60% in 2019, above the EU average and one of the highest in Europe (EC, 2021). The improvement of doctoral training indicators was driven by additional factors, including the implementation of the Bologna Process and the introduction, in 2007, of an accreditation process that verifies if higher education institutions meet a set of conditions, such as the existence of a qualified teaching staff and adequate human and material resources, to guarantee the level and quality of training.\n\nSeveral factors significantly influence the time to degree, including the scholarship holder’s nationality and the location of the host institution. Foreign scholarship holders took on average less time to obtain a doctorate than their Portuguese counterparts, as did scholarship holders who conducted their work outside Portugal. Previous publications reported similar observations, explained by the fact that expatriates with limited financial resources are more motivated to complete their work and obtain the degree (Espenshade & Rodriguez, 1997; Groenvynck et al., 2013). The time required to obtain a degree in the Humanities, Arts, and Social Sciences was longer than in the other fields. However, as observed in the overall sample, it consistently decreased from cohort 1 to cohort 4 also in the non-STEM areas.\n\nThe results indicate positive aspects regarding the impact of the investment policies in human resources training at the doctoral level implemented by the FCT over the last 25 years. Firstly, the efficient use of public funds, including European Structural and Investment Funds, which have supported part of this investment since 1987. In fact, the success rate (or efficacy) in obtaining the degree was high and comparable to other EU. Secondly, the efficiency of scholarship recipients in obtaining a doctorate has improved over time, as evidenced by a decrease in the time taken from the oldest to the most recent cohorts. This trend is consistent with findings from similar studies.\n\nIn the more recent cohorts, fewer scholarships were awarded exclusively abroad, and more foreign students chose to pursue their Ph.D. studies in Portugal. This evolution shows the increasing maturity and attractiveness of the national R&D system. In the 1990s and early 2000s, there were significant weaknesses in scientific capacity, both in terms of human resources and investment. These limitations have been mitigated by increased R&D funding, particularly between 2005 and 2009. During this period, R&D spending grew from 0.76% of GDP to 1.58%, and the number of researchers increased from 21126 to 39834 FTE, an investment that laid the foundations for the increase in doctoral studies in Portugal.\n\nIn the 2020 snapshot, 63% of the doctoral graduates from the four cohorts analysed were identified as having employment in higher education, where they worked as teachers, researchers or scholarship holders. The prominence of this sector aligns with official statistics regarding the overall Ph.D. population in Portugal. The cohorts exhibit significant differences, with doctoral graduates from the oldest cohort, whose fellowships began in 1995-1997 and who mostly obtained their degree by 2003, showing a remarkably high level of persistence in the national R&D ecosystem (almost 85%). In 2020, these former scholarship holders were assistant professors/assistant researchers (46%) or associate professors/principal researchers (25%). On the other hand, for the 2012 cohort, the vast majority of whom graduated in 2017, the most common situation in 2020 was a contract under the Scientific Employment Stimulus Programme, reported by 23% of individuals. The proportion of scholarships in this cohort was high, which is somewhat surprising given the policies implemented since 2016 that advocate for employment contracts as the preferred form of labour relations between doctoral graduates and R&D institutions. The number of fellowships suggests that institutions are still using this more precarious mechanism to secure their R&D workforce.\n\nOne significant observation from comparing cohorts 1 and 4 is the increasing prevalence of ‘other careers’ (6% versus 18%). This category includes senior technicians or managerial positions in public administration, doctors, nurses, senior health technicians, or military personnel in the armed forces. The 2020 snapshot indicates that FCT doctoral graduates are increasingly finding employment outside of higher education. The diversification of highly trained human resources across different sectors of society is a positive aspect and potential indicator of their growing impact. However, it is concerning that 37% of doctorate holders could not be located, raising questions about their professional status and sector of activity. It should be clarified whether they are in Portugal and what their professional status and sector of activity is. If they have left Portugal, it should be asked what they do in their host country. Answering these questions would entail the use of other research strategies, such as surveys, or additional administrative sources, such as records from the Social Security Information System.\n\nThe exercise to locate doctoral graduates at different times after their degree revealed that the proportion of individuals located was significantly higher for cohort 1 than for the other cohorts. For instance, 75% of the doctoral graduates in cohort 1 were engaged in R&D five years after their degree, a percentage that decreased to approximately 50% in cohorts 2 and 3 and reached 45% in cohort 4. After fifteen years since obtaining their PhD, 83% of cohort 1 graduates were engaged in R&D, a percentage that fell to 59% for cohort 2 graduates. This data raises questions about the ability of the national ecosystem to absorb recent doctorates. Additionally, the professional status of located doctoral graduates changed significantly with the time that elapsed after their degree and across cohorts; in cohort 1, 60% of the doctoral graduates located reported being teachers after 5 years, but in the following cohorts this percentage fell progressively, to 30% in cohort 4. Concomitantly, there was an increase in the number of researchers and post-doctoral fellows. The significance of the postdoctoral scholarships funded by the FCT as a means of ensuring continuation in the SNCT 5 years after obtaining a degree is evident in cohorts 2 and 3, while in cohort 4 the increase in researchers hired under the Scientific Employment Stimulus Programme, which has been in place since 2017, is noticeable, to the detriment of postdoctoral scholarships.\n\nThe IPCTN survey does not provide information on the type of contract, so it was not possible to determine the distribution of permanent and fixed-term contracts. However, according to the CDH survey, in 2020 65% of doctorate holders were on permanent contracts while 35% were on fixed-term contracts. The proportion of fixed-term contracts was much higher among younger doctorate holders.\n\nLess than 20% of individuals across all cohorts, at any time since obtaining their degree, had a position outside of academia. The Higher Education sector, particularly the Public University subsector, continues to dominate overwhelmingly across all cohorts. This confirms a well-known characteristic of the national scientific ecosystem. Furthermore, the proportion of doctoral graduates in the Business sector is considerably lower than in other economies. According to the CDH, only 8% of graduates were in the Business sector, compared to 30% in countries such as Belgium, Denmark or the United States. It is worth noting some initiatives aimed at addressing this issue and capitalising on the potential of highly qualified employment in other sectors. For example, since 1997, there has been a system of tax benefits for business R&D, and since 2004, FCT doctoral scholarships are available to be carried out in companies. However, the number of applications for this type of scholarship has been quite low, typically less than 2% of the total number of scholarships awarded each year. In 2023, the FCT launched a specific application line for scholarships in non-academic environments; a total of 332 scholarships were approved. The aim was to promote and leverage doctoral programmes in the business, social, and public administration sectors. This and other measures, such as fostering scientific employment in Collaborative Laboratories4, which have been in place since 2019, should contribute to reducing the imbalance between sectors in terms of the employment of doctoral graduates in the medium and long term. At the same time, other instruments, such as the “FCT Tenure” put in place in 2023, will play an important role in expanding the capacity of the scientific system to absorb doctoral graduates by providing co-funding to open-ended contracts in the teaching or research careers.\n\nThis retrospective study addressed a significant gap in evaluating the return on investment in advanced human resources training by the FCT over the last 25 years. It also established the methodological foundations for monitoring the career paths of FCT-funded doctorates in the future. However, the data has some limitations that prevent a more comprehensive description of the career paths of doctoral graduates. It lacks information on international mobility and contractual relationships after graduation. Additionally, it solely relied on statistical and administrative data, omitting personal aspirations and experiences encountered during and after the doctorate. These variables are also critical in determining career paths.\n\nThe study confirmed the challenges faced by doctoral graduates funded by the FCT in integrating into non-academic job markets. This is a well-known issue in Portugal and has been identified by national and international studies. On the other hand, it has demonstrated efficient use of public funds, with high success rates and time to degree within the average of other European countries. Undoubtedly, the observed evolution between cohorts indicates the maturity attained by the Portuguese scientific system in recent decades.\n\n\nEthics and consent\n\nPart of the data was supplied by a third party, the Directorate-General of Statistics of Education and Science (DGEEC, https://www.dgeec.medu.pt/) whose mission is to guarantee the production and statistical analysis about education and science, upon delegation of the national body for statistics production, Statistics Portugal (INE, www.ine.pt). Access to the data was governed by a protocol signed between the FCT and the DGEEC. The authors of this paper signed a confidentiality agreement and a term of responsibility of compliance with the General Data Protection Regulation (GDPR) and with the Law of the National Statistical System, Law n° 22/2008 of 13th May 2008. Data analysis was carried out in the safe center of the Directorate-General of Statistics of Education and Science. The underlying data published in Figshare complies with the above regulations and has been treated in accordance with the international Safe Harbour Privacy Principles.", "appendix": "Data availability\n\nThe underlying data has been deposited in Figshare: Obtaining a PhD in Portugal. Determinants of success and subsequent career paths. https://doi.org/10.6084/m9.figshare.26062966 (Ramos, A. & Ferreira, D,2024)\n\nIt contains the following data:\n\n• Time to Degree.cvs (Anonymised list of scholarship holders containing the following information: cohort number, sex, age at application year, scientific area, scientific field (ford), nationality (group), time to degree (y), degree, localinstdegree)\n\n• Professional Status After PhD.cvs (Anonymised list of scholarship holders containing the following information: cohort number, 5 years professional status, 5 years sector, 10 years professional status, 10 years sector, 15 years professional status, 15 years sector, 20 years professional status, 20 years sector)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank the Departamento de Formação Avançada and Arquivo de Ciência e Tecnologia of FCT for providing access to data, and António Esteves for assisting in determining the degree date of former scholarship holders. We also greatly acknowledge the collaboration of Direção-Geral de Estatísticas da Educação e Ciência in running the cross-checks needed to ascertain the professional situation of the graduates.\n\n\nReferences\n\nAuriol L, Misu M, Freeman R: Careers of Doctorate Holders: Analysis of Labour Market and Mobility Indicators. OECD Science, Technology and Industry Working Papers, No. 2013/04. Paris: OECD Publishing; 2013. Publisher Full Text\n\nBoman J, Beeson H, Sanchez Barrioluengo M, et al.: What comes after a PhD? Findings from the DocEnhance survey of doctorate holders on their employment situation, skills match, and the value of the doctorate. Strasbourg: European Science Foundation (ESF); 2021. Reference Source\n\nDebacker N: On the academic postdoctoral track in Flanders (Belgium) after obtaining a doctorate. Centre for Research & Development Monitoring, ECOOM Briefs; 2021; vol. 39. .\n\nDGEEC: Sumários estatísticos do Inquérito aos Doutorados 2009 (CDH09).2013.\n\nDGEEC: Sumários Estatísticos do Inquérito aos Doutorados 2015 (CDH15).2017.\n\nDGEEC: Resultados definitivos do Inquérito aos Doutorados 2020 (CDH20).2021.\n\nDGEEC: Diplomados no Ensino Superior 1996/1997 a 2021/2022.2023.\n\nEhrenberg RG, Mavros P: Do doctoral students’ financial support patterns affect their Times-To-Degree and completion probabilities? J. Hum. Resour. 1995; 30(3): 581. Publisher Full Text\n\nEspenshade TJ, Rodriguez G: Completing the Ph.D.: Comparative performances of U.S. and foreign students. Soc. Sci. Q. 1997; 78(2): 593–605. Reference Source\n\nEuropean Commission, Directorate-General Research and Innovation: MORE4 – Support data collection and analysis concerning mobility patterns and career paths of researchers – Survey on researchers outside Europe, Publications Office.2021; 2021. Publisher Full Text\n\nEuropean Commission: Directorate-General Research and Innovation, Science, Research and innovation performance of the EU (2018) – Strengthening the foundations for Europe’s future. Publications Office; 2017. Publisher Full Text\n\nFerreira A: Living on the edge: Continuous precarity undermines academic freedom but not academic identity in the neoliberal academia.Vatansever A, Kölemen Y, editors. Free as a Bird: Academic Precariat and the State of Academic Freedom in the Global North. London and New York: Routledge; 2023; pp. 79–100.\n\nGroenvynck H, Vandevelde K, Van Rossem R: The PhD track: Who succeeds, who drops out? Research Evaluation. 2013; 22(4): 199–209. Publisher Full Text\n\nHancock S: What is known about doctoral employment? Reflections from a UK study and directions for future research. J. High. Educ. Policy Manag. 2021; 43(5): 520–536. Publisher Full Text\n\nHancock S, Wakeling P, Chubb J: 21st Century PhDs: Why we need better methods of tracking doctoral access, experiences and outcomes (RoRI Working Paper No.2) (Version 3). Research on Research Institute; 2019. Publisher Full Text\n\nHasgall A, Saenen B, Borrell-Damian L, et al.: Doctoral education in Europe today: approaches and institutional structures. European University Association; 2019. Reference Source\n\nHorta H, Cattaneo M, Meoli M: PhD funding as a determinant of PhD and career research performance. Stud. High. Educ. 2018; 43(3): 542–570. Publisher Full Text\n\nKyvik S, Olsen TB: Increasing completion rates in Norwegian doctoral training: multiple causes for efficiency improvements. Stud. High. Educ. 2013; 39(9): 1668–1682. Publisher Full Text\n\nLarivière V: On the shoulders of students? The contribution of PhD students to the advancement of knowledge. Scientometrics. 2012; 90(2): 463–481. Publisher Full Text\n\nLong JS, Fox MF: Scientific Careers: universalism and particularism. Annu. Rev. Sociol. 1995; 21(1): 45–71. Publisher Full Text\n\nMastekaasa A: Gender differences in educational attainment: the case of doctoral degrees in Norway. Br. J. Sociol. Educ. 2005; 26(3): 375–394. Publisher Full Text\n\nMorais C, Gaio Alves M: Do doutoramento para o mercado de trabalho? O percurso de inserção profissional de um grupo altamente qualificado. Sociologia online. 2019; 20: 36–60. Publisher Full Text\n\nOECD: OECD Review of Higher Education, Research and Innovation: Portugal. Paris: OECD Publishing; 2019. Publisher Full Text\n\nOECD: Education at a Glance 2023: OECD Indicators. Paris: OECD Publishing; 2023. Publisher Full Text\n\nPedersen HS: New doctoral graduates in the knowledge economy: trends and key issues. J. High. Educ. Policy Manag. 2014; 36(6): 632–645. Publisher Full Text\n\nRamos A, Ferreira D: Obtaining a PhD in Portugal. Determinants of success and subsequent career paths. [Dataset]. figshare. 2024. Publisher Full Text\n\nRodrigues ML: Políticas de ciência em Portugal nos 40 anos de democracia. Revista Iberoamericana de Ciencia Tecnología y Sociedad. 2017; 12(36): 11–31.\n\nSmeby J: Disciplinary differences in Norwegian graduate education. Stud. High. Educ. 2000; 25(1): 53–67. Publisher Full Text\n\nSpognardi A, Matos A: Oferta e procura de investigadores doutorados; distorções no Sistema Científico e Tecnológico português.Sequeiros P, Carvalho MJ, Capinha G, Org. A investigação e a escrita - Publicar sem perecer. Imprensa da Universidade de Coimbra; 2021; pp. 215–248. Reference Source\n\nWollast R, Boudrenghien G, Van Der Linden N, et al.: Who Are the Doctoral Students Who Drop Out? Factors Associated with the Rate of Doctoral Degree Completion in Universities. Int. J. High. Educ. 2018; 7(4): 143. Publisher Full Text\n\nWoolston C: PhD career paths hold promise. Nature. 2018; 555: 277. PubMed Abstract \| Publisher Full Text\n\n\nFootnotes\n\n1 A permanent identifier for individuals carrying out scientific activity in Portugal, allowing authentication in various services related, such as CIÊNCIAVITAE.\n\n2 CIÊNCIAVITAE is the Portuguese scientific curriculum management system.\n\n3 FCT awarded master scholarships until 2007.\n\n4 Collaborative Laboratories involve businesses or private non-profit associations and R&D institution to foster the production, dissemination and transmission of knowledge. Based on a portfolio of products or systems with higher added value, CoLABs aim to facilitate the access of companies to global markets through exports, as well as to support the attraction of foreign investment in technology-intensive areas." }	[ { "id": "334906", "date": "13 Nov 2024", "name": "Sally Hancock", "expertise": [ "Reviewer Expertise Doctoral education", "doctoral employment", "higher education policy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article offers an important contribution to our understanding of the changing employment conditions for PhD holders in age of expansion. It does so through analysis of an extensive dataset on PhD holders in Portugal and is able to highlight shifts in employment destinations over time. The unique case of doctoral expansion in Portugal is well explained and the article is well positioned in relation to current literature. The study design and presentation of results are clear. The analysis appears to be sound. The most significant aspect for further development relates to the interpretation of the empirical data and concluding discussion. As a reviewer I remain somewhat undecided about the strength of the negative framing of the trend away from academic and R&D employment. Does this implicitly convey policy-makers' and employers' aspirations for growing the doctoral supply chain, and if so, should that aim be more explicit? Since the survey data are descriptive and do not robustly convey individual decision-making, it is not possible to say whether this shift is a disappointment for the PhD holders concerned, or whether it represents a broadening of horizons for action and a deliberate venture into non-academic employment. It seems, to me, unwarranted to valorise the empirical observations by referring to 'difficulties in retaining' PhDs in academic or research employment, or of the 'challenges of integrating' PhDs in the non-academic labour market. These trends may be an inevitable phase in the ongoing expansion of doctoral labour market and may lead to transformations in non-academic sectors. I think there is a wider point to acknowledge, which is that the contributions of PhD graduates beyond academic and research roles are not well understood, but that does not necessarily mean that value is not created here. Also, with regard to the way the trends over time are framed: the declining 'persistence' in R&D employment across cohorts may not necessarily be a cause for concern. It may be a purposeful turn away from precarious and deteriorating academic working conditions made by younger PhD holders. Finally, it may be worth some comment on the fact that although the data can show trends over time, they cannot capture individual trajectories. It is not clear if these trends will have permanence or if there may be individual movement between academic, R&D and non-academic occupations over the career (sector porosity) - meaning that some of these destinations are less static than might be implied.\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": "347736", "date": "15 Jan 2025", "name": "Maresi Nerad", "expertise": [ "Reviewer Expertise Doctoral education research and policies", "PhD career path studies", "globalization of doctoral education", "the history of women in higher education" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study is a useful analysis of doctoral completion rate, time-to-degree, and careers at 5, 10, 15 and 20 years out of 4 cohorts of Portuguese PhD fellowship holders funded by the Portuguese Foundation for Science and Technology between 1995 and 2012. It is useful as there seem to be a lack of such analyses of fellowship holders that can be compared to European data on PhDs. Specifically, the funding agency is finding out whether their monetary investment made a difference in completion rates and time-to-degree for PhDs and whether the PhDs joined R&D organizations, be there in business, industry, government of academia.\n\nThe article is well written and mostly clear. The data sources are well defined, and the method is clearly described. The findings are well supported, and the supplied tables and description are transparent. The conclusion drawn to answer the 3rd research question, particularly in terms of relevance for public policy could be more concise. The authors correctly mention three important limitations of the study. There are contradictions in the interpretation of the career findings.\nThe following suggestions and recommendations follow the sequence of the article:\nIntroduction and literature review To make it easier for non-Portuguese readers I would recommend providing at the beginning of the article explanations of the specific Portuguese context or refer in the introduction to the pages in the article where various new Portuguese policies are described.\nThe literature review could be improved by consulting a wider range of literature on PhD career paths, especially the US National Science Foundation reports (Survey of Doctoral Recipients – SDR biannual report, and the Survey of Earned Doctorates, SED annual report), both are analyzed, and data is provided in the NSF Science & Engineering Indicators Publication. Such studies have been going on since 1950s. Already in 1999 Science published an article on a national US PhD career path study, explaining the different patterns of choosing to undertake postdoc studies by selected science and engineering disciplines, Postdoctoral Patterns, Career Advancement, and Problems, in American Association for the Advancement of Science, Science, 285, Vol 285, pp.1533-1535). This article explained that gender needs to be carefully considered. The Center for Innovation and Research at the University of Washing, Seattle has further undertaken 2 more US national career path studies and advised European organizations on how to track researchers’ career. See for example in 2012 a meeting in Luxembourg under the leadership of the European Science Foundation (https://www.education.uw.edu/cirge/category/phd-career-path-tracking/).\nThe authors mention a publication by Ehrenberg and Mavros (1995). It is suggested to look further into Ehrenberg’s publications, such as the 2009 book Ehrenberg & Kuh (Eds) Doctoral Education and the Faculty of the Future, Ithaka, NY: Cornell University Press.) See also the reports from the US Council of Graduate Schools (CGS) on studies on doctoral completion. Similarly, the UK Council on Graduate Education (UKCGE) has published various PhD career path studies. Also note the Australian study on PhDs career path study of 2007 (Western et al. PhD Graduates 5 to 7 Years Out: Employment Outcomes, Job Attributes and the Quality of Research Training, Brisbane, Australia: The University of Queensland Social Research Center).\nThe authors write that “There is currently limited understanding of the expansion of doctoral training, including its causes, social and economic contributions, and medium to long-term.” It is advisable that the authors familiarize themselves better with the publication in the field of higher education, particularly doctoral education research. For example, Portuguese colleagues (Cardoso, et al) published a book in 2020, Structural and Institutional Transformations in Doctoral Education, Issues in Higher Education) that has several chapters explaining the expansion in doctoral education worldwide.\nMethods National career path studies solely relying on administrative and nationally collective data, are an intricate undertaken. The characterization of the cohorts and thus the analysis of the studies’ findings would benefit from disaggregating men and women by disciplines and age. For example, more women are fellowship holders among cohort 3 and 4, and in these cohorts the percentage of social sciences, humanities and arts has increases. Traditionally women tend to study to a larger degree in these fields, which could be an explanation of the increase of in the last two cohorts.\n\nThe cohorts are well described. It would be good to include the rationale for the grouping of sample sizes of the 4 cohorts (three years of graduates in the first cohort, two years in the second cohort, and one year in the fourth cohort). Once the readers see the numbers in the tables, they understand that the authors opted for an even cohort population.\n\nResults and Discussion The authors name the limitation of the study: lacking information on international mobility in the career, the kind of contractual appointment such a temporary or more permanent appointments, part time or full-time, and most importantly, the lack of information of personal career aspiration. However, further contextual information, such as being a parent and needing to provide income for the family, might restrict some newly completed PhDs to accept temporary postdoc positions in favor of other more permanent employment options.\nThe study’s research questions 1 and 2 are well answered with clear evidence in the data findings. The authors could be more explicit in answering the third study question in providing conclusions and possible recommendations that are relevant for public policies and that might lead to an increase of PhDs choosing R&D employment both within academia and in business and industry.\nMinor suggestions The term used for non-Portuguese citizens who have permanent residence in Portugal as “displaced citizen”, is not a commonly used term.\n\nIt would be good to define PhD “success”. What is considered a successful time for completing a PhD in Portugal? What is not mentioned in the article is the importance of the quality of the outcome, i.e. the trained doctorate as well as the quality of doctoral researcher for labour market analyses. In this study quality could not be assessed by using the existing data sources.\nOn page 17, could the underlying assumption in this sentence be explained? “The number of fellowships suggests that institutions are still using this more precarious mechanism to secure their R&D workforce.”\n\nA follow up study comparing fellowship holders with non-fellowship holders might be interesting and might provide another validation of the investment of money by the FCT in doctoral fellowships.\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": [] } ]	1	https://f1000research.com/articles/13-1101
https://f1000research.com/articles/12-410/v1	17 Apr 23	{ "type": "Research Article", "title": "A prolonged wait: The impact of COVID-19 on elective surgeries in India, a prospective study", "authors": [ "Heraa Islam", "Mohsin Nazeer Muhammed", "Aditi Kapoor", "Muhammed Ehsan", "Gowri Shankar", "Raadhika Agrawal", "Heraa Islam", "Aditi Kapoor", "Muhammed Ehsan", "Gowri Shankar", "Raadhika Agrawal" ], "abstract": "Background: The continuing Coronavirus Disease 2019 (COVID-19) pandemic has had a massive impact on healthcare systems all around the globe. There is no exception in the demographics of elective surgery also. Like any other medical professionals, surgeons and post-graduates are redirected to the management of patients with COVID-19. The purpose of this study is to determine how the COVID-19 pandemic affected elective surgeries, surgeon skills, and post-graduate training. Methods: This prospective study was done among 320 participants through a 15-question online cross-sectional survey sent primarily to surgeons practicing in six states of India that were most affected by the pandemic according to recent statistics and also to surgeons in other states via email or other online messaging services. Results: In our study, the following observations were made: Patient/ patient attendant dissatisfaction in a reduction in the availability of hospital beds, shortage of medical oxygen and lack of availability of surgical implants. Conclusions: All these factors showed significant p-values with statistical significance, thereby indicating the impact of the COVID-19 pandemic on the healthcare system and healthcare delivery. The pandemic also had a significant impact on post-graduate training.", "keywords": [ "COVID-19", "Pandemic", "elective surgery" ], "content": "Introduction\n\nThe World Health Organization (WHO) declared Coronavirus Disease 2019 (COVID-19) to be a pandemic on March 11, 2020.1 The government of India had adopted several measures to limit and stop the pandemic, including a nationwide lockdown, infection control standards including usage of masks and personal protective equipment (PPE) and social distancing.2,3 The pandemic had a massive impact on healthcare systems all around the world. Several healthcare practitioners were redirected to COVID management. Furthermore, due to resource reallocation and present economic constraints, hospitals throughout the world have been compelled to restructure to offer the best possible treatment for patients while avoiding the transmission of the coronavirus among patients and healthcare personnel. Hospital visits have decreased as a result of the cancellation of elective surgeries and routine outpatient department (OPD) treatments. Institutes and hospitals have cancelled in-person lectures, clinical rounds, seminars, and other educational events.4 This has had a significant impact on learning and teaching for post-graduates (PG). Elective operations are not optional procedures, but rather non-urgent procedures. In 50% of patients, cancelling or delaying elective surgery has unanticipated repercussions that might result in severe morbidity and mortality.5\n\nThe effect of the COVID-19 era on specific subspecialists is uncertain, particularly in epicentres where physician’s duties are changing to suit pandemic demands. Furthermore, while emergency and critical care professionals have received a lot of attention, surgeons are frequently overlooked. This cohort has extremely high baseline rates of burnout, and a worldwide pandemic could worsen any existing effects.6,7 Since most elective procedures and in-person clinics have been suspended across the world, many surgeons have had to quickly adapt their practices and help with frontline responsibilities. Moreover, surgeons operate in interdisciplinary teams, thus cancellations of elective surgeries have an impact on a variety of healthcare employees. COVID-19 has also proven to be a financial and social issue, in addition to a medical one.\n\nOncological surgery\n\nIt is important to rationalise every surgery performed because standard surgical procedures have been disrupted due to workforce issues. This is crucial in cancer surgery, when the physician must weigh the risks of both potential viral transmission to the surgical team and potential cancer patient progression.8 In the first instance, patients should be moved to hospitals with more financial resources available for operations, and it is suggested that local “COVID-19 free” surgical hubs be established to continue oncological surgery. General factors must also be taken into account for patients with cancer. Most complicated elective surgical procedures are frequently followed by post-operative care in a hospital ward. Patients occasionally experience postoperative problems that necessitate Intensive Therapy Unit (ITU) admission and/or re-operation, which could be difficult given the rising number of COVID-19 patients needing Level 3 care. It is advised to keep length of stay (LoS) to a minimal, particularly in critical care.9,10\n\nGeneral surgery\n\nThe provision of emergency general surgery is a crucial component of the planning of surgical services. Wherever possible, it is crucial to maintain the status quo for both COVID-19-infected patients and those who are not.11 To prevent nosocomial infections in COVID-negative patients, it has been suggested that separate “clean” and “dirty” emergency operating rooms be created. If conservative therapy has failed, poses a risk to the patient’s health, is likely to lengthen hospitalisation, or raises the possibility of readmission at a later time, operations or procedures should be carried out.12 Additionally, surgeons need to be on the lookout for a potential decline in the supply of blood products. Resources are already running out in the UK as a result of rising demand as well as a decline in blood donors brought on by social isolation and quarantine regulations.13 Therefore, it is advised that each particular centre should monitor the regional blood availability and, if necessary, support a restrictive transfusion strategy in both the operating room and the intensive care unit14 or intraoperative cell preservation.15\n\nCardiothoracic surgery\n\nThe impact of COVID-19 on cardiothoracic practise was inevitable. All elective and non-urgent surgeries have been delayed in the US and the UK, and resources have been shifted to the emergency and urgent cardiothoracic care. Additionally, cardiothoracic surgeons are excellent candidates for redeployment since they have general abilities that are typically transferrable to ITU. Based on the stage of the COVID-19 pandemic, the NHS in the UK has released recommendations on the management of cardiothoracic surgeries.10\n\nUrology\n\nClassification of urological surgery into oncological, emergency, and benign procedures by Ahmed et al.,16 included a number of prioritising suggestions. To reduce the impact on resource utilisation and labour shortages caused by the redeployment of anaesthetists, these recommendations include the extensive use of local anaesthesia and day-case surgery whenever possible. Additionally, they recommended the establishment of parallel urology services, with “hot” hospitals treating suspected COVID-19 patients and “cool” hospitals handling oncological and emergency work. Additionally, although the extent of urinary viral shedding is still not entirely understood, there is some preliminary evidence that SARS-CoV-2 Viral RNA can be detected in the urine, indicating that urology services must still take care.17\n\nOphthalmology\n\nThese procedures should be carried out as day cases whenever it is safe to do so. The surgical treatment with the shorter postoperative recovery duration and fewer postoperative follow-up visits should be chosen. Additionally, whenever possible, local anaesthesia is preferred to general anaesthesia.18\n\nOral and maxillofacial surgery (OMFS)\n\nNHS England and NHS Improvement have produced recommendations for treating OMFS and trauma patients.19 They recommend that senior team members make decisions about patient care at the initial point of contact with the patient in order to prevent unnecessary admissions and reduce nosocomial infections.\n\nPlastic surgery\n\nTo assist in the care of patients undergoing plastic surgery during COVID-19, the British Association of Plastic Surgery (BAPRAS) and NHS England have offered advice to its members. A plastic and reconstructive surgery escalation strategy has been published by the association.20 This offers advice to hospitals on how to handle an increase in COVID-19 prevalence. High prevalence requires limiting emergency surgery and ceasing all elective surgery. Minor surgeries should be carried out in outpatient clinics, where all emergency injuries should be triaged for treatment. Guidelines have been developed for the management of burns, breast reconstruction, and melanoma-specific issues, and advice has been developed to direct local services in order to deal with the anticipated significant reduction in clinical and surgical facilities. A referral letter is still necessary for patients whose melanoma diagnosis is suspected, and it will be examined by a multidisciplinary team (MDT). A recommendation will be made based on the image. The patient may then be immediately sent for surgery to remove the lesion after the pathology has been reviewed, and the results will be telephoned to them.21 NHS England has also provided details on how burn injuries during the COVID-19 epidemic should be managed.22\n\nPaediatric surgery\n\nAccording to the American College of Surgeons, the fundamental goal of paediatric surgery during the COVID-19 pandemic is to treat children with urgent surgical needs with the proper care while efficiently using patient care resources and safeguarding healthcare professionals. To prevent extended hospital stays or additional readmissions to the hospital, non-urgent surgery should only be done when absolutely necessary.23 Additionally, NHS England has advised against performing elective paediatric procedures on children unless they are ASA Grade 1 patients, with the exception of cancer situations.24,25 Paediatric surgical care should prioritise the efficient management of emergency situations, delaying any necessary elective procedures as possible. In order to shorten the preoperative period and guarantee an early discharge, this will provide greater access to theatres and an increase in staff capacity. While minimising the risk of infection transmission, the paediatric surgical team should provide ongoing management of urgent surgical situations. The utilisation of telemedicine as well as reorganising into two groups—one that works in hospitals and the other that operates remotely—are examples of such tactics. The attendance of parents during surgery should be taken into consideration whenever it is safe to do so.23\n\nThe purpose of this study is to see how the COVID pandemic affected elective operations, surgeon skills, and post-graduate training.\n\n\nMethods\n\nA prospective cross-sectional study was carried out from June to July 2021 in Kasturba Medical college, through an online cross-sectional survey questionnaire (Google forms) consisting of 15 questions circulated across India primarily to surgeons practising in six states of India that were most severely affected by the pandemic according to recent statistics and also to surgeons in other states of India. This was done through E-mail or any online messaging service. The questionnaire was made by the researchers, no specific program was used and no validity/reliability test was done.\n\nThe forms were sent to various surgeons across India. The responses we received from them were considered as their consent to participate in the study. The study was approved by the Institutional Human Ethics Committee (IHEC) clearance from KIMSHEALTH via letter no. KIMS/IHEC/APPROVAL/08/2021/03 dated September 7th, 2021.\n\nDue to the low risk nature of this study and the effects of COVID-19, retrospective ethical approval was obtained. The study was originally submitted to the IHEC at KIMSHEALTH on the 14th of August 2021. At KIMSHEALTH, there are two committees: the Scientific and Research Committee and the Ethics Committee. The Ethics Committee meets once every three months, while the Scientific Committee meets frequently. The Scientific and Research Committee’s approval allows the principal investigators of these projects to begin patient recruitment. For the purposes of the present study, surgeons across India—not patients—were the population under consideration and there were no ethical issues involved so before the study began we submitted it to the Scientific and Research Committee, which has been given the authorization to review and approve medical research and other observational studies. Three members of the Ethics Committee are represented on the committee to ensure that all ethical guidelines and rules are strictly followed. The Scientific and Research Committee approved the start of the study. The committee’s decision was then ratified by the Ethics Committee at a later date.\n\nSurgeons in the various surgical specialities in six states across India (Bihar, Delhi, Karnataka, Kerala, Maharashtra and Uttar Pradesh) that were most severely affected by the pandemic as per recent statistics and also other states in India.\n\nNon-surgical medical practitioners were excluded from the study.\n\nIn this study, the questionnaires were sent as Google forms to surgeons via Gmail and WhatsApp platform, out of which 320 responses were received by us, which became the primary data source. The combined responses were recorded and analysed statistically by the authors.\n\nFrequency and percentage were used to represent categorical variables, whereas the mean and standard deviation were used to represent continuous values. The Chi-squared test was used to examine associations between categorical variables. Unpaired t-test analysis was used to compare quantitative data between two groups. The ANOVA analysis was used to compare continuous variables between more than two groups. Comparison of continuous variable among more than two group was analysed by ANOVA with Post hoc tests of multiple comparison -LSD. p<0.05 was regarded as statistically significant. IBM SPSS Statistics (RRID:SCR_016479) version 24 was used for data analysis.\n\n\nResults\n\nIn this present study, a total of 320 participants were enrolled. The age groups were divided into 25-40 years old (170 participants), 40-60 years old (135 participants), and 15 participants were >60 years old (Table 1).29 A total of 241 participants were male and 79 were female (Table 2). In this study, various surgeons participated from various states in India, namely; Bihar (14), Delhi (16), Karnataka (89), Kerala (133), Maharashtra (14), Uttar Pradesh (20), and other states (34) (Table 3, Figure 1). Surgeons from various specialities have participated in this study, and the distribution was as follows: Cardiothoracic vascular surgery (CTVS), 5; General Surgery, 71; Neurosurgery, 5; Obstetrics and Gynaecology, 27; Ophthalmology, 17; Oral and Maxillofacial surgery, 20; Otorhinolaryngology, 31; Paediatric Surgery, 3; Plastic Surgery, 7; Surgical Oncology, 8; Trauma and Orthopaedic Surgery, 93; and Urology, 33 (Table 4).\n\nOverall, 59.7% of those participants who agreed that there was a reduction in bed availability also faced the brunt of patient or patient bystander’s dissatisfaction; whereas 40.3% of those who reacted that there was no reduction in the availability of beds also faced the brunt of patient or patient bystander’s dissatisfaction. With a p-value of 0.004, this showed a statistically significant association (Figure 2, Table 5 and Table 6).\n\nA total of 70.4% of those participants who agreed that there was a shortage of oxygen also faced the brunt of patient or bystander’s dissatisfaction; whereas 29.6% of those who reacted that there was no shortage of oxygen also faced the brunt of patient or patient bystanders dissatisfaction, With a p-value <0.001, this showed a statistically significant association (Figure 3, Table 7, Table 8 and Table 9).\n\nOverall, 78.8% of those participants who agreed that there was a shortage of PPE kits also faced the brunt of patient or bystander’s dissatisfaction; whereas 21.2% of those who reacted that there was no shortage of PPE kits also faced the brunt of patient or patient bystanders dissatisfaction. With a p-value <0.001, this showed a statistically significant association (Figure 4 and Figure 5, Table 10, and Table 11).\n\nPPE, personal protective equipment.\n\nGuidelines for the care of acute OMFS and trauma patients have been issued by NHS England and NHS Improvement.19 They recommend that senior team members make decisions about patient care at the initial point of contact with the patient in order to prevent unnecessary admissions and reduce nosocomial infections. Moreover, results showed that doctors found it challenging to get accustomed to the new pre-op guidelines in line with the pandemic (Figure 6, Table 12).\n\nOverall, 60.7% of those participants who agreed that there was a delay in procurement of surgical implants also faced the brunt of patient or bystander’s dissatisfaction, whereas 40.3% of those who reacted that there was no delay in procurement of surgical implants also faced the brunt of patient or bystander’s dissatisfaction. With a p-value of 0.041, this showed a statistical association (Figure 7, Table 13 and Table 14).\n\nA total of 64% of participants also agreed that the COVID-19 pandemic had affected the post-graduate teaching program (Figure 8 and Table 15).\n\nPG, post-graduates.\n\nPG, post-graduates.\n\nMore than half of the participants agreed to the fact that they were affected by the fear of contracting COVID-19 during high-risk invasive procedures and there was an increase in the rate of post-operative complications in surgically operated COVID-19 patients (Figure 9 and Figure 10, Table 16 and Table 17). Overall, 74.7% of surgeons felt that there was a decline in aerosol generating procedures during the pandemic (Figure 11, Table 18). A total of 54.1% of surgeons felt that deferral of surgeries in patients with comorbidities led to ‘grave consequences’ (Figure 12, Table 19). Most of the surgeons did not face a personal financial crisis during the pandemic (Figure 13, Table 20). Overall, 46.6% of doctors noticed deterring influence on surgical skills due to abstinence from conducting surgeries whereas, the rest were not affected by it (Figure 14, Table 21).\n\nCOVID-19, Coronavirus Disease 2019.\n\nCOVID-19, Coronavirus Disease 2019.\n\nSurgeons identified that hospital administration made significant changes in healthcare and employment policies during the pandemic (Figure 15, Table 22).\n\n\nDiscussion\n\nA survey of 611 orthopaedic physicians from 140 Indian cities was conducted by Sahu et al.26 Orthopaedic surgeons reported being slightly stressed 40.5% of the time and being very worried 22.5% of the time. The proportion of orthopaedic surgeons who reported feeling “certainly stressed out” rose as age declined.\n\nIn the survey conducted by Upadhyaya et al.27 138 (77.5) PG trainees participated, and 65.1% of them said that there are currently no clinical classes being held. The majority (94%) agreed that COVID-19 had impacted their training in surgery and clinical practise. Overall, 71.6% of students reported dissertation completion issues, and 96% expressed mental health worries.\n\nIn a study by Khan et al.,28 15 (53.6%) of the 44 trainees that answered (28/44; 63.6%) were CST/IST. A total of 15 (53.6%) participants worked in general surgery, while 14 (50.0%) were employed by teaching hospitals. In total, 20 participants (71.4%) believed they had less opportunities to serve as the primary surgeon as a result of the pandemic. Only 21 participants (75.0%) had never visited an outpatient clinic. Eight people (28.6%) had no access at all to the laparoscopic box-trainer. Overall, 20 (71.4%) people thought that their degree of trust in their ability to perform surgical skills had been lowered. In total, 18 (64.3%) people felt it challenging to show improvement in their portfolio. A total of 21 trainees (75.0%) had not participated in any instruction. Overall, 10 (35.7%) trainees missed class due to illness. Eight (286%) trainees reported feeling somewhat or much more pressured.\n\nSome of the suggestions and recommendations put forth by the participating surgeons include: i) Anticipation and better preparation for future pandemic waves; ii) at least 10% of GDP to be allotted for health care sector in India; iii) decentralization of COVID care and monitoring system; iv) to promote good COVID appropriate sanitation habits like hand washing; v) prompt completion of all vaccination doses; vi) postponement of elective surgeries (Figure 10, Table 19); vii) adopt newer methods for teaching in the medical education department; viii) reduce the length of hospital stay; ix) parallel training of more health care workers and paramedics to handle pandemics in future; x) peripheral healthcare centres are to be better equipped; and xi) transparency of documentation, periodic pandemic evaluation and amendment of policies and protocols based on evidence-based medicine.\n\n\nConclusions\n\nWith the effect of the COVID-19 pandemic, all doctors with diverse specializations were used to handle patients with COVID-19, as predicted. Due to a shortage of available manpower and materials, elective procedures were different, resulting in a substantial defect in the hands-on and learning process of the surgeons as well as the post-graduate teaching programs. In the future, digital learning should be a part of learning in all specialities so preparedness for the same should be projected. Module and stimulation teaching should be a part of the medical curriculum.", "appendix": "Data availability\n\nFigshare: A prolonged wait: The impact of COVID-19 on elective surgeries in India, a prospective study. https://doi.org/10.6084/m9.figshare.22347268. 29\n\nThis project contains the following underlying data:\n\n- COVID elective surgery responses for analysis.xlsx (spreadsheet data)\n\n- Study on Impact of COVID-19 on Elective Surgeries in India.pdf (blank questionnaire)\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 writing of this article was supported by a medical writer at Medwiz Healthcare Communications Private Ltd.\n\n\nReferences\n\nWHO: Coronavirus disease (COVID-19) pandemic. Accessed on June 13, 2021. Reference Source\n\nCOVID-19 India: Accessed on June 13, 2021. Reference Source\n\nMinistry of Health and Family Welfare: Government of India (MOHFW) eSanjeevani- an integrated telemedicine solution. Accessed on June 13, 2021. Reference Source\n\nHaleem A, Javaid M, Vaishya R, et al.: Effects of COVID-19 pandemic in the field of orthopaedics. J. Clin. Orthop. Trauma. 2020 May-Jun; 11(3): 498–499. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStahel PF: How to risk-stratify elective surgery during the COVID-19 pandemic? Patient Saf. Surg. 2020 Mar 31; 14: 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDimou FM, Eckelbarger D, Riall TS: Surgeon Burnout: A Systematic Review. J. Am. Coll. Surg. 2016 Jun; 222(6): 1230–1239. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRotenstein LS, Torre M, Ramos MA, et al.: Prevalence of Burnout Among Physicians: A Systematic Review. JAMA. 2018 Sep 18; 320(11): 1131–1150. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBartlett DL, Howe JR, Chang G, et al.: Society of Surgical Oncology. Management of Cancer Surgery Cases during the COVID-19 Pandemic: Considerations. Ann. Surg. Oncol. 2020 Jun; 27(6): 1717–1720. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNHS England, Clinical Guide for the Management of Noncoronavirus Patients Requiring Acute Treatment: Cancer: 2020. Accessed on April 2, 2020. Reference Source\n\nNHS England, Clinical Guide for the Management of Cardiothoracic Surgery Patients during the Coronavirus Pandemic: 2020. Accessed on April 2, 2020. Reference Source\n\nSpinelli A, Pellino G: COVID-19 pandemic: perspectives on an unfolding crisis. Br. J. Surg. 2020 Jun; 107(7): 785–787. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmerican College of Surgeons, COVID-19 Guidelines for Triage of Emergency General Surgery Patients: 2020. Accessed on April 2, 2020. Reference Source\n\nKurihara H, Bisagni P, Faccincani R, et al.: COVID-19 outbreak in Northern Italy: Viewpoint of the Milan area surgical community. J. Trauma Acute Care Surg. 2020 Jun; 88(6): 719–724. PubMed Abstract \| Publisher Full Text\n\nAmerican College of Surgeons Committee on Trauma, Maintaining Trauma Center Access & Care during the COVID-19 Pandemic: Guidance Document for Trauma Medical Directors: 2020. Accessed on April 12, 2020. Reference Source\n\nDoughty H, Chowdhury F: National Blood Transfusion Committee Emergency Planning Working Group. Emergency preparedness, resilience and response guidance for UK hospital transfusion teams. Transfus. Med. 2020 Jun; 30(3): 177–185. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhmed K, Hayat S, Dasgupta P: Global challenges to urology practice during the COVID-19 pandemic. BJU Int. 2020 Jun; 125(6): E5–E6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLing Y, Xu SB, Lin YX, et al.: Persistence and clearance of viral RNA in 2019 novel coronavirus disease rehabilitation patients. Chin. Med. J. 2020 May 5; 133(9): 1039–1043. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThe Royal College of Ophthalmologists, Glaucoma Management Plans during COVID-19: 2020. Accessed on April 2, 2020. Reference Source\n\nNHS England, Clinical Guide for the Management of Patients Requiring Oral and Maxillofacial Surgery during the Coronavirus Pandemic: 2020. Accessed on April 2, 2020. Reference Source\n\nNHS England, Clinical Guide for the Management of Patients Requiring Plastic Treatment during the Coronavirus Pandemic: 2020. Accessed on April 2, 2020. Reference Source\n\nBritish Association of Plastic, Reconstructive and Aesthetic Surgeons, Advice for Managing Melanoma Patients during Coronavirus Pandemic: 2020. Accessed on April 9, 2020. Reference Source\n\nNHS England, Clinical Guide for the Management of Acute Burns Patients during the Coronavirus Pandemic: 2020. Accessed on April 2, 2020. Reference Source\n\nAmerican College of Surgeons, COVID-19 Guidelines for Triage of Pediatric Surgery Patients: 2020. Accessed on April 2, 2020. Reference Source\n\nNHS England, Clinical Guide for the Management of Paediatric Patients during the Coronavirus Pandemic: 2020. Accessed on April 2, 2020. Reference Source\n\nNHS England, Clinical Guide for the Management of Paediatric Critical Care Patients during the Coronavirus Pandemic: 2020. Accessed on April 12, 2020. Reference Source\n\nSahu D, Agrawal T, Rathod V, et al.: Impact of COVID 19 lockdown on orthopaedic surgeons in India: A survey. J Clin Orthop Trauma. 2020 May; 11(Suppl 3): S283–S290. Erratum in: J Clin Orthop Trauma. 2020 Nov-Dec;11(6):1169-1171. Erratum in: J Clin Orthop Trauma. 2020 Nov-Dec;11(6):1172-1174. Erratum in: J Clin Orthop Trauma. 2021 Oct;21:101561. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUpadhyaya GK, Jain VK, Iyengar KP, et al.: Impact of COVID-19 on post-graduate orthopaedic training in Delhi-NCR. J. Clin. Orthop. Trauma. 2020; 11(Suppl 5): S687–S695. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan KS, Keay R, McLellan M: Impact of the COVID-19 pandemic on core surgical training.August 9, 2020. Publisher Full Text\n\nMuhammed MN: A prolonged wait: The impact of COVID-19 on elective surgeries in India, a prospective study. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "212762", "date": "12 Oct 2023", "name": "Fitzgerald Anazor", "expertise": [ "Reviewer Expertise Trauma and orthopaedic surgery", "major trauma", "Mmedical education" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nABSTRACT\nThe purpose of the study applies to which population? The Indian population, UK population, worldwide population? This is not clear especially as one goes through the abstract down to the introduction.\n\nPlease revise the abstract to include a brief statement on the results from the study in-relation to the \"purpose\" you mentioned. Your current abstract tells a reader nothing really about what this study achieved.\n\nFurthermore, include the dates when this study was conducted in your abstract.\n\nFinally, correct the significant language errors that makes it difficult to understand the \"results\" section of the abstract.\nKEYWORDS\nPlease include at least 5 key words relevant to this paper.\nINTRODUCTION\nI do not understand who formulated the guidelines you mentioned. Are these UK, global or Indian guidelines?\n\nPlease include a reference for your statement in the first sentence of paragraph 2 (regarding surgeons being ignored).\n\nPlease use reported speech that reflects the fact that this study was conducted in 2021 (most of the statements you put forward no longer hold true in 2023).\n\nPlease edit this sentence: \"If conservative therapy has failed, poses a risk to the patient’s health, is likely to lengthen hospitalisation, or raises the possibility of readmission at a later time, operations or procedures should be carried out\".12\nMETHODS\nPlease what is the full meaning of KIMSHEALTH? Is this the same as Kasturba Medical College?\n\nYou collected data for this study between June and July 2021, but obtained REC approval on Sept 7, 2021. Based on your explanation, its either you require REC approval or you don't. The extensive explanation you provided is not clear enough in my opinion. Please clarify this or attach the REC approval letter to the Appendix or additional materials for this manuscript.\nRESULTS\nPlease exclude tables 1-4 and figure 1 as the information has already been provided in the text. This avoids duplication.\n\nPlease edit this statement to make it easier to comprehend in universally accepted research language: \"Overall, 59.7% of those participants who agreed that there was a reduction in bed availability also faced the brunt of patient or patient bystander’s dissatisfaction; whereas 40.3% of those who reacted that there was no reduction in the availability of beds also faced the brunt of patient or patient bystander’s dissatisfaction. With a p-value of 0.004, this showed a statistically significant association\".\n\nFigure 2 and table 5 represent the same information. Please exclude one of them.\n\nPlease edit this statement to make it easier to comprehend in universally accepted research language \"A total of 70.4% of those participants who agreed that there was a shortage of oxygen also faced the brunt of patient or bystander’s dissatisfaction; whereas 29.6% of those who reacted that there was no shortage of oxygen also faced the brunt of patient or patient bystanders dissatisfaction, With a p-value <0.001, this showed a statistically significant association\".\n\nCorrections for the above paragraph also applies to your summary paragraph for oxygen availability.\n\nFigure 3 and table 7 represent the same information. Please exclude one of them.\n\nFigure 6 and table 12 represent the same information. Please exclude one of them.\n\nFigure 7 and table 13 represent the same information. Please exclude one of them.\n\nFigure 8 and table 15 represent the same information. Please exclude one of them.\n\nWhat do you mean by \"impact on the PG teaching programme\"? Positive or negative impact? In what way exactly? For example, teaching time, resources, faculty availability due to sickness etc.\n\nPlease go through the rest of the results section and remove any table or figure that duplicates information already presented in the manuscript text.\nDISCUSSION\nBetter to start your discussion by summarising the key findings from the study.\n\nPlease expand your discussion to also correlate your countrywide findings to what happened with COVID-19 in other countries as it relates to elective surgery (this is where you compare your results with local and international published evidence as applicable). Check the literature as there are other recent (2022-2023) Pubmed-indexed papers relevant to the effects of COVID-19 on elective surgery and surgical practice from a global perspective (a few suggested references: https://doi.org/10.1308/rcsann.2021.01891; https://doi.org/10.5435/jaaosglobal-d-22-002762; https://doi.org/10.1002/msc.17163; https://doi.org/10.1093/bjsopen/zraa0514; https://doi.org/10.1007/s10151-020-02404-55).\n\nFor your recommendations, they appear relatively shallow (more quantity than quality). I suggest you pick a maximum of 5-6 recommendations and provide details of how they should be implemented in real-practice as it relates to the aim of this paper.\n\nPlease include a paragraph with an extensive discussion of the limitations of this study and how you tried to address these.\n\nPlease re-write the conclusion to reflect the key messages from this paper and any future directions in-relation to the topic.\nACKNOWLEDGEMENTS\nPlease state what exact \"writing role\" was offered by Medwiz Healthcare communications. Was this language editing, scientific content writing, data analysis, etc? Please include the name of the writer from this company.\nCONFLICT OF INTEREST/DISCLOSURE:\nThe conflict of interest/disclosure statement has been included by the authors and is acceptable.\n\nAUTHOR CONTRIBUTIONS:\nNo issues noticed as authorship was well-delineated in the authorship section as per ICMJE guidelines.\nREFERENCE LIST:\nWill suggest an inclusion of the digital object identifiers (DOI) for all articles available online. Otherwise, no issues.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10590", "date": "05 Jan 2024", "name": "Mohsin Naseer Muhammed", "role": "Author Response", "response": "ABSTRACT 1. The purpose of the study applies to which population? The Indian population, UK population, worldwide population? This is not clear especially as one goes through the abstract down to the introduction. Response: This study applies to Indian population. 2. Please revise the abstract to include a brief statement on the results from the study in relation to the \"purpose\" you mentioned. Your current abstract tells a reader nothing really about what this study achieved. Response: Abstract is revised now accordingly. 3. Furthermore, include the dates when this study was conducted in your abstract. Response: Date included in Abstract 4. Finally, correct the significant language errors that makes it difficult to understand the \"results\" section of the abstract. Response: Result section of the Abstract is completely modified as suggested. KEYWORDS 1. Please include at least 5 key words relevant to this paper. Response: 5 key words included in relevant to our study INTRODUCTION 1. I do not understand who formulated the guidelines you mentioned. Are these UK, global or Indian guidelines? Response: The formulated guidelines mentioned in our study is related to Indian guidelines released by Government of India. 2. Please include a reference for your statement in the first sentence of paragraph 2 (regarding surgeons being ignored). Response: Reference included with Pubmed citation 3. Please use reported speech that reflects the fact that this study was conducted in 2021 Response: The statements mentioned are modified accordingly. 4. Please edit this sentence: \"If conservative therapy has failed, poses a risk to the patient’s health, is likely to lengthen hospitalisation, or raises the possibility of readmission at a later time, operations or procedures should be carried out\". Response: Sentence edited as suggested METHODS 1. Please what is the full meaning of KIMSHEALTH? Is this the same as Kasturba Medical College? Response: Both are same. Have changed to Kasturba Medical College. 2. You collected data for this study between June and July 2021, but obtained REC approval on Sept 7, 2021. Based on your explanation, its either you require REC approval or you don't. The extensive explanation you provided is not clear enough in my opinion. Please clarify this or attach the REC approval letter to the Appendix or additional materials for this manuscript. Response: REC approval letter will be attached RESULTS 1. Please exclude tables 1-4 and figure 1 as the information has already been provided in the text. This avoids duplication. Response: Tables 1-4 and figure 1 was deleted as suggested. 2. Please edit this statement to make it easier to comprehend in universally accepted research language: \"Overall, 59.7% of those participants who agreed that there was a reduction in bed availability also faced the brunt of patient or patient bystander’s dissatisfaction; whereas 40.3% of those who reacted that there was no reduction in the availability of beds also faced the brunt of patient or patient bystander’s dissatisfaction. With a p-value of 0.004, this showed a statistically significant association\". Response: Statement edited accordingly 3. Figure 2 and table 5 represent the same information. Please exclude one of them Response: Table 5 was deleted as per suggestions. 4. Please edit this statement to make it easier to comprehend in universally accepted research language \"A total of 70.4% of those participants who agreed that there was a shortage of oxygen also faced the brunt of patient or bystander’s dissatisfaction; whereas 29.6% of those who reacted that there was no shortage of oxygen also faced the brunt of patient or patient bystanders dissatisfaction, With a p-value <0.001, this showed a statistically significant association\". Response: Statement edited accordingly 5. Figure 3 and table 7 represent the same information. Please exclude one of them. Response: Table 7 was deleted 6. Figure 6 and table 12 represent the same information. Please exclude one of them. Response: Table 12 was deleted 7. Figure 7 and table 13 represent the same information. Please exclude one of them. Response: Figure 7 was deleted 8. Figure 8 and table 15 represent the same information. Please exclude one of them. Response: Table 15 was deleted 9. What do you mean by \"impact on the PG teaching programme\"? Positive or negative impact? In what way exactly? For example, teaching time, resources, faculty availability due to sickness etc. Response: A Negative Impact has occurred on the PG teaching programme due to loss of direct contact classes, decrease in faculty strength due to sickness, lack of bed side clinical teaching. 10. Please go through the rest of the results section and remove any table or figure that duplicates information already presented in the manuscript text. Response: Tables and Figures with Duplication checked and removed as suggested. DISCUSSION 1. Better to start your discussion by summarising the key findings from the study. Response: Discussion modified accordingly 2. Please expand your discussion to also correlate your countrywide findings to what happened with COVID-19 in other countries as it relates to elective surgery (this is where you compare your results with local and international published evidence as applicable). Check the literature as there are other recent (2022-2023). Pubmed-indexed papers relevant to the effects of COVID-19 on elective surgery and surgical practice from a global perspective Response: Discussion expanded as suggested 3. For your recommendations, they appear relatively shallow (more quantity than quality). I suggest you pick a maximum of 5-6 recommendations and provide details of how they should be implemented in real-practice as it relates to the aim of this paper. Response: Further references and details are provided 4. Please include a paragraph with an extensive discussion of the limitations of this study and how you tried to address these. Response: Paragraph included as suggested 5. Please re-write the conclusion to reflect the key messages from this paper and any future directions in-relation to the topic. Response: Conclusion modified fully ACKNOWLEDGEMENTS 1. Please state what exact \"writing role\" was offered by Medwiz Healthcare communications. Was this language editing, scientific content writing, data analysis, etc? Please include the name of the writer from this company. Response: Modified as suggested REFERENCE LIST: 1. Will suggest an inclusion of the digital object identifiers (DOI) for all articles available online. Response: DOI included as suggested" } ] } ]	1	https://f1000research.com/articles/12-410
https://f1000research.com/articles/10-50/v1	27 Jan 21	{ "type": "Research Article", "title": "Evidence for immunity to SARS-CoV-2 from epidemiological data series", "authors": [ "Pablo Yubero", "Alvar A. Lavin", "Juan F. Poyatos", "Pablo Yubero", "Alvar A. Lavin" ], "abstract": "The duration of immunity to SARS-CoV-2 is uncertain. Delineating immune memory typically requires longitudinal serological studies that track antibody prevalence in the same cohort for an extended time. However, this information is needed in faster timescales. Notably, the dynamics of an epidemic where recovered patients become immune for any period should differ significantly from those of one where the recovered promptly become susceptible. Here, we exploit this difference to provide a reliable protocol that can estimate immunity early in an epidemic. We verify this protocol with synthetic data, discuss its limitations, and then apply it to evaluate human immunity to SARS-CoV-2 in mortality data series from New York City. Our results indicate that New York’s mortality figures are incompatible with immunity lasting anything below 105 or above 211 days (90% CI.), and set an example on how to assess immune memory in emerging pandemics before serological studies can be deployed.", "keywords": [ "COVID-19", "immunological memory", "compartmentalized epidemiological models", "data assimilation" ], "content": "Introduction\n\nThe presence and duration of immunity to novel viruses is traditionally determined through longitudinal serological studies. By characterizing antibodies against a problem virus and tracking the serum levels of these antibodies in a population, for a long enough period, it can be determined with a solid standard of evidence whether the virus induces immunity and how long that immunity lasts.\n\nThis method for studying immunity is statistically reliable, but it can demand a very long time and requires ample human and technical resources. Such caveats do not usually pose a problem, but they have become relevant in the case of the recent 2019 coronavirus outbreak. COVID-19 presents the right combination of infectivity and mortality to cause a pandemic of unprecedented global proportions that became clinically and economically relevant in very short timescales, far exceeded by those required for longitudinal serological studies.\n\nCommon human coronaviruses causing cold and ﬂu-like symptoms of mild degree typically leave an immune memory lasting from six to twenty-eight months1. The determinants of coronavirus and rhinovirus immunity have been widely studied for decades and are moderately well understood, as are those of inﬂuenza2. These diseases leave some immunity, but they can reinfect patients as soon as half a year after.\n\nThe mechanisms enabling reinfection strive from simple to elaborate. In the case of inﬂuenza and rhinoviruses, highly polymorphic proteins change yearly or faster and thus pathogens escape immune memory through mutation: they are virtually a new pathogen2,3. There is also some evidence that homologous reinfection may contribute to multi-wave inﬂuenza outbreaks. Due to previous infections generating an insufficient or non-lasting immune response, recovered patients can become infected again4. Other human pathogens such as herpes virus, human cytomegalovirus (HCMV), and human immunodeficiency virus (HIV) elude immunity without fully leaving the human body. This persistence in the face of immune surveillance and medicine is not unique to viruses, as it is well documented in bacteria and tumor cells5–8. The populations of these cellular pathogens achieve persistence through the complex interplay of different factors, including extrinsic and intrinsic noise in therapeutic targets, mutation, directly compromising immune function, subpopulations with distinct growth rates, and other phenomena. In viruses, lysogeny often plays a pivotal role, as may do infection of immune cell types.\n\nSARS-CoV-2 is phylogenetically a coronavirus, so the standard of evidence by default would indicate that it induces immunity lasting from one to two years. However, since early in the pandemic, recovered patients have tested positive after previously testing negative. For a while, this rose concerns that SARS-CoV-2 could be not inducing immunity, or persisting in the body after recovery. It is now becoming evident that these positives at least were induced by harmless remains of viral material that endure in the human bloodstream weeks after disease has subsided. But, could immunity after infection be virtually non-existing after all? The presence, extent, and particularities of human immunity to SARS-CoV-2 are still relevant for academics, health professionals and the broader public, and require further research.\n\nSerological studies are the main tool to that aim and continue to unfold as we write this study, with preliminary results already being published9,10. In the meantime, lack of further evidence on human immunity to SARS-CoV-2 delays our full understanding of COVID-19, leads to mismanagement of medical resources such as masks in conditions of scarcity (as the ones we have seen during this pandemic), and sets recovered patients as putative contagion sources, among other undesirable outcomes.\n\nTheoretical alternative approaches to detecting immunity would be desirable in these circumstances; and in principle identifying immunity times should be as simple as inferring the value of a free parameter by fitting an epidemiological model to field data. However, nonlinear dynamical systems like those characteristic of epidemics have a high degree of inherent uncertainty, which makes prediction through conventional, deterministic means inefficient. System variables such as the population of infectious or recovered patients may follow any of a wide array of possible trajectories, and we cannot know which one they will take until they do so11.\n\nDespite these hurdles, data assimilation techniques are a set of mathematical tools that have provided success in forecasting epidemics12. Within these methods, ensemble adjustment Kalman filters (EAKF) have shown capable of providing accurate predictions in a system with many variables13.\n\nBy using Bayes’s theorem to update a model’s predictions with observations at a series of points, uncertainty in a further forecast is reduced, and the span of possible posterior trajectories is limited14. The better the measurements (having less uncertainty themselves than the predictions) and the closer in time to the present, the better the updated forecast will be. These Bayesian approaches were originally developed in the context of large-scale geophysical problems and readily and most notably applied to weather predictions15,16. More recently, they have been adapted to epidemiology too, where they became the state of the art in epidemiological forecasting, also in the COVID-19 pandemic, e.g., 17, see also 18 for a related method.\n\nHere, we first examine the impact of immunity memory in the dynamics of a sound epidemiological model of COVID-19. We then estimate the capacity of EAKF techniques to infer the duration of this memory and then apply this approach to mortality time series from New York City (NYC), discerning immunity times against SARS-CoV-2 with reasonable accuracy. Finally, we examine the implications of the presence of immunity in the post-pandemic dynamics. This work thus provides reliable information about human immunity to SARS-CoV-2 and also represents an alternative to longitudinal serological studies for use against future emergent pandemics.\n\n\nResults\n\nWe used an epidemiological model in which the total population is divided into a number of classes19 (Figure 1). The specific compartments represent our current understanding of COVID-19 progression. Note that the infected population is divided into five (right column in Figure 1) and that we also included two different mortality rates for critical cases because mortality depends strongly on whether there are available beds in Intensive Care Units (ICUs; Methods and Extended data for the model details). All associated parameters in this model are available except for the infection rate β and the immunity memory τ (Extended data). The fundamental categories resemble those of the wellknown SEIRS model20 in that the recovered population becomes susceptible after some duration of immunity (τ). However, the particularities of the COVID-19 progression are such that a minimal SEIRS cannot predict the mid- and long-term dynamics of the population well enough (Extended data and Figure S1).\n\nWe introduce a compartmentalized epidemiological model with five infected categories (gray shading). Note that the accessibility of ICUs determines the rate to deceased and that those individuals recovered after infection may lose their immunity and become again susceptible after a finite time τ (red arrow). See Extended data for model details.\n\nIn addition, we performed a variance-based global sensitivity analysis21,22 of the model (Extended data and Figure S2). In particular, it illustrates the importance of the parameters related to the mild cases in shaping the deceases time series, the peak height and the total number of deceases after a year of pandemic whereas the infection rate tunes mainly the timing of the pandemic peak.\n\nFirst, we study how the loss of immunity after infection impacts daily deaths (dD/dt) in our COVID-19 epidemiological model. The initial condition is a single exposed case, with a constant and intermediate value of the infection rate (Figure 2A). We find analytically that in the short term, i.e., during the exponential growth of infected cases, the development of immunity has no effect on the initial number of secondary infections R0 (Extended data): there is not enough time for the re-circulation of the recovered back to the susceptible population.\n\nHowever, in the mid-term of the epidemic starting at the departure from exponential growth and up to the first noticeable reduction in daily deceases, a shorter immunity memory time raises the overall number of daily deceases. It also promotes a more prolonged duration of the epidemic as estimated by the time daily deceases stay above 75% of the maximum. Finally, in the long term, beyond the first peak, a finite immunity memory promotes the appearance of new epidemic waves.\n\nThe duration of the immunity time also shapes the dependence with β of the peak number of daily cases dD/dtmax and the duration of the epidemic (Figure 2B). As expected, dD/dtmax increases with the infection rate β but decreases for increasing τ. In addition, we observe that dD/dtmax for τs beyond a threshold are hardly distinguishable, e.g., data for τ = 3 months and τ = 1 year. Moreover, the duration of the first peak decreases together with both increasing β and τ. Figure 2C displays the intrinsic seasonality derived from a finite immunity time. The height and timing of the secondary peaks are strongly dependent on both β and τ, data shown is for a fixed value of τ = 3 months. This subscribes earlier projections obtained with a multi-strain model23.\n\n(A) Different time series of daily deceases depending on the value of the immunity memory τ (β = 0.5 days−1). (B) The peak height, i.e. maximum number of deceased individuals in a single day, and the duration of the \"first-wave\" (inset) increase with shorter immunity times. However, the former increases with the infection rate, as opposed to the latter. (C) A finite value of immunity memory induces intrinsic seasonality on the model what produces subsequent epidemic peaks with time. This seasonality depends heavily on the interplay between the infection rate and the immune memory. Data shown for τ = 3 months.\n\nA finite value of the immunity time impacts the time series of daily deceases only after the exponential growth, and starting around the peak of the first wave. To notice these implications, we required a considerably advanced epidemic. What about an ongoing epidemic? This would need the real-time assessment of the epidemic parameters and the ability to forecast the short-term dynamics after the epidemic passes the peak.\n\nWhile this kind of forecasting is intrinsically difficult13, it is now possible to apply filtering techniques that recently demonstrated valid in this problem by integrating model predictions and data13,17,23,24. We thus adopted a specific recursive filtering technique known as EAKF to infer the immunity memory duration in the course of an ongoing epidemic (see Extended data for a brief intro to EAKF)11,14.\n\nTo describe a typical scenario, we first simulated a synthetic time-series with the deterministic model that would represent real data (Figure 3A–C). We then ran 100 independent iterations of the EAKF protocol, with different initial conditions, to estimate dD/dt (everyday deaths) and the \"hidden\" parameters (βsynth and τsynth). To assess the performance of our protocol, we compute the relative errors between the target values and the median of predictions. The similarity between the predicted and real curve of dD/dt is evident (Figure 3A). Note that the estimates of β and τ improve mostly before and after the epidemic peak, respectively (Figure 3B–C). This trend is in agreement with our results from the previous section.\n\nWe tested the performance of the EAKF-based protocol over a test bed of synthetic data made of 100 time-series generated with the model and random values of β and τ. Panels A–C illustrate the analysis of a single example whereas panels D–F show the overall performance on the entire test bed. (A) Our protocol (blue) is able to accurately capture data of daily deceases (red), with a linear correlation between data and model ρ > 0.99. (B) The value of the synthetic infection rate βsynth (dotted line) is captured by the protocol βmodel (blue) after some data assimilation steps, and prior to the pandemic peak. Accordingly, the relative error between βsynth and βmodel decreases as more data is assimilated (purple solid, right y-axis). (C) The immune memory τmodel (blue) follows similar dynamics as βmodel and approaches the synthetic value τsynth (dotted line). However, its relative error (purple solid, right y-axis) drops later than βmodel, at about the epidemic’s peak, in agreement with the results of our previous section. In panels A–C, shadings represent 95%CI, while vertical lines denote time of peak. (D) Histogram of linear correlations between model and data of daily deceases (as in panel A) for the entire test bed. (E–F) Synthetic values and EAKF estimates of the infection rate and immune memory largely correlate, ρ = 0.99 and ρ = 0.98, respectively. We find however that our protocol tends to overestimate larger infection rates when βsynth > 1.\n\nTo further evaluate the limits of this approach, we generated a test bed of 100 synthetic data series for a range of parameters (note that for each series we ran again 100 iterations). Specifically, each series correspond to random values of βsynth ∈ [0.2, 1.5] days−1 and τsynth ∈ [0, 360] days to which we added relative random noise normally distributed with zero mean and standard deviation up to 10%. The initial exposed population is also selected randomly from a uniform distribution Esynth(t = 0) ∈ [0, 10]. The goal is to apply EAKF within this range to estimate once again the dD/dt series and the \"hidden\" parameters. Figure 3D–E shows the performance of our protocol when applied to the entire test bed of synthetic data. On the one hand, we find that infection rates β < 1 are excellently captured whereas β > 1 are slightly overestimated (Figure 3E). On the other hand, τ is more difficult to estimate in its entire range (smaller correlation between model and synthetic values), but the estimates are not biased towards upper/lower values (Figure 3F). Moreover we found that the errors between estimates of τ and β barely correlate (ρ = −0.18, not shown), so a better estimation of β does not necessarily lead to a worse estimation of τ. Also, neither errors in the estimates of τ nor β correlate with the magnitude of the noise added to dD/dt (ρ = 0.04 and ρ = −0.12, respectively; not shown).\n\nIn sum, filtering and data assimilation techniques successfully identify the values of the infection rate, β, and immunity memory, τ, when enough data points are available. The value estimates are robustly captured for different initial conditions. Finally, we also found that our protocol can handle up to 10% relative errors with little to no impact on the estimation of β and τ.\n\nWe now apply the protocol used in the previous section to real time series of new daily deceases reported for COVID-19 in different heavily-affected regions. We performed a preliminary test to rank these regions (world-wide countries and counties/cities within the US) to narrow down potential candidates for signal detection. From over 30 regions, we selected NYC because it had the largest number of deceases per 105 inhabitants and it did not exhibit volatile field data like other regions, e.g. Nassau (NY, USA) or Belgium, (Extended data: Figures S3 and S4).\n\nTo be certain that the signal in τ is not an artifact, we added to the protocol a control variable δ that has no effect on the model, it is initialized as a different sample of the same initial distribution as τ and follows the same update rules as τ. Whether immunity should be considered in the model will depend on its behavior relative to the control variable. The influence of τ becomes relevant in the model whenever its distribution deviates significantly from that of δ. On the contrary, if immunity mimics the behavior of the control variable it demonstrates that τ has no role in shaping the epidemiological dynamics. Thus, statistically significant deviations between the distributions of τ and δ highlight the influence of τ in the results.\n\nIn Figure 4A–C we show the results of NYC. The success of the EAKF protocol to capture the dynamics of dD/dt is apparent with a root mean squared error RMSE= 18 deceases and a linear correlation between data and the model median ρ > 0.99 (Figure 4A). In particular, our protocol also captures the time-dynamics of the infection rate, which is well aligned with the days on which NYC promoted social distancing measures: schools and library closings on March 16th, and the pause order of March 22nd (Figure 4).\n\n(A) Data (red dots) and algorithm estimate (blue solid, median and 95% CI) of New York City’s daily deceases of COVID-19. Data and prediction are in good agreement, with a root mean squared error RMSE=18 deceases and with a linear correlation coefficient ρ => 0.99. (B) Estimate of the infection rate, β, dynamics (median and 95% CI). Drops in β are well aligned with the days on which social distancing measures took place: school closings (black dashed) and the pause order (black dotted). (C) Estimate of the immune memory duration τ (median and 95% CI). The distribution of τ becomes significantly different from that of a control variable δ (two-sample Kolmogorov-Smirnov test p= 0.017) and sets the lower and upper bounds to τ ∈ [80, 288] days with (95% CI). We also simulated a hypothetical scenario based on NYC data with (D) lockdowns established on different days since the first decease, and with (E) different decreases in β due to the lockdown. As a proxy for the difficulty of detecting τ, we use the number of potential reinfections, i.e. the number of recovered people that has lost its immunity by the 50th day since the start of the epidemic, for different values of τ. Observe that specific data for NYC (black vertical lines in panels D and E) illustrates how their quick action in closing schools and passing a pause order (on March 22nd 2020) and their large effectiveness (with β decreasing > −90%) ensure a small amount of possible reinfections, and hence the difficulty to capture τ with fitting methods.\n\nMost importantly, we found a final estimate of 105 < τ < 211 days with 90% confidence (80 < τ < 288 days with 95% CI). We obtained this estimate from a statistically significant change in the distribution of τ with respect to the control variable δ (two-sample Kolmogorov Smirnov, p= 0.017). The upper bound should be considered with caution, given the limited availability of COVID-19 data due to its recent appearance, and future data assimilation steps could alter this bound.\n\nWe attribute the difficulty to capture the value of τ in real data as opposed to synthetic data to the ubiquity of a strong reduction of the infection rate during the initial days of the epidemic in all data sets that we studied (results of Belgium, Spain and France are available in Figure. S5). We tested this idea by computing the number of recovered cases that have lost their immunity against the virus after 50 days of the start of the epidemic. This number, which we call potential reinfections, is a proxy for the difficulty of capturing τ. We consider a scenario similar to NYC, with equal population and equal initial and final infection rates β, but with different timing and effectiveness of lockdowns (Figure 4DE). The effectiveness is measured by the relative change between the infection rate pre- and post-lockdown. Simulation data supports our hypothesis since the number of potential reinfections is both close to zero and independent of τ when lockdowns are quickly established and/or when they are very effective with infection rate drops > 90%.\n\nAlthough we confirmed the potential of EAKF algorithms to distinguish the duration of immune memory during an ongoing epidemic, we also noted that the application of our methods is bounded by the expected control measures that are aimed to reduce epidemic progression, i.e., to decrease the infection rate.\n\nHow could the immune memory for COVID-19 affect a secondary wave of infection? We tackle this by integrating the final state of the EAKF ensembles of NYC with our COVID-19 model deterministically. To account for the relaxation of social distancing measures we include a linear increase of the infection rate during the month of July, specifically, β doubles by the 1st of August and remains constant from then on, which is a conservative scenario. In terms of the effective number of secondary infections Re, a doubling of β is equivalent to an Re increase from ~ 0.7 to ~ 1.3 (Extended data).\n\nFigure 5 shows the model forecast of daily deceases due to COVID-19 considering the lower and upper bounds of the 95% CI, τ = 80 and τ = 288 days, respectively. First, in this scenario where social distancing is only slightly relaxed and where the infection rate remains constant from then on, a new epidemic wave in terms of deceases would shortly take place. Its precise timing will depend strongly on the number of ICU beds available, but it can be expected to start in mid September. Moreover, without further social distancing measures during this second epidemic wave, we anticipate that it could last up until January and beyond.\n\nWe show the forecast of a second epidemic wave starting in early September if the infection rate β doubles its value during July, for two cases of immune memory τ = 80 and τ = 288 days (purple and orange respectively, shadings denote 95% CI). Observe that τ slightly affects the timing of the second wave: the shorter τ has a narrower CI. The second wave becomes quickly a real problem due to the little immunity developed during the first (black).\n\nThis is due to the fact that, during the first wave, most of the population did not develop immunity to the virus and hence is yet susceptible through the second wave. Such a secondary peak has already been suggested in other specific scenarios23,25.\n\nHowever, if we focus on the maximum effect that different τs have in the short run, we find that, although the median trajectory is independent of τ, the confidence region is narrower for τ = 80 days. In fact, we expect the immune memory to be relevant only after a considerable fraction of the population has undergone a first infection by COVID-19, or in the case that the time between epidemic waves (or intermittent social distancing) is shorter than that of τ where there is enough time to build a sufficiently large pool of immune population.\n\n\nDiscussion\n\nWe propose an alternative approach for estimating the duration of immunity. The protocol relies on the computational analysis of epidemiological time series, which requires far fewer resources and may be deployed faster than its alternatives. Although longitudinal serological studies may be preferred, the evidence for immunity they provide is as indirect as the one we may detect in epidemiological data series. In fact, a direct experimental test of human immunity to SARS-CoV-2 would require intentionally infecting and monitoring recovered human patients with the virus, which would be highly controversial, although this approach has been tested in monkeys26.\n\nTo circumvent this, serological studies obtain indirect evidence based on the premise that antibody prevalence equates immunity, which is generally accurate. However, this is not the case for all diseases. Different mechanisms of persistence deployed by pathogens can uncouple antibody memory from actually being protected against the disease and/or being asymptomatic. Moreover, the effect of immunity on mortality series can hardly be mimicked by any other factors and draws information from field data. Thus, its standard of evidence for immunity is not necessarily lower than the one traditionally employed.\n\nDespite all these points in its favor, the reach of the protocol in its current form is limited, and some requirements must be satisfied to discern immunity. Data series must have surpassed the peak following social distancing measures, which will increase the time necessary to begin a proper examination. In this regard, it is worth noting that capturing τ was highly dependent on lockdown policies, as evidenced by our potential reinfections metric. The maximum portion of infected people in the population must be sufficiently large for there to be a signal. However, most regions will implement comparable measures to reduce the number of deceased and its growth that make the signal barely distinguishable. In some cases, different stages of social alarm stratified with political or legal restrictions of varying strength are what makes for very volatile infection rates or completely renders changes in immunity irrelevant to early population mortality.\n\nHowever, segregating exposure and likeliness of infection should improve signal detection as all individuals are not equally likely to be infected. On the one hand, long-lasting cross-immunity with other coronaviruses can significantly reduce the susceptible population27,28, and on the other hand, re-infections are most likely occurring in only a subset of the population (such as the working as opposed to the non-working population, age-based classifications, or metropolitan vs suburban or rural). A second way of improving immunity would be to use another observable on top of the deceased during data assimilation. In fact, predictions would improve considerably should data of the infected population be reliable and independent of the limited availability of PCR tests. In addition, the improper mapping of field-measured variables (the \"confirmed\", sampling-biased metric) to model variables (exposed, asymptomatic, mild, severe and critical populations) prevents predictability.\n\nBut leaving aside reliability in the field tracking of epidemiological variables, it is also worth noting that the protocol is unworkable without a moderately predictive model. Concomitantly, having an accurate model requires some knowledge of the disease’s progression, symptomatology, and outcomes, as well as any notable resources or clinical agents involved in them (as in this case were ICU beds or oxygen). Still, none of these requirements is particularly unlikely to be reached during emergent pandemics. For instance, all of them had been satisfied after 3 months of COVID-19. And the information needed to produce a reasonable model was already public after the second month.\n\nLastly, perhaps the most significant obstacle in this and more conventional approaches is their inability to discriminate heterogeneity in immunity29 from groups of recovered patients that have experienced varying degrees of symptomatology. Indeed, patients with many kinds of symptoms and/or peak viral loads may vary in their development of immunity. It could be, for instance, that mild cases do not result in enduring immunity, or result in a shorter immune span, than severe or critical cases. If that were the case, our approach would similarly identify a single overall value for immunity from the statistical overlap of different genuine immunity times, offering a weighed, non-real centrality measure of all immune times in the population.\n\nAll these things considered, the present protocol can be thought of as an additional first-hand tool that can always provide necessary evidence in the early stages of a pandemic, until more and varied methods can be deployed.\n\nNow, several issues have arisen surrounding persistence and immunity in COVID-19 throughout the last months. For the majority of the time, the best estimate for immunity to SARS-CoV-2 the community could work with was a presumed range stemming from phylogenetic comparisons pertaining seasonal human coronaviruses like HCoV-OC43 and HCoV-HKU123. Nevertheless, the standard of evidence of phylogenetic assumptions is not very reliable, particularly with regards to microorganisms. According to these suppositions, COVID-19 may elicit immunity lasting from 6 months to 2 years.\n\nBecause these were potentially inaccurate measures, early cases of apparent reinfection sparked controversies, and even now as some countries are re-experiencing outbreaks recurring positives are a concern. Our work adds on to other very recent publications that appear to indicate immunity will last at least several months10. In particular, a study has observed T cell immunity for SARS-CoV-2 not only in asymptomatic and mild patients, but also in unexposed individuals. This suggests both that the susceptible population has been overestimated and that there are signs of lasting immune memory30. In fact, they find similarities with immunity to SARS-CoV-1, pointing that SARS-CoV-2 is likely to have a comparable immune response. Moreover, recent experimental results show that although antibody production depends strongly on disease severity, it lasts at least three months31 in line with our results. In this context, we provide further evidence that the currently recovered patients will maintain, on average, at the very least 3.5 months of immunity, most likely around 5, and possibly no more than 7; so long as there are no significant differences due to case severity and cross immunity does not provide a far better protection to SARS-CoV-2 than exposition to SARS-CoV-2 itself.\n\nFurthermore, we find that reinfections are a fundamental cornerstone of the current debate on immunity to SARS-CoV-2, especially concerning the development of a vaccine32,33. Although the criteria to label reinfections as such have recently been settled34, these are demanding. Indeed, to prove a reinfection the patient must have followed a positive-negative-positive PCR testing pattern with at least 28 days between the first and second positives to discard cases of viral remnants35. Additionally, it is desirable to have samples of both positives be sequenced and compared to further improve accuracy of re-infection labeling36. Also, as in other human coronaviruses, it is highly probable that reinfections produce asymptomatic or mild symptoms37,38, in which cases re-testing is hardly expected or not provided by health institutions. However, this might not always be the case, and re-infections can lead to worse symptoms39. In general, the probability that a person is symptomatic during both infections, that has been tested negative in between and that samples of both positives are kept and sequenced is rare at best, which highlights the need for surveillance of SARS-CoV-2 reinfections (see also Addendum for further comments on our results).\n\nWhile we recognize the complexity of the human immune response to SARS-CoV-2, as it is to many other viruses, we trust that our work contributes to a more solid comprehension of the epidemiological implications of this response.\n\n\nMethods\n\nWe obtained death counts of COVID-19 aggregated by country and USA county from the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University40 (last updated on July 9th), and information of ICU beds from a variety of sources depending on the region of study (for the case of NYC see the city’s coronavirus tracker). We used Worldometer to obtain the populations of the regions and countries we selected for analysis41. We also used data from the Oxford COVID-19 Government Response Tracker to find the days that different social distancing measures took place in some countries42.\n\nWe introduced a compartmental model that exploits what is currently known about COVID-19 progression and associated accessible data such as the fraction and times at which different infected cases recover or worsen (Extended data: Table S1). Namely the compartments are: susceptible (S), exposed to the virus but not yet contagious (E), infected and contagious but asymptomatic (IA), with mild symptoms (IM), with severe symptoms (needs hospitalization - IS), and critical symptoms (requires urgent admittance to an ICU - IC); recovered cases (R) and the deceased (D).\n\nThe basic reproductive number, R0, and its temporal-dependent counterpart Re (effective reproductive number) are composite parameters that integrate information on not only the infection rate but also the contact rate, susceptible population, and most importantly model architecture43,44. For this reason, we have prioritized the use of the infection rate β throughout. However, we have used Re sparingly due to its biological relevance, which lies in whether it is larger/smaller than the unit, indicating whether the outbreak is expected to continue. To compute Re we have applied the Next Generation Matrices (NGM) algorithm to our model45, hence Re is the largest eigenvalue of the NGM KL=-T S-1 where T and S are respectively the transmissions and transitions matrices (see Extended data for more details). A sensitivity analysis of R0 with respect to the model parameters is available in Figure S6.\n\nThe EAKF filtering method consists in propagating and updating ensemble members, which constitute a probabilistic description of the state variables and model parameters13. Ensembles are samples of the distributions that the variables are expected to have. In our case, the time-dependent state variables are the infection rate β, the immunity memory τ and the population in each compartment of the model. We also introduced a dummy variable δ that does not affect the model results against which to test the ensemble dynamics of τ. The time-dependent observable is the number of daily deceases officially reported, to which we applied a 2 week running average to account for miscommunications and reporting delays.\n\nIn the data assimilation step, the ensemble members are integrated with the model to obtain their expected state at the time of the succeeding observation. Next, together with the likelihood distribution of the actual observation, the algorithm calculates the posterior probability assuming that all distributions are normal. Lastly, the unobserved state variables are updated according to their correlation with the observable. For the assimilation of the next data-point, the posterior probability then becomes the prior. A more detailed description of the protocol is available in the Extended data.\n\nImportantly, considering that τ did not correlate linearly with the observable, we used rank correlations instead to update both τ and δ. We also used a 3% inﬂation in the ensemble variance of all variables except τ and δ since they showed no convergence problems. We have run 100 EAKF instances with ensemble sizes of 200 members. The days in which confinement measures took place (school closing, lockdown...) we added a 200% inﬂation to better accommodate parameter discontinuities.\n\n\nAddendum\n\nDecember 17, 2020\n\nAfter the publication of this manuscript in the medRxiv repository by the end of July 2020 (https://doi.org/10.1101/2020.07.22.20160028), we decided to submit it to several scientific journals for peer review. Some reviewers raised a few issues that unfortunately led to a rejecting editorial consideration even though, in our opinion, they could be argued in their entirety. We take this opportunity to provide a precise answer to these issues further explaining the contributions of this work and also its limitations.\n\nBy January 2020 both the scientific community and the broader public were already aware of the novel coronavirus SARS-CoV-2, by February it spread without difficulty, and on March 11th the World Health Organization declared the COVID-19 pandemic. During March, most of the countries closed schools, public transport and established a variety of social distancing measures. Initial debates focused on sources of infection (contact surfaces, aerosols), its infectivity (the now well-known R0), the importance of social distancing, geographical dynamics and, the development of immunity after recovery46,47.\n\nWhile some of these debates have been already clarified, questions around SARS-CoV-2 immunity remain nowadays greatly unresolved48. In this work, we provided an early estimate of the duration of immunity developed by recovered people after SARS-CoV-2 infections, it being between 3 and 7 months with a 90% CI from New York City (NYC) data. The main concerns raised by readers were\n\n1. the major conclusion is ﬂawed as we obtain a short duration of immunity,\n\n2. this question can only be resolved with approaches characteristic of Molecular Biology,\n\n3. many, many factors determine immunity as to be defined with a single parameter,\n\nwhich, although already examined in the introduction and the discussion, we will now further review.\n\nThe principal aim of this work was to explore alternative approaches to assess the duration of immunity given that longitudinal serological studies are time- and resource-consuming. Its main result, which is the duration of immunity, has been questioned for two reasons: immunity appears to last only a few months, and should that be the case, the number of reinfections reported is far less than expected.\n\nFirstly, our estimate of an immune memory lasting several months is in line with initially published results10. Moreover, as in the manuscript’s discussion, while we provide a defined range of immunity duration it has to be considered with caution. Partly because not a single range nor a single value can fully describe the high complexity of immunity derived from the ample heterogeneity in viral charges, secondary exposures, disease severity and, individual immune responses29. Note that reports on reinfections within a few months after the first infection also support our lower bound to the duration of immunity39.\n\nSecondly, while some propose that reinfections are a rare event, others argue that most of them are going unnoticed. However, we believe both stances are appropriate as suggests the COVID-19 reinfection tracker49. Confirmed reinfections are indeed rare, but the figure grows two orders of magnitude if we also consider suspected reinfections: from 30 vs. 1700, respectively. This disparity is partly explained by the lack of genetic proof in suspected cases of reinfections. In addition, most reinfections are hardly detectable as they might present even milder symptoms compared to the first infection.\n\nThe fundamental methodological handicap of our approach is the difficulty with which the duration of immunity is captured during an intense epidemic in which most regions will implement social distancing and confinements as principal contention measures.\n\nIn fact, our protocol can only robustly obtain the duration of immunity if reinfections are a significant driver of the epidemic dynamics, as evidenced by the success in treating synthetic data and by our reinfections metric for the case of NYC. Although this poses a major obstacle to an accurate estimation of the duration of immunity for experimental data of the COVID-19, we found that NYC data deviated significantly from a reinfection-free scenario, which led to a significant estimation of this parameter.\n\nThe estimate we provide relies on a simple compartmentalized model, a common approach in the study of epidemics with its limitations, yet tailored to the typical stages of SARS-CoV-2 infection in which the effects of reinfections produced by immunity loss cannot be mimicked by any other factor. To this model, we applied state-of-the-art probabilistic methods that have already been applied previously with success to highly non-linear systems like weather forecasting, and other epidemics13,24. For this reasons, we believe that although limited by data, we provided a sound initial estimate on immunity duration of comparable value to other approaches after only four months since the declaration of the pandemic.\n\n\nConclusion\n\nIn this work, we demonstrate that epidemiological models together with state-of-the-art numerical methods are complementary to traditional approaches in providing estimates of the duration of immunity during the COVID-19 pandemic. Finally, the success in analysing synthetic data highlights the potential of this methodology for epidemiological studies beyond COVID-19. We hope that this and other lessons will contribute to a better response to future pandemics.\n\n\nData availability\n\nDaily time series summary tables, including confirmed, deaths and recovered are available from: https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series\n\nArchived time series data as at time of publication: http://doi.org/10.5281/zenodo.445212450\n\nRepository name: Zenodo: Supplementary Material and Code of Evidence for immunity to SARS-CoV-2 from epidemiological data series, http://doi.org/10.5281/zenodo.445212450.\n\nThis project contains the following extended data:\n\nCOVID-19 epidemiological model\n\nIntroduction to Ensemble Adjustment Kalman Filter algorithms\n\nFigure S1. A minimal SEIRS model is not completely equivalent to our COVID-19 model.\n\nFigure S2. Model sensitivity analysis.\n\nFigure S3. Impact of COVID-19 upon different countries and regions.\n\nFigure S4. Daily deceases of COVID-19 upon different countries and regions.\n\nFigure S5. EAKF results for Belgium, Spain and France.\n\nFigure S6. Parameter sensitivity of R0.\n\nTable S1. List of parameters and their values references used throughout.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nEdridge ADE, Kaczorowska J, Hoste ACR, et al.: Seasonal coronavirus protective immunity is short-lasting. Nat Med. 2020; 26(11): 1691–1693. PubMed Abstract \| Publisher Full Text\n\nJones S, Nelson-Sathi S, Wang Y, et al.: Evolutionary, genetic, structural characterization and its functional implications forthe inﬂuenza a (H1N1) infection outbreak in india from2009 to 2017. Sci Rep. 2019; 9(1): 14690. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPalmenberg AC, Spiro D, Kuzmickas R, et al.: Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science. 2009; 324(5923): 55–59. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCamacho A, Cazelles B: Does homologous reinfection drive multiple-wave inﬂuenza outbreaks? Accounting for immunodynamics in epidemiological models. Epidemics. 2013; 5(4): 187–196. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeste DJV, Espasa M, Bonde B, et al.: The genetic requirements for fast and slow growth in mycobacteria. PLoS One. 2009; 4(4): e5349–e5349. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Y, Zhang Y: PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli. Antimicrob Agents Chemother. 2007; 51(6): 2092–2099. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharma SV, Lee DY, Li B, et al.: A chromatin-mediated reversible drug tolerant state in cancer cell subpopulations. Cell. 2010; 141(1): 69–80. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCohen AA, Geva-Zatorsky N, Eden E, et al.: Dynamic proteomics of individual cancer cells in response to a drug. Science. 2008; 322(5907): 1511–1516. PubMed Abstract \| Publisher Full Text\n\nBobrovitz N, Arora RK, Yan T, et al.: Lessons from a rapid systematic review of early SARS-CoV-2 serosurveys. medRxiv. 2020. Publisher Full Text\n\nSeow J, Graham C, Merrick M, et al.: Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans. Nat Microbiol. 2020; 5(12): 1598–1607. PubMed Abstract \| Publisher Full Text\n\nGandon S, Day T, Metcalf CJE, et al.: Forecasting epidemiological and evolutionary dynamics of infectious diseases. Trends Ecol Evol. 2016; 31(10): 776–788. PubMed Abstract \| Publisher Full Text\n\nIonides EL, Breto C, King AA: Inference for nonlinear dynamical systems. Proc Natl Acad Sci U S A. 2006; 103(49): 18438–18443. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShaman J, Karspeck A: Forecasting seasonal outbreaks of inﬂuenza. Proc Natl Acad Sci U S A. 2012; 109(50): 20425–20430. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEvensen G: Data assimilation: the ensemble Kalman ﬁlter. Springer, Dordrecht; New York, 2nd ed edition, 2009. Reference Source\n\nAnderson JL: An Ensemble Adjustment Kalman Filter for Data Assimilation. Mon Weather Rev. 2001; 129(12): 2884–2903. Publisher Full Text\n\nKalnay E: Atmospheric modeling, data assimilation, and predictability. Cambridge University Press, New York, 2003. Publisher Full Text\n\nLi R, Pei S, Chen B, et al.: Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2). Science. 2020; 368(6490): 489–493. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDehning J, Zierenberg J, Spitzner FP, et al.: Inferring change points in the spread of COVID-19 reveals the effectiveness of interventions. Science. 2020; 369(6500): eabb9789. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKermack WO, McKendrick AG: Contributions to the mathematical theory of epidemics–I. 1927. Bull Math Biol. 1991; 53(1–2): 33–55. Publisher Full Text\n\nBjørnstad ON, Shea K, Krzywinski M, et al.: The SEIRS model for infectious disease dynamics. Nat Methods. 2020; 17(6): 557–558. PubMed Abstract \| Publisher Full Text\n\nSobol IM: Global sensitivity indices for nonlinear mathematical models and their monte carlo estimates. Math Comput Simul. 2001; 55(1–3): 271–280. Publisher Full Text\n\nSaltelli A, Annoni P, Azzini I, et al.: Variance based sensitivity analysis of model output. design and estimator for the total sensitivity index. Comput Phys Commun. 2010; 181(2): 259–270. Publisher Full Text\n\nKissler SM, Tedijanto C, Goldstein E, et al.: Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science. 2020; 368(6493): 860–868. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang W, Lipsitch M, Shaman J: Inference of seasonal and pandemic influenza transmission dynamics. Proc Natl Acad Sci U S A. 2015; 112(9): 2723–2728. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYamana T, Pei S, Kandula S, et al.: Projection of COVID-19 cases and deaths in the us as individual states re-open may 4,2020. medRxiv. 2020. Publisher Full Text\n\nDeng W, Bao L, Liu J, et al.: Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques. Science. 2020; 369(6505): 818–823. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBert NL, Tan AT, Kunasegaran K, et al.: SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature. 2020; 584(7821): 457–462. PubMed Abstract \| Publisher Full Text\n\nBraun J, Loyal L, Frentsch M, et al.: SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19. Nature. 2020; 587(7833): 270–274. PubMed Abstract \| Publisher Full Text\n\nAntia A, Ahmed H, Handel A, et al.: Heterogeneity and longevity of antibody memory to viruses and vaccines. PLoS Biol. 2018; 16(8): e2006601. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSekine T, Perez-Potti A, Rivera-Ballesteros O, et al.: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19. Cell. 2020; 183(1): 158–168.e14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRipperger TJ, Uhrlaub JL, Watanabe M, et al.: Detection, prevalence, and duration of humoral responses to SARS-CoV-2 under conditions of limited population exposure. medRxiv. 2020; 2020.08.14.20174490. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIwasaki A: What reinfections mean for COVID-19. Lancet Infect Dis. 2021; 21(1): 3–5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOverbaugh J: Understanding protection from SARS-CoV-2 by studying reinfection. Nat Med. 2020; 26(11): 1680–1681. PubMed Abstract \| Publisher Full Text\n\nTomassini S, Kotecha D, Bird PW, et al.: Setting the criteria for SARS-CoV-2 reinfection – six possible cases. J Infect. 2020; S0163-4453(20)30546-6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWölfel R, Corman VM, Guggemos W, et al.: Virological assessment of hospitalized patients with COVID-2019. Nature. 2020; 581(7809): 465–469. PubMed Abstract \| Publisher Full Text\n\nTo KKW, Hung IFN, Ip JD, et al.: COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing. Clin Infect Dis. 2020; ciaa1275. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNachmias V, Fusman R, Mann S, et al.: The first case of documented COVID-19 reinfection in israel. IDCases. 2020; 22: e00970. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGupta V, Bhoyar RC, Jain A, et al.: Asymptomatic reinfection in two healthcare workers from India with genetically distinct SARS-CoV-2. Clin Infect Dis. 2020; ciaa1451. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTillett RL, Sevinsky JR, Hartley PD, et al.: Genomic evidence for reinfection with SARS-CoV-2: a case study. Lancet Infect Dis. 2021; 21(1): 52–58. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCOVID-19 Data Repository by the Center for Systems Science and Engineering at Johns Hopkins University. Reference Source\n\nWorldometer. Reference Source\n\nBlavatnik School of Government: Oxford covid-19 government response tracker. 2020. Reference Source\n\nDelamater PL, Street EJ, Leslie TF, et al.: Complexity of the Basic Reproduction Number (R 0). Emerg Infect Dis. 2019; 25(1): 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKevin L, Mathias P, Ellen K: The reproduction number of COVID-19 and its correlation with public health interventions. medRxiv. 2020. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDiekmann O, Heesterbeek JAP, Roberts MG: The construction of next-generation matrices for compartmental epidemic models. J R Soc Interface. 2010; 7(47): 873–885. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLayne SP, Hyman JM, Morens DM, et al.: New coronavirus outbreak: Framing questions for pandemic prevention. Sci Transl Med. 2020; 12(534): eabb1469. PubMed Abstract \| Publisher Full Text\n\nDaniel MA, Rosemary JB: SARS-CoV-2 T cell immunity: Specificity, function, durability, and role in protection. Sci Immunol. 2020; 5(49): eabd6160. PubMed Abstract \| Publisher Full Text\n\nSaad-Roy CM, Wagner CE, Baker RE, et al.: Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years. Science. 2020; 370(6518): 811–818. PubMed Abstract \| Publisher Full Text\n\nBNO News: COVID-19 reinfection tracker. BreakingNewsOn, 2020. Reference Source\n\nYubero P, Lavin AA, Poyatos JF: Supplementary Material and Code of Evidence for immunity to SARS-CoV-2 from epidemiological data series. [Data set]. Zenodo. 2021. http://www.doi.org/10.5281/zenodo.4452124" }	[ { "id": "80253", "date": "26 Apr 2021", "name": "Juliane F. Oliveira", "expertise": [ "Reviewer Expertise Mathematics", "Dynamical systems", "Singularity Theory", "Mathematical Modeling of Infectious Diseases" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nUsing mathematical modelling, the work submitted by Poyatos and colleagues tries to estimate from series of death and hospitalisations need the interval of acquired immunity by an infected individual by SARS-CoV-2.\n\nAs pointed out by the authors, longitudinal serological studies are required to determine the duration of immunity to a virus. Such studies consider individual response levels for the disease, which for many diseases it is also influenced by age. These characteristics can not be studied from ecological data of counts of mortalities, or cases, or hospitalisation needs.\nAdditionally, the authors carry out significant misinterpretations on the model construction, which invalidate the analysis performed. For instance, they fail to interpret the disease's dynamics and draw the pathway of the individuals from susceptibility to an outcome as recovered or death. There is a transition between exposed and mild infections where asymptomatic infections compulsory will be a mild infection. Other confusions are seen between the basic reproduction number, a value estimated at the beginning of the disease dissemination, and the effective reproduction numbers.\n\nThe methods and data analysed cannot estimate such a complex measure: the immunity period for a disease.\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?\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": "6640", "date": "14 May 2021", "name": "Juan Poyatos", "role": "Author Response", "response": "Comment. As pointed out by the authors, longitudinal serological studies are required to determine the duration of immunity to a virus. Such studies consider individual response levels for the disease, which for many diseases it is also influenced by age. These characteristics can not be studied from ecological data of counts of mortalities, or cases, or hospitalisation needs. Response. The reviewer's main concern is that immunity time can only be ascertained through longitudinal serological studies. The reviewer appears to overlook in this argument the analyses that we performed on synthetic data before studying actual coronavirus mortality. These analyses demonstrate the opening premise that immunity time can be discerned significantly despite intrinsic limitations and an obscure infection rate. Thus, the results of this part of the manuscript (section 2) constitute statistical proof of how our approach quantifies immunity time. Furthermore, we at no point say in our manuscript that serological studies are the only way to estimate immunity time. Indeed, note that a posterior study concocted and added to the repositories after this manuscript of ours was, replicated part of our approach and obtained some information on immunity. This study was recently published in Science [Saad-Roy et al., Science 370, 6518, 811-8, 2020] and thus represents a bibliographical endorsement of our approach. Comment. Additionally, the authors carry out significant misinterpretations on the model construction, which invalidate the analysis performed. For instance, they fail to interpret the disease's dynamics and draw the pathway of the individuals from susceptibility to an outcome as recovered or death. There is a transition between exposed and mild infections where asymptomatic infections compulsory will be a mild infection. Response. The reviewer takes exception to a feature that seems to be the absence of an explicit transition between two compartments of the model, the “asymptomatic” and recovered patients. The criticisms seem to refer to said diverging feature between our rendition of covid19 etiology and her co-authored modeling work [Oliveira et al., Nat Comm 12, 333,19798-3,2021]. The feature in question, the transition between asymptomatic and recovered patients, is present in their model but not explicit in ours. Oliveira et al. consider that some people are exposed to the virus, infected, and promptly become immune without showing any symptoms at all (something that has been profusely taken for granted since the beginning of the pandemic, but rarely well demonstrated), and writes this as a specific term in their equations. In contrast, we consider that all infected patients will develop either headache, digestive problems, fever, or a slight cough during 0 to 15 days. Both things are not incompatible and, as a matter of fact, the nature of our bibliographical parameters as measures of centrality is not incompatible with a subset of these asymptomatic patients indeed becoming immune. Therefore, our model does not fail the reality being modelled any more than one whereby this transition is explicitly represented. But, even if it was the case that our model was compartmentalized differently, this would not necessarily change anything. When using models for prediction, not every change to the model is relevant for predictivity. Indeed, a conventional SEIRS model, which we evaluated in our study before the analyses with the advanced one that the reviewer takes exception to, is well beyond capable of predicting coronavirus mortality when combined with ensemble filtering approaches. And it does so with a structure more general and uninformed than either our model or other aesthetically different iterations used, such as the reviewer's very own. Comment. Other confusions are seen between the basic reproduction number, a value estimated at the beginning of the disease dissemination, and the effective reproduction numbers. Response. We kindly, but again strongly, disagree with the reviewer in the existence of any kind of confusion regarding the basic reproduction number (R0) and the effective reproduction number (Re) along our manuscript. The first time we mention R0 we call it \"initial number of secondary infections\" (Results section 1, paragraph 3) and is totally equivalent to the basic reproduction number as defined by the reviewer and as evidenced by the standardized nomenclature R0. Later, we mention \"the effective number of secondary infections Re\" (Results section 4, paragraph 1), which is totally equivalent to the \"effective reproduction number\" that the reviewer mentions. In this case, we are describing the reproduction number after the start of the disease in agreement with the reviewer's description and, again, as evidenced by the use of the standard nomenclature Re. Moreover, in the methods section we refer to R0 as the \"basic reproductive number\" and Re as the \"effective reproductive number\" in literal agreement with the reviewer description of these parameters. Furthermore, that we call Re the \"temporal-dependent counterpart\" of R0 highlights what the reviewer points out: that R0 is fixed while Re is time-dependent. Finally, our computation of R0 and Re follow the standard procedure using the Next Generation Matrices, which unsurprisingly is the same method the reviewer used in a co-authored work [Oliveria et al, Nat Comm 12, 333,19798-3,2021]. Hence, we regret that using \"number of secondary infections\" instead of \"reproductive number\" even when preserving the standard notation R0 and Re might have caused such confusion in the reviewer. We have added a brief note in a new version of our manuscript to make this clear when mentioning both R0 and Re (link to reference [23] in Results section 1, paragraph 3 and Results section 4 paragraph 1). We thank the reviewer for her time. We hope that our clarifications in this response will be positively valued and that she now considers our manuscript approved for publication." } ] } ]	1	https://f1000research.com/articles/10-50
https://f1000research.com/articles/13-788/v1	10 Jul 24	{ "type": "Systematic Review", "title": "Cheating and plagiarism in higher education institutions (HEIs): A literature review", "authors": [ "Md Sozon", "Omar Hamdan Mohammad Alkharabsheh", "Pok Wei Fong", "Sia Bee Chuan", "Pok Wei Fong", "Sia Bee Chuan" ], "abstract": "Cheating and plagiarism have become serious problems in higher education institutions (HEIs). It affects educational quality as well as the reputation of higher education. The purpose of this study is to identify the most prevalent types of cheating and plagiarism, as well as the elements that contribute to cheating and plagiarism, and to present solutions to this recurring problem. This paper systematically reviews 45 articles published from 2018, to 2022, aligned with the PRISMA guidelines in the selection, filtering, and reporting of the papers. This review shows that factors such as increased pressure on students, poor academic integrity awareness, lack of up-to-date academic honor codes, and the unethical application of AI tools are prime contributing factors to cheating and plagiarism in HEIs. In a broader sense, all these factors are classified as individual, social, cultural, institutional, and technological factors that are responsible for this problem. This problem can be reduced by establishing ethical and moral development tutorials as well as formulating up-to-date honor codes considering AI tools. Furthermore, higher education institutions must develop anti-plagiarism detection software in order to detect plagiarism and aid students in improving academic writing and paraphrasing approaches. The findings of this systematic literature review provide useful insights for educators and policymakers to solve the complicated issue of cheating and plagiarism in higher education institutions.", "keywords": [ "students", "cheating", "plagiarism", "higher education institutions", "academic integrity." ], "content": "1. Introduction\n\nAcademic integrity is an essential element for higher education institutions (HEIs) all over the world (Vasylkevych & Lomak, 2020; Hölscher, 2021). Academic integrity is a commitment not only to uphold ethical values, but also to demonstrate behaviors that promote six fundamental principles “honesty, trust, fairness, respect, responsibility, and courage” in all aspects of education, research, and scholarly communication within the context of higher education (International Center for Academic Integrity [ICAI], (2021). In this sense, 97% of guardians in the United States of America believe that moral values such as honesty and integrity should be incorporated into the academic curriculum (Pavela, 1993; Shrivastava, 2017) and higher education institutions are responsible for promoting academic integrity (Mattar, 2022) and producing ethically and morally sound graduates (Alhamuddin et al., 2023).\n\nHowever, higher education institutions around the world are struggling to maintain academic integrity due to the recurrent occurrence of cheating and plagiarism. Cheating and plagiarism are prevalent problems in HEIs that threaten the core principles of education and undermine the student's ethical and moral values (Sozon et al., 2024). The availability of technology-driven artificial intelligence tool, for example, Chat Generative Pre-trained Transformer (ChatGPT) supports to violate academic integrity (Susnjak, 2022) and corrupts user judgment (Krügel et al., 2023), raises concern about ethics and professionalism (Currie, 2023), promotes high-tech plagiarism (Gefen & Arinze, 2023), students not considered as high-risk technology tool about cheat (Fergus et al., 2023), teachers find hard to detect the authenticity of students assignments and exams (Crawford et al., 2023), users may publish the paper as their own (Oravec, 2023), raises ethical and privacy issues (Shahriar & Hayawi, 2023) and sparks controversy among higher education community. In the future, AI is more likely to develop (Tomlinson et al., 2023) and produce more customized educational materials, which may disrupt students' motivation for acquiring knowledge and higher education institutions' learning environment. Moreover, it may also discourage students from developing new skills and abilities by putting in an effort and investing time to sharpen their expertise. AI tool (ChatGPT) is a potential threat to academic integrity in all levels of higher education (Williams & Fadda, 2023) because all types of cheating raise questions regarding the quality of an institution's academic curriculum, the value of its degrees, and the skill of its graduates (Wideman, 2008).\n\nThis scope of this study covers various forms of academic integrity violations, from classic exam cheating to sophisticated cases of plagiarism made possible by digital technology. It is crucial to recognize that combating academic misconduct such as cheating, and plagiarism requires a variety of approaches. The authors intend to examine the strategies and interventions that universities can implement to combat cheating and plagiarism. Therefore, understanding the effectiveness of these measures is critical for institutions seeking to protect the integrity of their academic programs.\n\nWith this systematic literature review, the authors aim not only to comprehensively synthesize existing knowledge but also to identify gaps in the literature, thereby paving the way for future research efforts. The authors also consider the scope of different studies, the geographical location of the selected papers, research methods, their impact on citations, reasons for cheating and plagiarism, and ways to prevent cheating and plagiarism in higher education institutions and contribute to the ongoing discourse on academic integrity, providing educators, administrators, and researchers with valuable insights to inform evidence-based policies and practices.\n\nThe four research questions listed below served as the study’s compass in meeting its objectives and identifying the untapped research fields:\n\n1. What are the characteristics of research and publication on the prevalence of plagiarism and cheating in HEIs (volume of publications, pattern of papers, field of study, etc.) of the reviewed papers published from 2018 to 2022?\n\n2. What are the top prevalent types of plagiarism and cheating in HEIs?\n\n3. What factors contribute to the prevalence of cheating and plagiarism in Higher education institutions?\n\n4. What strategies have been employed to reduce the prevalence of cheating and plagiarism in HEIs\n\nThis research will provide evidence-based guidance to educators and other responsible stakeholders for the formulation and modification of academic integrity policies and procedures within educational institutions to combat students’ inappropriate academic behavior (cheating and plagiarism). This study will also explore the design and development of plagiarism detection software and innovation assessment systems that encourage critical thinking, originality, and ethical research practices. Thus, the purpose of this literature review is to explore the existing body of knowledge and summarize the results of various academic studies to reveal a comprehensive picture of the prevalence of cheating and plagiarism in higher education institutions.\n\n\n2. Literature review\n\nCheating and plagiarism are prevalent issues in higher education institutions around the world. HEIs have become increasingly concerned about the prevalence of cheating and plagiarism in recent years. It has further increased due to the unethical application of artificial intelligence tools (AI) in manipulating the examination and writing assignments, reports, case studies, thesis, and research papers. The scholarly publication shows that students are easily able to cheat and plagiarize written assignments through inappropriate applications of technology and AI tools.\n\nCheating is defined as the use of data, resources, equipment, or methods for the completion of academic tasks in a dishonest manner (Salamah, 2022). The duplication and submission of the work of another student without their permission also come under the umbrella of cheating and it describes the exploitation of prohibited materials, work plagiarizing, or dishonest behavior such as telling lies of being ill or injured as leverage in tests (Hodgkinson et al., 2016). In short, cheating is often adopted to gain an unfair advantage over other students from the teachers.\n\nCheating is a growing concern in higher education institutions. In the past, many scholarly papers were published to identify and provide solutions to this problem. However, this problem bv hgbvbv cheating.\n\nOn the other hand, the term plagiarism stems from the root Latin term “plagiarism” which means “kidnapper/abductor”. Plagiarism is the unauthorized use of a source in situations where there is a legitimate expectation of authorship. Plagiarism is using another individual’s thoughts, words, phrases, sentences, or facts and taking them as one’s own (Thomas, 2020). According to Sutton et al. (2014) plagiarism is considered as academic dishonesty or contribution to misleading while taking credit for work that is owned by someone else. In the same way, other authors (Farook et al., 2020; Mbutho & Hutchings, 2021) defined it as a type of academic dishonesty that is considered fraudulent behavior, undermining the intellectual property of the author and obtaining a reward for another’s work. Viewed from a legal perspective, plagiarism is an act of theft of intellectual work ownership (Gullifer & Tyson, 2010, p. 463). It is a violation of intellectual property rights that are protected through copyright laws. It appears that plagiarism has legal as well as ethical ramifications and is sometimes viewed as a violation of moral-ethical aspects as opposed to legal aspects owing to its nature of being outside of the copyright infringement rights boundaries (Mbutho & Hutchings, 2021).\n\nPlagiarism is the top frequently used method in academia which breaches the integrity of HEIs. According to the opinion of (Butakov et al., 2012), this has become a huge concern in several fields, namely education, research, and industry and it is deemed to be a significant misbehavior breaching academic ethics and intellectual thought. Moreover, (Gullifer & Tyson, 2010) described the issue as increasingly worsening among institutions, urging them to focus more on its resolution. The issue is being focused on due to the increasing prevalence of plagiarism in the technological era, aiding students in claiming someone else’s work as their own. Information and communication technologies (ICT) development has led to the promotion of plagiarism among students at higher educational institutions (Rozar et al., 2020). Stealing another’s work breaches the fundamental foundations of the academic community (Helgesson & Eriksson, 2015; Eret & Gokmenoglu, 2010) as it is dishonesty, and a normal and decent person possessing morals and values would never engage in plagiarism behavior.\n\nVarious sources are attributable to the rise of plagiarism, among which are the failure to cite sources properly, honest mistakes, and divergent views on what comprises suitable academic behavior/scholastic integrity in different cultures (Sarlauskiene & Stabingis, 2014). This stresses the consideration behind the phenomenon’s motivation when addressing the issue and the fact that evidence-based reasoning may not be effective in clarifying the low levels of students who are penalized or expelled from educational institutions for plagiarizing. This era of internet technology has abetted fraudulent and corrupt behaviors among higher learning institution students, which has become a source of concern. Consequently, the increasing and extensive prevalence of plagiarism in several colleges of industrialized nations has focused on technology to prevent the behavior among students (Thompsett & Ahluwalia, 2010). Regardless of such technological detection of plagiarism, institutions in developed nations are still not leveraging effective plagiarism detection software. Therefore, further study is essential to determine the contributing factors of student plagiarism and design a solution to solve this burning issue.\n\nCheating and plagiarism in universities have far-reaching consequences. It not only disrupts classroom decorum but also affects students' ethics and professionalism. Cheating and plagiarism can hurt educational institutions, teachers, and learners both domestically and internationally (Pettyjohn et al., 2020). Students who commit academic dishonesty in their educational institutions are likely to continue to engage in similar unethical activities in their professional lives (Ozcan et al., 2022). Moreover, violations of students' academic integrity harm not only students' learning outcomes but also the reputation of educational institutions. Furthermore, students' cheating and plagiarism may lead teachers, prospective students, and researchers to engage in similar inappropriate activities in their fields (Waigand, 2019). Therefore, every effort should be made to detect and prevent students' cheating and plagiarism that affect various stakeholders.\n\nHigher education institutions must address cheating and plagiarism issues seriously. Institutions must put in place effective rules and processes to ensure academic standards and integrity Darman, 2022). To address these challenges, institutions must deploy robust plagiarism detection tools, secure online exam platforms, and clear academic integrity policies, while also fostering a culture of ethical AI use and digital literacy among students (Jenkins et al., 2022). Striking a balance between the benefits and risks of AI in higher education requires a comprehensive and proactive approach to maintaining academic integrity and upholding the ethical standards of education. Failure to do so will destroy the inclusive learning environment designed for ethical practice. Higher education institutions are also required to initiate a combination of educational, technical, and supportive measures to reduce recurrent incidents (Abbasi et al., 2021). One potential solution to address this issue is to increase awareness about the negative consequences of cheating and plagiarism (Kier & Ives, 2022). Another solution is to implement stricter consequences for those who engage in these practices. Additionally, encouraging ethical behavior through education and mentorship can help prevent cheating and plagiarism (Mutongoza & Olawale, 2022). The solution aims to promote a culture of integrity, responsibility, and intellectual growth, and ensure the integrity of the educational experience for all involved. All stakeholders must work closely together to foster a culture of academic integrity in higher education institutions.\n\nOverall, the literature review highlights the significance of sustaining educational ethics and taking action to prevent and address cheating and plagiarism in HEIs. Institutions and individuals must prioritize academic integrity to ensure that students receive a quality education and obtain legitimate qualifications. This research may help to address the challenges relating to students cheating and plagiarism behaviors in educational contexts by offering useful findings to education institutions, policymakers, and professionals. Furthermore, this study will reinforce the necessity to upgrade the existing plagiarism detection software and make it more diversified to detect AI and software-produced write-ups. In summary, this study is critical given the present state of higher education, and it will significantly advance our knowledge of students' unethical behavior in the classroom and teach them to uphold the institution's code of ethics.\n\n\n3. Methods\n\nA systematic literature review (SLR) refers to a process involving analyses, condensing, and interpretation of research inferences according to sources, while complying with the established rules (Tawfik et al., 2019). This study follows PRISMA framework (Mckenzie, et al., 2021; Moher, et al., 2021; Sozon et al., 2024). The PRISMA framework presents a core foundation for the systematic articulation and visualization of the way the study results are acknowledged and reached during the process of review and meta-analysis (Surahman & Wang, 2022). SLR is justifying the conditions for information sources utilized, the procedures of collecting data, providing descriptions of data and reaching conclusions.\n\nThis study considered articles published from2018, to 2022, in the Scopus database. This database was chosen due to its availability and easy access to internationally recognized articles including peer-reviewed papers, and scientific literature published worldwide and in various disciplines. The search technique centred around key concepts linked to the subject of study topic (cheating, plagiarism, academic dishonesty, academic misconduct, academic integrity violation in Higher education institutions” OR “tertiary education institutions), and simple operators’ Boolean operators (AND, OR) were used based on a research question.\n\nThe study was limited to peer-reviewed articles, which helped it become more reliable and comprehensive. As the search continues, additional parameters are used in the database to search based on the inclusion and exclusion criteria described in section 3.2, To provide the broadest possible overview, no specific journals were selected during the search strategy stage. In the continuation of the search, additional parameters (document type: articles, review articles; language: English) to refine the search results were used in the database based on the inclusion and exclusion described in section 3.2. To offer the widest possible view, particular journals were not chosen during the search strategy phase.\n\nClear inclusion and exclusion criteria were established to choose and incorporate only pertinent papers that were found in the database related to our study subject.\n\n3.2.1 Inclusion criteria\n\nIC1: Journal articles published in Scopus Database only.\n\nIC2: Research papers published between 2018, and 2022.\n\nIC3: The research paper is written in English Language only.\n\nIC4: The research is related to the Social Sciences, Arts and Humanities, and Psychology field.\n\nIC5: The study was carried out in an educational setting (higher education institutions, tertiary education).\n\nIC6: Only available complete papers.\n\nIC7: The research address (cheating, plagiarism, academic dishonesty, academic misconduct, academic integrity violation).\n\n3.2.2 Exclusion criteria\n\nEX1: Journal editorials, books, book chapters, conference article and other nonpeer-reviewed publications.\n\nEX2: The journal paper is not written in English Language.\n\nEX3: The journal paper is not peer-reviewed\n\nEX4: The journal paper is listed in other databases.\n\nEX5: The research is not conducted in an education environment (higher education institutions, Tertiary education).\n\nEX6: The journal paper is not related to the Social Sciences, Arts and Humanities, and Psychology field.\n\nEX7: The study does not address (cheating, plagiarism, academic dishonesty, academic misconduct, academic integrity violation).\n\nEX8: Non-availability of complete peer-reviwed papers\n\nEX9: The articles published beyond the selected time frame between 2018, and 2022.\n\nEX10: Duplication of data: The search strings generated the same papers more than once.\n\nThe systematic literature review was carried out in five phases by two researchers following the PRISMA guidelines. The first phase consisted of an initial search of the literature included in the Scopus Database (n=1376). In the second phase, a total of 163 studies were dropped because of duplication of data (EX10). A total of 729 papers were eliminated in the third phase based on the exclusion criteria (EX2: 51; EX9: 678). Subsequent stage, A total of 439 papers were dropped due to the above-written exclusion criteria (EX3:125; EX5: 103; EX6:12; EX7:139; EX8:60). In the fifth phase, consequently, 45 articles were selected based on the inclusion criteria. A list of selected papers is shown in PRISMA flow diagram (Figure 1). Moreover, all the selected 45 articles were publications in 34 well-known global index journals for the years 2018-2022, distributed as follows 7 in 2018 (16%), 2 in 2019 (4%), 7 in 2020 (16%), 10 in 2021 (22%), and finally, 19 in 2022 (42%). Besides, these papers also encompass an extensive array of academic subjects, from Social Sciences (84%) to Psychology (7%) and Humanities (9%).\n\nThe 45 papers that were included in the SLR are available in Extended data file 3. All 45 eligible articles were entered into Microsoft Excel and alphabetically arranged based on authors’ names. Each article was then coded serving as a building block for the content analysis method.\n\nResearch findings were thoroughly examined by going through the discussion section, after which thematic and sub-thematic data analysis approach was utilized. Thematic analysis is an analysis that determines new themes and sub-themes. This ensured a better and more organized presentation of results. After a manual analysis method through content analysis strategy, the direction of future studies was mapped out by reading the discussion and conclusion sections of the articles. In a qualitative data analysis, such as this study, the acquisition, compilation, and evaluation of data is conducted in a non-numerical and unstructured method using a grounded theory method. The articles were categorized based on the study question topic, namely, to reduce cheating and plagiarism in HEIs. Data was arranged based on the questions following the manual analysis method which constitutes qualitative data acquisition, data organization and connection to the research subject, data coding and analyzing insights, and drawing up the findings in the form of a report.\n\nTo ensure the authenticity, reliability, and credibility of the research and included paper for this study, the authors conducted a risk bias assessment (see Figure 2) by applying the Cochrane ‘Risk of bias’ tool for randomized trials (RoB 2.0) (McGuinness & Higgins, 2020). A bias is a “systematic error, or deviation from the truth, in results or interferences”. A study may be at risk of bias due to issues with the conceptualization, design, conduct, or interpretation of the study and this may lead to misleading estimates of effect\n\nIn this process, the authors tried to address the five specific domains where the biases may occur: “bias arising from the randomization process, bias due to deviation from intended intervention, bias due to missing outcome data, bias in the measurement of the outcome, and bias in the selection of the reported results”. Two authors (i and iv) independently applied this tool to each included study to provide supporting information and rationale for assessing the risk of bias in each area (low, high, and moderately concerning). Any conflicts in the decision that risked biasing or justifying the verdicts were resolved through discussion to reach an agreement The authors created a risk of bias summary (low, moderately concerned, high) for each included article Finally, the authors used the Robvis software to summarize the risk assessment and create a risk chart for this systematic review, as shown in Extended data file 2.\n\nThis review is therefore fully transparent and able to provide free, fair, natural, and reliable research results to resolve issues related to violations of academic integrity in higher education institutions.\n\nThe findings in the articles concerning cheating and plagiarism among HEIs were examined in a systematic literature review in compliance with the PRISMA paradigm, specifically ensuring that the inclusion and exclusion criteria were met Extended data file 1, along with data searching and selection, and the synthesis of the results. Based on the research questions, the result section provided a summarized version of each answer. The results have implications for educators and researchers as to the creation and implementation of effective practical solutions for minimizing the incidents of cheating and plagiarism among HEIs.\n\n\n4. Results\n\nThe column graph (see Figure 3) shows the annual published papers selected for this review from 2018 to 2022.\n\nThe data represent the frequency of publication of cheating and plagiarism for the years 2018 through 2022. To compare the periods before and after the onset of the COVID-19 pandemic (which began in late 2019), we can split the data into two groups: pre-COVID (2018-2019) and post-COVID (2020-2022). It seems that the frequency of publications on cheating and plagiarism increased (80%) in the post-COVID period compared to the pre-COVID period (20%). This could be due to various factors, such as changes in educational settings, increased reliance on online learning, or other pandemic-related challenges.\n\nIn terms of methodological point of view, a variety of research approaches (Figure 4) were used by earlier scholars to study academic integrity violations. According to the findings, 49% of the studies were based on qualitative research methods, while 36% of studies used quantitative research methods. Furthermore, mixed research approaches were used in 16% of the investigations. Figure 5 displays the methods mostly utilized to obtain research data: Casy study (4%). Survey (67%), Interview (2%), Mixed Literature and Interview (7%), and Mixed Literature and Survey (20%).\n\nAccording to the study, researchers have previously investigated a variety of topics to identify the root causes of academic integrity violations. To pinpoint the cause of this problem, they conducted tests on students, teachers, and staff (see Figure 6). The majority of research is centered around students (78%), indicating a significant emphasis on understanding their experiences, motivations, and methods related to cheating and plagiarism. Teachers and staff collectively constitute a small percentage (2%) of the respondents. This suggests that, compared to students, there may be less emphasis on exploring the perspectives of educators and administrative staff in cheating and plagiarism research. The category of both teachers and students (13%) reflects an interest in investigating the relationships and interactions between these two groups. This may involve studying how educators perceive and address cheating among their students. The subset of teachers-only (7%) respondents indicate a targeted focus on understanding the role of educators in the context of cheating and plagiarism, potentially exploring their awareness, preventive measures, and reactions.\n\nTrends in authorship analysis\n\nThe analysis focused on authorship patterns that represent breaches of academic integrity in higher education research. The authors read and evaluated the articles. As shown in Table 1, analysis showed that 7% of the database's articles were produced by female scholars, whereas 51% of the articles were published by males. 42% of the papers featured both male and female scholars. Additionally, the study revealed that 29% of the publications had a single author and 71% of the papers had two or more authors.\n\nThe distribution of articles by selected journals\n\nBetween 2018 and 2022, a sizable number of research papers were published in high-impact journals (see Figure 7). The researcher had expressed great interest in publishing articles on cheating and plagiarism.\n\nAnalysis of citation impact of the selected papers\n\nThe citation count exhibits some fluctuation from 2018 and 2022, suggesting that interest or effect levels were not constant over this time. Nonetheless, in comparison to the years that surround them, 2018, 2019, and 2021 stand out with comparatively larger citation counts. Perhaps throughout these years, there has been a rise in interest in the work or its increasing significance in the area (See Figure 8).\n\nThe highest citation count was observed in 2018, suggesting a peak in the impact or interest in research during that year. There was a substantial drop in citations in 2019 followed by a gradual increase in 2020, and a subsequent slight decrease in 2021 and 2022. The fluctuating pattern in citation counts across the years could be influenced by various factors, including the novelty and significance of the research, changes in the academic landscape, or the emergence of competing works.\n\nPublication of papers selected papers across countries\n\nA map was produced to determine the source of publications in every nation, and it was categorized by the specific location of data collection. The map shows 45 papers were selected which originated from 28 different countries. More publications were from such as Turkey (n=3), USA (n=2), Indonesia (n=2) Canada (n=2), China (n=2), Saudi Arabia (n=2), South Africa (n=2). Other publications (n =30) were distributed across 21 countries i.e., “Kosovo, New Zealand, Australia, Ethiopia, Ghana, Greece, Honduras, Iran, Israel, Kuwait, Malaysia, Mexico, Oman, Qatar, Romania, United Kingdom, Norway, Rwanda, and Switzerland, United Arab Emirates” with one paper for each country (See Figure 9).\n\nFrom the available statistics, it is clear that a varied range of nations appear to be represented, with each producing a distinct quantity of articles related to academic integrity violations. These review articles may certainly contribute to reaching an actionable solution for achieving this research objective.\n\nWhat are the top prevalent types of plagiarism and cheating in HEIs?\n\nIn higher education institutions, academic dishonesty has grown in importance recently, especially when it comes to cheating and plagiarism. Research has indicated a rise in the frequency of cheating and plagiarism, particularly since the use of electronic assessments. This unethical behavior erodes the principles of academic honesty and jeopardizes the integrity of the educational system. The review of 45 articles following cheating and plagiarism forms in HEIs is tabulated in Table 2.\n\nWhat factors contribute to the prevalence of academic cheating and plagiarism in higher education institutions?\n\nIn higher education institutions, cheating and plagiarism have become prevalent issues. It's concerning because these immoral actions compromise the integrity of education and diminish the hard work of sincere learners. Academic cheating and plagiarism are common in higher education institutions for several reasons. Table 3 summarizes the key factors contributing to cheating and plagiarism in higher education institutions.\n\nWhat strategies have been employed to mitigate academic cheating and plagiarism in higher educational institutions?\n\nReducing the prevalence of cheating and plagiarism in Higher Education Institutions (HEIs) involves implementing a combination of preventive measures, educational initiatives, and disciplinary actions. Here are some common strategies that have been employe. The article review concerning plagiarism and cheating in HEIs also indicated the way they can be mitigated (see Table 4).\n\n\n5. Discussion\n\nThis systematic literature review was conducted to provide an overview and insight into the research literature on cheating and plagiarism in HEIs to improve the quality of education and help students to develop ethical and moral skills. In this study a total of 45 papers (see Extended data file 3) were analyzed to answer the set of objectives and proposed research questions. The result indicates that from 2021 onwards, there was a significant wave of publications of papers about cheating and plagiarism.\n\nThe results of the literature review suggest that students have often broken the rules and regulations of the institutions they are enrolled in. Some students make it a habit to engage in dishonest behaviors like cheating and plagiarism (Amzalag et al., 2021). Besides, cheating and plagiarism, students are also involved in other forms of academic dishonesty such as contract cheating (Ali & Alhassan, 2021), collusion (Chen, 2022), falsification (Mâță et al., 2020), fabrication (Khan, 2022), fraud, corruption, and unjustified absences. These are the top prevalent types of academic integrity violations in HEIs. Therefore, it has become challenging for higher educational institutions to maintain academic integrity and ensure quality education for all students.\n\nThere is a high contextual basis for the causes behind cheating and plagiarism and this differs, from one individual to another and from one nation to the next. Based on the study, there are several contributors to students' infractions of academic honesty and integrity and this includes peer pressure, internet availability, societal norms, and individual mindset (Abbasi et al., 2021). These factors are categorized as individual factors, institutional factors, social, cultural, and technological factors which are summarized in the following paragraphs.\n\nIndividual factors: individual factors may contribute to the student’s choice to breach academic honesty. It is related to students' motivation. About this, motivation is an English word that stems from the word, “moveo”, which means to arouse, urge someone to act, or annoy. In other words, the system can sometimes initiate, stimulate, and maintain a particular behavior among individuals (Landa-Blanco et al., 2020; Usher, 2018). Motivation is a tool that can urge someone to act in a certain way and academic motivation is thus the root behind the behaviors relating to the performance and function of academic behavior (Kuhlmann et al., 2023) like the low level of students’ efforts, management of workload among students, their selected activities and their persistence in their academic development.\n\nA range of studies have explored the relationship between student motivation and academic dishonesty such as cheating and plagiarism. According to Landa-Blanco et al. (2020), academic dishonesty is negatively associated with intrinsic motivation and self-efficacy, and positively linked with motivation and extrinsic goal orientation. There is a significant connection between academic dishonesty and both intrinsic and extrinsic motivation. (Abbasi et al., 2021) further delved into the role of personality traits in academic dishonesty, finding that impulsivity and fight-flight-freeze behaviors were positively associated with engagement in dishonest academic behaviors. These studies collectively suggest that both intrinsic and extrinsic motivation, as well as certain personality traits, play a role in influencing cheating and plagiarism.\n\nInstitutional factors: This category of factors covers undermining practices to the academic integrity in the classroom, namely external assistance, collaboration, plagiarizing, and technology used for cheating. The environment in the classroom and the atmosphere within it reflects the students’ personalities and through the usage of academic materials, such an environment becomes a specific setting for learning advancement and promotion of creativity (Thomas, 2020). Studies show that a positive classroom atmosphere supports the learning outcomes of the students in light of their success and content level (Chang et al., 2018). Various physical environments, contexts, and cultures within which students learn are referred to as the academic environment (and such a learning environment, directly impacts the drive of the students to study.\n\nSocial factors: A range of social factors have been identified as significant contributors to academic integrity violations such as competition, social rejection, and societal pressure while (Șercan & Voicu, 2022) highlighted the influence of performance goals and social norms. These studies collectively underscore the complex interplay of social influences on academic integrity, suggesting the need for targeted interventions and support mechanisms. Moreover, cultural differences were also found to play a role, wit Roe (2022) and Nabee et al. (2020) both identifying the influence of perceived peer dishonesty and the acceptability of cheating, as well as the impact of cultural and psychological variables such as distress, perfectionism, and self-control. These findings underscore the complex interplay of social and individual factors in shaping academic dishonesty.\n\nCultural factors: The origin of cultural factors is the home, and the main source is parental pressure. Generally, parents pressure their children towards academic excellence notwithstanding the latter’s abilities and capabilities. Hence, students may turn to academic integrity breaches to satisfy their parents (Won & Lee, 2023). Studies showed that some students feel that obtaining high academic standards is a must to meet their parents’ expectations (Farahat, 2022). Added to this, parents force their children to obtain high marks despite their actual ability to do so and as such, parental expectations could make students compromise their academic integrity. A related study by Rozar et al. (2020) revealed that plagiarizing attempts among students usually occur when faced with tough tasks when obtaining a good score would call for extra effort and time, and when there is pressure from family. Their belief in the impossibility of obtaining good scores in limited time drives students to engage in cheating after which this becomes a part of their culture. Bretag & Mahmud (2014). found that institutionalizing a culture in the academic policy and practice context can promote academic integrity among students. In other words, understanding the way academic culture influences the inclination of students to breach academic integrity is the key.\n\nTechnological factors: Technology advancements have been dynamic over time and technology use among students has unfortunately taken a turn for the worst when it comes to cheating and stealing other’s work. In other words, ICTs have made it possible for students to easily plagiarize and cheat in HEIs. These infractions may also be brought on by improper and illegal ICT usage. It is thus important for students to understand and respect the rights and obligations of using and sharing intellectual property by adhering to the copyright and fair use, citing resources, obtaining or providing permission for use, steering clear of plagiarism, and understanding and using creative commons (Coldwell-Neilson, 2020). Morrison (2018), stated that the California Model School Library Standards indicate the need for students to respect intellectual property its fair use, and public performance rights when it comes to media downloading and duplication.\n\nCheating and plagiarism are a recurrent issue in higher education institutions. The reasons for cheating and plagiarism vary from person to person. Higher education institutions are required to take preventive measures to stop cheating and plagiarism as they hurt institutions' reputations, undermine the institutional code of ethics, and sideline the sustainability of the ethics and morality of higher education institutions. There is no one-stop solution for reducing the reasons for cheating and plagiarism in higher education institutions. Therefore, higher education institutions need to adopt a adopt a comprehensive strategy to safeguard against student cheating and plagiarism behavior.\n\nThe initial step is to reform and reinforce academic honor code and ethical guidelines which every student must follow. Students need to be informed and aware of the appropriate and inappropriate conduct in the classroom and based on past studies, the majority of the learning institutions do not stress the importance of academic integrity, which provides the impression that it is not a crucial issue. Through academic policies, the academic integrity level of HEI students may be enhanced. Moreover, this honor code needs to be regularly reviewed and updated to adapt to the evolving landscape of academic dishonesty. At the same time, higher education institutions must promote a culture of ethical behavior and educate both students and faculty on the importance of maintaining integrity by implementing academic integrity awareness programs. New students can be the recipients of customized course to inculcate within them the basics when it comes to academic dishonesty and its consequences. Cooperation between teachers, writing center directors, library directors, and academic specialists to develop such a course for students could be the key (Darmansyah & Darman, 2022). New incoming students would be required to take the course to enhance their academic integrity in what could be a first-year requirement (Stephens et al., 2021). HEIs need to play a key role in inculcating the habit of honesty, fair dealing, and integrity into students considering one of their major aims is to generate highly qualified graduates who can uphold the highest standards of integrity and professional ethics to contribute to society. Besides, higher education institutions must strengthen policy and invest resources to develop anti-plagiarism detection software using algorithms to scan and analyze submitted work, identify cases of plagiarism, and promote originality. Although the existing plagiarism prevention software (Turnitin, Authenticate, and Plagiarism Checker) has proven to be effective in the fight against academic cheating and plagiarism however this need to be modified further to detect AI generated contents. Furthermore, higher education institutions must introduce counselling and advisory services in shaping students' understanding of ethical boundaries. This counselling service will provide opportunities to understand the consequences of their actions for cheating and plagiarism. Fundamentally, the synergy of policy improvements, awareness initiatives, technical solutions and supportive advice will not only prevent cheating and plagiarism, but also improve academic integrity within higher education institutions (Farahat, 2022). This creates a comprehensive framework that fosters genuine engagement in higher education institutions.\n\nImplications of the study\n\nCheating and plagiarism are major issues in higher education institutions. The misuse of technology and artificial intelligence tools has made these problems even more challenging. Based on a comprehensive literature review, it is evident that higher education institutions must make it a priority to combat cheating and plagiarism. Additionally, it is essential to educate and raise awareness among students about the severe consequences that come with these actions.\n\n\n6. Conclusions\n\nCheating and plagiarism are serious problems in higher education institutions around the world. This systematic literature review found that there are different forms of academic integrity violations in higher education institutions. Students cheating and plagiarism are the most common form of academic integrity violation.\n\nSeveral factors contribute to this problem, including academic environment, cultural, social, and individual factors. The study also revealed that cheating and plagiarism are also caused by other variety of factors, including lack of student motivation to study, peer approval of cheating, laziness, strict submission deadline, course difficulty, lack of integrity awareness, and illegal use of cutting-edge technology, and increased pressure on students to improve their academic performance. The literature analysis also revealed that cheating and plagiarism increased further when higher education institutions moved to virtual assessments and evaluations during the Covid-19 pandemic. The introduction of electronic assessments has been found to increase the prevalence of cheating and plagiarism. Therefore, there is an urgent necessity to address this problem by designing effective policies and interventions.\n\nSolving the issues related to cheating and plagiarism requires a comprehensive approach among faculty, administrators, and students is paramount. Moreover, universities need to create environments where students are motivated to learn and enhance ethical and moral values to become positive contributors to society. In such a learning environment, students are more likely to act and work with integrity and demonstrate the highest level of integrity. Besides, to improve students' academic integrity, educational institutions should invest in educational initiatives that promote ethical behavior, critical thinking, and the development of strong research and writing skills. Additionally, there is an urgent need to implement advanced plagiarism detection tools to make students understand their current level of skills and offer them a solution to develop skills and produce a revised version of the copy with an accepted version of plagiarism in academic writing. Overall, the results of this systematic literature review highlight the urgent need for higher education institutions to prioritize efforts to combat cheating and plagiarism and increase student knowledge and awareness about the consequences of cheating and plagiarism.\n\nThis systematic literature review provided valuable insight into the prevalence of cheating and plagiarism in higher education institutions. However, there are certain limitations of this study. The main limitation is that relevant studies published in journals not indexed in Scopus are excluded. This can lead to biased literature selection and the loss of valuable articles from reliable journals that are not included in the Scopus database. Scopus primarily indexes English-language journals and may exclude valuable research published in other languages. This limitation can lead to an incomplete understanding of the global landscape of cheating and plagiarism in higher education, especially in regions where English is not the primary publication language.\n\nAnother limitation is the different research methods and definitions of cheating and plagiarism in studied studies. Different researchers have different approaches, which can make it difficult to accurately compare and generalize results. Differences in survey instruments, assessment methods, and cultural backgrounds can lead to inconsistencies in the reported prevalence, making it difficult to draw consistent conclusions. Despite these limitations, the Scopus framework provides a structured approach and allows access to a wide range of peer-reviewed literature. Future researchers should consider these limitations and take them into account when interpreting and generalizing the results of the review.\n\nEthical approval and Consent were not required.\n\nThe Qualitative Data Repository: PRISMA checklist for ‘Cheating and plagiarism in higher education institutions (HEIs): A literature review’, (Sozon et al., 2024) https://data.qdr.syr.edu/dataset.xhtml?persistentId=doi:10.5064/F6NEGI7I.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nThe Qualitative Data Repository: Extended data for ‘Cheating and plagiarism in higher education institutions (HEIs): A literature review’. https://www.doi.org/10.5064/F6NEGI7I (Sozon et al., 2024).\n\nThis project contains the following extended data:\n\n1. A list of inclusion and exclusion criteria for the study.\n\n2. Assessment of risk of bias for the included papers.\n\n3. List of included papers for the study (n=45).\n\n\nReferences\n\nAbbasi P, Yoosefi-Lebni J, Jalali A, et al.: Causes of the plagiarism: A grounded theory study. Nurs. Ethics. 2021; 28(2): 282–296. PubMed Abstract \| Publisher Full Text\n\nAlhamuddin A, Inten DN, Adwiyah R, et al.: Academic fraud during the covid-19 pandemic for high school students. Indonesian Journal of Islamic Education Studies (IJIES). 2023; 5(2): 233–251. Publisher Full Text\n\nAli HIH, Alhassan A: Fighting contract cheating and ghostwriting in Higher Education: Moving towards a multidimensional approach. Cogent Education. 2021; 8(1): 1885837. Publisher Full Text\n\nAmzalag M, Shapira N, Dolev N: Two sides of the coin: lack of academic integrity in exams during the corona pandemic, students' and lecturers' perceptions. Journal of Academic Ethics. 2021; 20: 243–263. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBretag T, Mahmud S: Embedding and extending exemplary academic integrity policy and support frameworks across the higher education sector. Department of Education, Skills and Employment; 2014.\n\nButakov S, Dyagilev V, Tskhay A: Protecting students’ intellectual property in the web plagiarism detection process. Int. Rev. Res. Open Dist. Learn. 2012; 13(5): 1–19. Publisher Full Text\n\nChang J, Faikhamta C, Na J, et al.: A comparison of science classroom environments between Korea and Thailand with a focus on their cultural features. Asia Pac. Sci. Educ. 2018; 4(1): 1–22. Publisher Full Text\n\nChen L: The Concepts of Academic Dishonesty of Undergraduate Students in China in the Situation of Online Education. Journal of Higher Education Theory and Practice. 2022; 22(6). Publisher Full Text\n\nCheating and plagiarism in higher education institutions (HEIs): A literature review. DOI: 10.5064/F6NEGI7I\n\nChiam CC, Lim YW, Kue WL: Academic cheating behaviour among students in higher education institutions in Malaysia. Journal of Social Sciences and Humanities. 2021; 7(2): 108–113.\n\nColdwell-Neilson J: Unlocking the code to digital literacy. Department of Education, Skills and Employment; 2020.\n\nCrawford J, Cowling M, Allen KA: Leadership is needed for ethical ChatGPT: Character, assessment, and learning using artificial intelligence (AI). J. Univ. Teach. Learn. Pract. 2023; 20(3): 02. Publisher Full Text\n\nCurrie GM: Academic integrity and artificial intelligence: is ChatGPT hype, hero or heresy? Seminars in Nuclear Medicine. WB Saunders; 2023, May. Publisher Full Text\n\nDarman RA: Plagiarism level analysis of online take-home examination results and its correlation with doctoral program students learning outcome. Int. J. Instr. 2022; 15(2): 243–256. Publisher Full Text\n\nDesalegn AA, Berhan A: Cheating on examinations and its predictors among undergraduate students at Hawassa University College of Medicine and Health Science, Hawassa, Ethiopia. BMC Med. Educ. 2014; 14: 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEret E, Gokmenoglu T: Plagiarism in higher education: A case study with prospective academicians. Procedia Soc. Behav. Sci. 2010; 2(2): 3303–3307. Publisher Full Text\n\nFarahat A: Elements of academic integrity in a cross-cultural middle eastern educational system: Saudi Arabia, Egypt, and Jordan case study. Int. J. Educ. Integr. 2022; 18(1): 9. Publisher Full Text\n\nFarook TH, Radford J, Alam MK, et al.: Plagiarism in dentistry-a systematic review. Br. Dent. J. 2020; 1–7. PubMed Abstract \| Publisher Full Text\n\nFergus S, Botha M, Ostovar M: Evaluating academic answers generated using ChatGPT. J. Chem. Educ. 2023; 100(4): 1672–1675. Publisher Full Text\n\nGefen D, Arinze O: ChatGPT and usurping academic authority. J. Inf. Technol. Case Appl. Res. 2023; 25(1): 3–9. Publisher Full Text\n\nGullifer J, Tyson GA: Exploring university students' perceptions of plagiarism: A focus group study. Stud. High. Educ. 2010; 35(4): 463–481. Publisher Full Text\n\nHabiburrahim H, Trisnawati IK, Yuniarti Y, et al.: Scrutinizing cheating behavior among EFL students at Islamic higher education institutions in Indonesia. Qual. Rep. 2021; 26(3): 1033–1053. Publisher Full Text\n\nHelgesson G, Eriksson S: Plagiarism in research. Med. Health Care Philos. 2015; 18: 91–101. Publisher Full Text\n\nHodgkinson T, Curtis H, MacAlister D, et al.: Student academic dishonesty: The potential for situational prevention. Journal of Criminal Justice Education. 2016; 27(1): 1–18. Publisher Full Text\n\nHölscher M: “A Question of Integrity”: Academic Values Torn Between Organizational Affiliation, National Competitiveness and the Global Academic Community. The Promise of Higher Education: Essays in Honour of 70 Years of IAU. 2021; 139–143. Publisher Full Text\n\nInternational Center for Academic Integrity (ICAI): The fundamental values of academic integrity. 3rd ed.2021. Reference Source\n\nJenkins BD, Golding JM, Le Grand AM, et al.: When opportunity knocks: College students’ cheating amid the COVID-19 pandemic. Teach. Psychol. 2022; 50(4): 407–419. Publisher Full Text\n\nKhan ZR: The devil’s in the detail–counting unique and organic contract cheating sites targeting higher education students in the UAE as a call to delegitimize them. Int. J. Educ. Integr. 2022; 18(1): 21. Publisher Full Text\n\nKier CA, Ives C: Recommendations for a balanced approach to supporting academic integrity: perspectives from a survey of students, faculty, and tutors. Int. J. Educ. Integr. 2022; 18(1): 22. Publisher Full Text\n\nKrügel S, Ostermaier A, Uhl M: The moral authority of ChatGPT. arXiv preprint arXiv:2301.07098. 2023. Reference Source\n\nKuhlmann SL, Bernacki ML, Greene JA, et al.: How do students’ achievement goals relate to learning from well-designed instructional videos and subsequent exam performance?. Contemp. Educ. Psychol. 2023; 73: 102162. Publisher Full Text\n\nLanda-Blanco M, Santos-Midence C, Blanco AL: Academic integrity: attitudes and practices of students of a public university in Honduras. Academia. 2020; 20-21: 202–217. Publisher Full Text\n\nMâță L, Lazăr IM, Ghiațău R: Exploring academic dishonesty practices among science education university students. J. Balt. Sci. Educ. 2020; 19(1): 91–107. Publisher Full Text\n\nMattar MY: Combating academic corruption and enhancing academic integrity through international accreditation standards: The model of Qatar University. Journal of Academic Ethics. 2022; 20(2): 119–146. Publisher Full Text\n\nMbutho NP, Hutchings C: The complex concept of plagiarism: undergraduate and postgraduate student perspectives. Perspect. Educ. 2021; 39(2): 67–81. Publisher Full Text\n\nMcGuinness LA, Higgins JPT: Risk-of-bias VISualization (robvis): An R package and Shiny web app for visualizing risk-of-bias assessments. Res. Synth. Methods. 2020; 12: 55–61. Publisher Full Text\n\nMorrison C: Copyright and digital literacy: rules, risk and creativity.2018. Publisher Full Text\n\nMutongoza BH, Olawale BE: Safeguarding academic integrity in the face of emergency remote teaching and learning in developing countries. Perspect. Educ. 2022; 40(1): 234–249. Publisher Full Text\n\nNabee SG, Mageto J, Pisa N: Investigating predictors of academic plagiarism among university students. International Journal of Learning, Teaching and Educational Research. 2020; 19(12): 264–280. Publisher Full Text\n\nOravec JA: Artificial intelligence implications for academic cheating: Expanding the dimensions of responsible human-AI collaboration with ChatGPT. J. Interact. Learn. Res. 2023; 34(2): 213–237.\n\nOzcan CC, Gerceker M, Ozmen I, et al.: The effect of globalization, income and tourism on environment: An empirical analysis. European Journal of Tourism Research. 2022; 32: 3210–3210. Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: Updating guidance for reporting systematic reviews: development of the PRISMA 2020 statement. J. Clin. Epidemiol. 2021a; 134: 103–112. PubMed Abstract \| Publisher Full Text\n\nPage MJ, Moher D, Bossuyt PM, et al.: PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. BMJ. 2021b; 372. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPavela G: Applying the power of association campus: a model code of academic integrity. Law and Policy. 1993; 24(1): 1–22. Reference Source\n\nPettyjohn H, Dyer JM, Pettyjohn HC, et al.: Academic dishonesty and testing: How student beliefs and test settings impact decisions to cheat. Journal of the National College Testing Association. 2020; 4(1): 1–30.\n\nRozar N, Sidik MH, Razik MA, et al.: Why do university students perpetrate internet plagiarism? A multiple linear regression analysis. Systematic Reviews in Pharmacy. 2020; 11(12).\n\nRoe J: Reconceptualizing academic dishonesty as a struggle for intersubjective recognition: A new theoretical model. Humanities and Social Sciences Communications. 2022; 9(1). Publisher Full Text\n\nSalamah I: Factors influencing academic dishonesty among Sriwijaya State Polytechnic students. International Journal of Science, Technology & Management. 2022; 3(2): 357–362. Publisher Full Text\n\nSarlauskiene L, Stabingis L: Understanding of Plagiarism by the Students in HEIs of Lithuania. Procedia Soc. Behav. Sci. 2014; 110: 638–646. Publisher Full Text\n\nȘercan E, Voicu B: Patterns of Academic Integrity Definitions among BA Romanian Students. The Impact of Rising Enrolments. Revista de Cercetare si Interventie Sociala. 2022; 78: 87–106. Publisher Full Text\n\nShahriar S, Hayawi K: Let’s Have a Chat! A Conversation with ChatGPT: Technology, Applications, and Limitations. Artificial Intelligence and Applications. 2023; 2(1): 11–20. Publisher Full Text\n\nShrivastava SK: Promotion of moral values through education. International journal of research in social sciences. 2017; 7(6): 103–108.\n\nSozon M, Alkarabsheh OHM, Pok WF, et al.: Data for: Cheating and Plagiarism in Higher Education Institutions (HEIs): A Literature Review. Qualitative Data Repository. 2024. Publisher Full Text\n\nStephens JM, Watson PWSJ, Alansari M, et al.: Can online academic integrity instruction affect university students’ perceptions of and engagement in academic dishonesty? Results from a natural experiment in New Zealand. Front. Psychol. 2021; 12: 569133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSurahman E, Wang TH: Academic dishonesty and trustworthy assessment in online learning: A systematic literature review. J. Comput. Assist. Learn. 2022; 38(6): 1535–1553. Publisher Full Text\n\nSusnjak T: ChatGPT: The end of online exam integrity?. arXiv preprint arXiv:2212.09292. 2022. Reference Source\n\nSutton A, Taylor D, Johnston C: A model for exploring student understandings of plagiarism. J. Furth. High. Educ. 2014; 38(1): 129–146. Publisher Full Text\n\nTawfik GM, Dila KAS, Mohamed MYF, et al.: A step by step guide for conducting a systematic review and meta-analysis with simulation data. Tropical medicine and health. 2019; 47: 46–49. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThomas D: Academic dishonesty, religious fundamentalism, among students at a religious university. International Forum Journal. 2020, June; 23(1): 126–138.\n\nThompsett A, Ahluwalia J: Students turned off by Turnitin? Perception of plagiarism and collusion by undergraduate bioscience students. Bioscience Education. 2010; 16(1): 1–15. Publisher Full Text\n\nTomlinson B, Torrance AW, Black RW: Chatgpt and works scholarly: Best practices and legal pitfalls in writing with ai. SMU L. Rev. F. 2023; 76: 108. Publisher Full Text\n\nUsher EL: Acknowledging the whiteness of motivation research: Seeking cultural relevance. EducationalPsychologist. 2018; 53(2): 131–144. Publisher Full Text\n\nVasylkevych Y, Lomak O: Formation of academic integrity as a component of professional competence of future professionals. HUMANITARIUM. 2020; 44(1): 25–34. Publisher Full Text\n\nWaigand AU: Using Turnitin to help students understand plagiarism. Learning and Teaching in Higher Education: Gulf Perspectives. 2019; 16(1): 2–13. Publisher Full Text\n\nWideman MA: Academic dishonesty in postsecondary education: A literature review. Transformative Dialogues: Teaching & Learning Journal. 2008; 2(1): 1–12.\n\nWilliams DO, Fadda E: Can ChatGPT pass Glycobiology?. Glycobiology. 2023; 33(8): 606–614. PubMed Abstract \| Publisher Full Text\n\nWon S, Lee YJ: Adolescent students’ grit: Do parents’ grit and educational expectations matter?. Contemp. Educ. Psychol. 2023; 72: 102137. Publisher Full Text" }	[ { "id": "311995", "date": "20 Aug 2024", "name": "Adva Margaliot", "expertise": [ "Reviewer Expertise Integrity & creativity", "Creativity in teachers' education", "Online learning and teaching" ], "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 clearly stated the importance of the need for this wide literature review of Plagiarism and Cheating in Higher education institution. The researchers did very wide literature scanning and convinced by the centric issue and its future influencing on the skills and the performances of the generation of students that uses the affordance of technology smart tools, they provide the high scale of the phenomena of cheating and Plagiarism at HEIs across the globe. The spread of such phenomena is well expressed and well examined along with this paper. The discussion section well detailed the phenomena as well as the urgent need to find some new directions so as to connect between the theoretical versus practical knowledge construction, so that academic knowledge construct will be better realize as relevant and worth for upload the self effectiveness for the promotion of livelihood.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] }, { "id": "308208", "date": "09 Sep 2024", "name": "Ceceilia Parnther", "expertise": [ "Reviewer Expertise Academic integrity", "student success", "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 your submission. Your global study is helpful and needed. The rationale and objectives are clear , the analysis section is very thorough and complete, and the four research questions are straightforward. Your methodological choices and descriptions are clear and maintain rigor. Your conclusions are logical and suggestions, while broad, align with the findings.\nSeveral uncited studies popularized the PRISM technique in academic integrity research before 2021 . I suggest mentioning one or more given the shift in approach.\nIn terms of added clarity, defining subsections in the technological factors section would be helpful. In addition the cheating types discussion section would benefit from with additional context. It is surprising that only one study uses the term academic misconduct. Providing more context on the factor types, specifically institutional and social factors as described would provide a more comprehensive understanding of the topic. I suggest you consider the absence of findings a finding, and explaining what is will yield stronger future research and implications. Please consider connecting the findings to the research questions. I also recommend potential elaboration of prior literature specific to cheating. 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? Not applicable\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": "12449", "date": "26 Sep 2024", "name": "Md Sozon", "role": "Author Response", "response": "Dear esteemed reviewer, Thank you so much for reviewing our paper. We appreciate your time and effort in providing constructive feedback and suggestions. Your input has greatly improved the paper. We are pleased to inform you that we have incorporated your suggestions into version II of the paper. Kindly, let us know if any further revisions are required. Thank you once again for your valuable input. Sincerely, Md. Sozon [PhD Candidate] Faculty of Accountancy and Management, Universiti Tunku Abdul Rahman, Malaysia Reviewer Comment 1: Several uncited studies popularized the PRISM technique in academic integrity research before 2021. I suggest mentioning one or more given the shift in approach. Our reply: We have included one pertinent research paper in the study, as per your suggestion. Revised text: After conducting a comprehensive review of the existing literature, it is clear that the PRISM technique has become widely popular in the field of academic integrity. Zawacki-Richter's (2020) study, in particular, has been instrumental in bringing clarity, replicability, and a comprehensive synthesis of the literature to academic integrity research. Zawacki-Richter, O., Kerres, M., Bedenlier, S., Bond, M., & Buntins, K. (2020). Systematic reviews in educational research: Methodology, perspectives and application (p. 161). Springer Nature. https://library.oapen.org/handle/20.500.12657/23142 Reviewer Comment 2: In terms of added clarity, defining subsections in the technological factors section would be helpful. In addition the cheating types discussion section would benefit from with additional context. Our reply: We have revised this section to enhance its professional tone. Firstly, we offer a comprehensive definition of the technology and its significant impact on the prevalence of cheating and plagiarism in higher education. Following that, we delve into the critical technological factors in four distinct subsections. Lastly, we support each subsection by incorporating relevant statistics and citing credible sources. Technology advancements have been dynamic over time and technology use among students has unfortunately taken a turn for the worst when it comes to cheating and stealing other’s work. In other words, ICTs have made it possible for students to plagiarize and cheat in HEIs easily. These infractions may also be brought on by improper and illegal ICT usage. It is thus important for students to understand and respect the rights and obligations of using and sharing intellectual property by adhering to the copyright and fair use, citing resources, obtaining or providing permission for use, steering clear of plagiarism, and understanding and using creative commons (Coldwell-Neilson, 2020). Morrison (2018), stated that the California Model School Library Standards indicate the need for students to respect intellectual property its fair use, and public performance rights when it comes to media downloading and duplication. Cheating and plagiarism through the misuse of technology can be further divided into three subsections such as the availability of computer and& AI tools, limitations of existing tools in detecting cheating and plagiarism, internet and Internet and web-based unauthorized collaboration Availability of computer and& AI tools: Computer and artificial intelligence tools have been shown to have a double-edged effect on higher education institutions. Recent research conducted by Hasanein & Sobaih (2023) has highlighted that students frequently misuse these tools, particularly ChatGPT, within the realm of higher education. Consequently, there has been a notable increase in instances of AI-driven cheating, plagiarism, contract cheating, and various forms of academic dishonesty, including falsification, collusion, and unauthorized collaboration. These challenges present significant obstacles to maintaining academic integrity (Wang & Cornely, 2023). Limitations of existing tools in detecting cheating and plagiarism: The study conducted by Do Ba (2017) reported that higher education institutions are applying software and technological tools, like Turnitin, to assess the similarity index of students' written assignments/reports. However, the study conducted by Lines (2016) highlighted that these tools are often incapable of detecting assignments and reports written by ghostwriters. Therefore, the students who engage in committing cheating and plagiarism often go undetected because of the limitations of the existing tools for detecting such behavior. Internet and web-based unauthorized collaboration: The study conducted by Wang & Cornely (2023) reported that students frequently engage in unauthorized Internet and web-based collaboration while completing their reports, theses, and assignments. In this connection, Tabsh (2019) emphasized that this type of unauthorized collaboration encourages cheating and plagiarism and diminishes the overall learning outcomes in higher education. Moreover, the unapproved and dishonest behaviors exhibited by students have raised concerns about data security and privacy. Therefore, it is necessary for higher education institutions to promptly take action to reduce these unethical student behaviors. Newly added references: Hasanein, A. M., & Sobaih, A. E. E. (2023). Drivers and consequences of ChatGPT use in higher education: Key stakeholder perspectives. European journal of investigation in health, psychology and education, 13(11), 2599-2614. . https://doi.org/ 10.3390/ejihpe13110181 Wang, J., & Cornely, P. R. (2023, November). Addressing Academic Misconduct in the Age of ChatGPT: Strategies and Solutions. In Proceedings of the 2023 7th International Conference on Education and E-Learning (pp. 19-25). https://doi.org/10.1145/3637989.3638014 Do Ba, K., Do Ba, K., Lam, Q. D., Le, D. T. B. A., Nguyen, P. L., Nguyen, P. Q., & Pham, Q. L. (2017). Student plagiarism in higher education in Vietnam: an empirical study. Higher Education Research & Development, 36(5), 934-946. https://doi.org/10.1080/07294360.2016.1263829 Lines, L. (2016). Ghostwriters guaranteeing grades? The quality of online ghostwriting services available to tertiary students in Australia. Teaching in Higher Education, 21(8), 889-914. https://doi.org/10.1080/13562517.2016.1198759 Tabsh, S. W., El Kadi, H. A., & Abdelfatah, A. S. (2019, April). Faculty perception of engineering student cheating and effective measures to curb it. In 2019 IEEE Global Engineering Education Conference (EDUCON) (pp. 806-810). IEEE. Reviewer Comment 3: It is surprising that only one study uses the term academic misconduct. Providing more context on the factor types, specifically institutional and social factors as described would provide a more comprehensive understanding of the topic. Cheating and plagiarism continue to be persistent issues in higher education. A study by Singh et al (2016) revealed a prevalent occurrence of cheating among undergraduates. Approximately 39% of participants admitted to cheating on tests, and a majority of 62% admitted to cheating on written assignments. Among graduate students, 17% admitted to cheating on tests, while 40% admitted to cheating on written assignments. Furthermore, according to Curtis et al. (2021), the percentage of Australian students who buy assignments from ghostwriting services is estimated to be 7.9%, which is considerably higher than previous self-reported numbers. Previous research conducted by Cuadrado et al. (2019) has shown that these acts not only hinder students' learning outcomes but also damage the reputation of educational institutions. Moreover, students' cheating and plagiarism incidents undermine the institutional code of ethics and jeopardize the sustainability of ethical values and principles within these institutions. The causes of cheating and plagiarism can vary from person to person. According to Sozon et al. (2024), individual causes include laziness, lack of motivation for learning, and insufficient time to study. In terms of institutional factors, Solmon (2018) revealed that a poor academic integrity policy, ineffective implementation of an honor code, and a lack of technological tools for detecting cheating and plagiarism contribute to the issue. Tanveer et al. (2012). Additionally, Sozon et al. (2024) highlighted those social factors, such as peer influences, pressure to achieve higher grades, intense competition, cultural norms, and the perceived acceptance of cheating, also play significant roles in shaping student behavior. There is no one-stop solution for reducing the reasons for cheating and plagiarism in higher education institutions. Therefore, higher education institutions need to adopt a comprehensive strategy to safeguard against student cheating and plagiarism behavior. Parnther (2022) recommends increasing student engagement, providing more opportunities for part-time faculty to share and disseminate ideas, demonstrating student learning, and establishing a clear policy and shared mission to address the issue of academic misconduct, such as cheating and plagiarism, in higher education institutions. The scope of this study covers various forms of academic integrity violations, from classic exam cheating to sophisticated cases of plagiarism made possible by digital technology. It is crucial to recognize that combating academic misconduct such as cheating, and plagiarism requires a variety of approaches. While investigating academic misconduct in higher education, Parnther (2020) conducted a study to identify the characteristics of students who engage in academically dishonest behaviors and suggested best practices and challenges in preventing academic misconduct and promoting academic integrity. Newly added references: Singh, P., Thambusamy, R. X., & Druckman, Z. A. (2016). Insidious, invasive, invisible: academic dishonesty and on-going assessments in higher education. The European Journal of Social & Behavioural Sciences. DOI: 10.15405/ejsbs.193 Curtis, G. J., McNeill, M., Slade, C., Tremayne, K., Harper, R., Rundle, K., & Greenaway, R. (2022). Moving beyond self-reports to estimate the prevalence of commercial contract cheating: An Australian study. Studies in Higher Education, 47(9), 1844-1856. DOI: 10.1080/03075079.2021.1972093 Cuadrado, D., Salgado, J. F., & Moscoso, S. (2019). Prevalence and correlates of academic dishonesty: Towards a sustainable university. Sustainability, 11(21), 6062. https://doi.org/10.3390/su11216062 Sozon, M., Chuan, S. B., Fong, P. W., Alkharabsheh, O. H. M., & Rahman, M. A. (2024). Factors influencing academic dishonesty among undergraduate students in higher education institutions (HEIs) in Malaysia. Journal of Management Info, 11(2), 137-159. DOI: https://doi.org/10.31580/jmi.v11i2.3039 Solmon, M. A. (2018). Promoting academic integrity in the context of 21st century technology. Kinesiology Review, 7(4), 314-320. DOI: https://doi.org/10.1123/kr.2018-0042 Tanveer, M. A., Gill, H., & Ahmed, I. (2012). Why business students cheat? A study from Pakistan. American Journal of Scientific Research, 78, 24-32. Sozon, M., Sia, B.C., Pok, W.F. and Alkharabsheh, O.H.M. (2024), \"Academic integrity violations in higher education: a systematic literature review from 2013–2023\", Journal of Applied Research in Higher Education, Vol. ahead-of-print No. ahead-of-print. https://doi.org/10.1108/JARHE-12-2023-0559 Parnther C. (2020). Academic Misconduct in Higher Education: A Comprehensive Review. johepal. 1(1), 25-45. doi:10.29252/johepal.1.1.25 URL: http://johepal.com/article-1-31-en.html Parnther, C. (2022). The Rise of Contract Cheating in Graduate Education. In: Eaton, S.E., Curtis, G.J., Stoesz, B.M., Clare, J., Rundle, K., Seeland, J. (eds) Contract Cheating in Higher Education. Palgrave Macmillan, Cham. https://doi.org/10.1007/978-3-031-12680-2_17 Reviewer Comment 4: I suggest you consider the absence of findings a finding, and explaining what is will yield stronger future research and implications. Our Reply: The absence of significant findings can provide valuable insights by revealing gaps in the literature. These gaps can then be used to guide future research and improve academic integrity. Reviewer comment 5:Please consider connecting the findings to the research questions. I also recommend potential elaboration. Our reply: We have expanded on the findings pertaining to the research questions and additionally provided potential explanations. Thank you" } ] } ]	1	https://f1000research.com/articles/13-788
https://f1000research.com/articles/13-1097/v1	26 Sep 24	{ "type": "Software Tool Article", "title": "A high-throughput gene expression analysis software tool for developmental time series and gene signature analysis of human cardiomyocyte differentiation", "authors": [ "Isaiah Bartlett", "Jeff Kinne", "Grace Martin", "Kevin Coombes", "Kristopher R. Schwab", "Isaiah Bartlett", "Jeff Kinne", "Grace Martin", "Kevin Coombes" ], "abstract": "Publicly available high-throughput gene expression data enable the investigation of biological processes by the scientific community. Although several bioinformatics tools offer methodologies for basic differential gene expression analysis, difficulties arise in the analysis of multiple sample groups comprising a developmental time series, especially when the identification and classification of unique gene expression patterns is the primary goal of the study. Data analysis using these tools requires programming experience, which limits the accessibility of these tools to the broader community. To streamline developmental time-series investigations, we created the Developmental Gene Expression Analysis (devGEA) tool. This environment can be implemented locally or via web browsers to expedite differential gene expression analysis. This tool provides gene signature determination methods that can classify differentially expressed genes based on their correlation with gene expression patterns. devGEA was used to characterize cardiac development gene expression signatures from high-throughput RNA-seq datasets profiling small-molecule directed cardiomyocyte differentiation of human pluripotent stem cell lines (hiPSCs). After pre-processing, discrete gene expression criteria-based expected changes were used to classify the genes into developmental signatures. Several cardiomyocyte differentiation markers and candidate cardiac genes representing different developmental signatures were experimentally validated using the GIBCOTM hiPSC line. This method was then compared to a gene signature correlation approach that classified expressed genes based on their degree of similarity with key cardiac developmental signatures representing the stages of cardiomyocyte differentiation. Therefore, devGEA provides a robust workflow for investigator-driven analysis of developmental time series, allowing for the identification of differentially expressed genes and gene signatures for extensive experimental investigation. We also introduced a method for classifying genes by their correlation with genes or developmental patterns of interest. Our correlation-based method takes advantage of a priori knowledge of an experiment and is conceptually simpler than unsupervised clustering approaches.", "keywords": [ "transcriptomics", "differential gene expression", "RNA-seq", "heart development", "cardiomyocyte differentiation", "clustering", "shiny application" ], "content": "Introduction\n\nDifferential gene expression analysis of developmental processes during embryogenesis can be enhanced by combining online resources that provide curated data from the scientific literature with independent investigations of previously published data. Several online databases exist, such as the Mouse Genome Informatics (MGI) online database, which aggregates in situ hybridization gene expression data (Genepaint), high-throughput gene expression datasets profiling a diverse set of tissues (Genotype-Tissue Expression (GTEx) Project), and the biocuration of gene expression data from diverse sources integrating anatomy and expression.1–3 However, the expression profiles of many genes remain ambiguous or poorly characterized during the spatiotemporal expression changes that occur during organogenesis. For example, according to the MGI Gene Expression Database (GXD), only 8,660 of the 16,038 genes identified by the resource have annotated gene expression data for the developing heart at any stage or expression level, using conventional molecular techniques.3,4 To fill these gaps in gene expression knowledge, the large quantity of high-throughput gene expression data aggregated within the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) provides an incredible opportunity for investigators to enhance their investigation of differential gene expression during developmental processes and thereby obtain preliminary data to develop new hypotheses for future investigations.\n\nData analyses involving two experimental groups are relatively straightforward to complete using GEO2R, a differential analysis software integrated into GEO.5 However, an in-depth study of the differentiation and development of a tissue or organ involves analysis of multiple experimental conditions comprising a developmental time series. Several bioinformatics tools and the requisite programming experience are required to complete the appropriate differential gene expression analysis and data visualization. We introduced developmental Gene Expression Analysis (devGEA), a new software solution that combines common bioinformatics tools necessary to investigate gene expression changes during cellular differentiation or other developmental processes, with an emphasis on classifying unique gene expression signatures. The workflow provides an investigator with the ability to evaluate and classify gene expression changes in a developmental or time-series dataset, such as differentiation from a pluripotent cell to a terminally differentiated cellular state. DevGEA extends the common steps of raw data processing by introducing several methods for analysis and classification based on a gene model or specific developmental gene expression. These methods are direct, reproducible, and conceptually simpler than many other clustering methods often used in this area. devGEA can be run in the browser from http://cs.indstate.edu/devgea or downloaded as an R source code from https://gitlab.com/jkinne/devgea and executed locally. The Gitlab repository also contains a standalone R Markdown file that performs the analysis in this study.\n\nTo demonstrate the use of this software tool, we used devGEA to perform differential gene expression analysis and developmental gene signature classification of cardiomyocyte differentiation from human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESC) and human induced pluripotent stem cell (hiPSC) lines. The two prior datasets utilized in our investigation profile the cardiomyocyte differentiation of several cell lines, providing an opportunity to classify cardiac developmental signature genes that are reproducible across multiple cell lines. Genes identified within these developmental signatures were validated in the laboratory for comparable expression changes in an independent hiPSC line.\n\nhPSCs have revolutionized biology, allowing in vitro investigation of developmental, physiological, and pathological processes within a human tissue-based experimental system.6,7 The study of heart development and disease has undergone a paradigm shift in the last decade, evolving from the use of experimental organisms as models of mammalian heart development, such as the mouse, to the use of in vitro hPSC differentiation procedures to directly investigate human cardiac development.8–10 Furthermore, these breakthroughs have enabled scientists to study human cardiomyocyte differentiation and the physiology of hiPSCs in both healthy patients and those with congenital heart defects. Directed differentiation of hESCs or hiPSCs using either recombinant growth factors or small-molecule modulators of the WNT signaling pathway enables robust and efficient differentiation of hPSCs into cardiomyocytes, which recapitulates the differentiation of the cardiac lineage in vivo.11–14 Similar to embryonic heart development, hPSCs undergo mesoderm, cardiac progenitor, and cardiomyocyte differentiation, which are characterized by the stepwise expression of specific developmental mesodermal and cardiac regulatory genes.8,9,11 In this study, the devGEA analysis suite was used to classify gene expression profiles during human cardiomyocyte differentiation based on known cardiac developmental regulators. Together, these results aid our understanding of discrete gene expression profiles representing the major gene expression states of cardiomyocyte differentiation, and form a robust method to investigate novel cardiac genes.\n\nin vitro directed cardiomyocyte differentiation using small molecule modulators of the WNT signaling pathway has greatly enhanced our ability to study human cardiomyocyte development.13,15,16 This procedure offers a robust and reproducible experimental assay for studying cardiomyocyte differentiation that recapitulates the in vivo cardiac developmental gene regulatory network. Compared to previous methods, such as embryoid body generation, which produces a heterogeneous mixture of developing tissues, directed cardiomyocyte differentiation enables the generation of cardiomyocytes at an efficiency varying from 80 to 98%.8,15,16 Since directed cardiomyocyte differentiation involves the introduction of defined culture media, developmental gene expression changes can be correlated with the introduction of new media formulations containing specific small molecules and supplements. These datasets consist of at least four developmental time points that correspond to specific culture media that induce a stepwise cardiomyocyte differentiation program. Standard bioinformatic analyses using pairwise statistical tests and fold-change cutoff criteria between groups can be unwieldy and difficult to interpret. Thus, differential gene expression analyses of such datasets have traditionally used statistical tools consisting of the ANOVA statistical test and pair-wise fold-change cutoff criteria, followed by data visualization using clustering tools such as k-means or hierarchical clustering. Given our prior knowledge of key regulatory genes within the cardiac network, a guided analytical approach can instead be employed to classify cardiac genes based on their unique developmental gene expression signatures. Figures 1 and 2 summarize the key timepoints of the cardiomyocyte differentiation experiment: the two prior datasets that we used for analysis and expression patterns of key genes from our study.\n\nA) Methods of small molecule-directed cardiomyocyte differentiation of hiPSCs in prior studies and the present study. Wnt signaling pathway modulators are utilized in a stepwise manner to induce cardiomyocyte differentiation and to maintain contractile cardiomyocytes over the course of several days. Although the addition of specific small-molecule inhibitors and supplements varies slightly, the overall result efficiently generated a large population of autorhythmic contractile cardiomyocytes.\n\nB) Gene expression profiling of three experimental datasets used in this study. The major developmental time points were identified along the cardiac differentiation stage timeline with comparable dates of gene expression profiling in each experiment identified in the table above. Key cardiomyocyte gene expression signatures as well as the expected cardiac developmental markers were identified.\n\nA) Micrographs of morphological changes in hiPSCs during cardiomyocyte differentiation. hiPSC colonies, characteristic of feeder-free human PSCs, were identifiable on day 0. Cell morphological changes are identifiable as differentiating cells proliferate to confluency by days 2 and 4, generating significant cellular debris. By day 8, the confluent multilayer cellular morphology of the well had undergone remodeling into rhythmically contractile cardiomyocyte syncytia.\n\nB) Relative gene expression profiling using RT-qPCR of key cardiomyocyte differentiation markers obtained from the basic gene expression signature analysis for pluripotency and mesodermal, early-cardiomyocyte, mid-cardiomyocyte, and late-cardiomyocyte signatures within the GSE85331 (Liu et al., 2017) dataset. Note that ISL1 is the only mid-cardiomyocyte expression signature, whereas MEF2C, NKX2-5, and TBX5 exhibit late-cardiomyocyte expression.\n\nTo begin the in silico analysis of directed cardiomyocyte differentiation, we identified two publicly available GEO datasets that profile human cardiomyocyte differentiation (Figure 1). Both Refs. 17 and 18 utilize Illumina RNA-seq technology to profile gene expression changes during hPSC-directed cardiomyocyte differentiation. Although these reports utilized slightly different modifications to the original procedure, similar results were obtained with the robust and efficient differentiation of cardiomyocytes.11,13,17,18 Both datasets evaluated the major differentiation steps that were initiated by the addition of GSK3 inhibitors (day 0), the addition of WNT inhibitors (day 2 or 3), the addition of media supplemented with B27 and insulin (day 4 or 5), and then beating cardiomyocyte syncytia at the end of differentiation (day 15 or 30). Furthermore, these high-quality datasets evaluate cardiomyocyte differentiation using multiple hPSC lines, which allows the identification of cardiac developmental genes demonstrating consistent regulation and the exclusion of genes that exhibit variable expression between cell lines. Note that the bioinformatics analysis within these papers used specialized scripts in R and other languages to conduct their experimental analyses. The GEO-provided analysis software GEO2R can be used to define sample groups for analysis, set P value and fold change cutoff thresholds, select pairs of sample groups for differential expression analysis, and allow minimal plot functionality, data export, and the ability to download an R script that can be run locally. devGEA provides enhanced functionality for developmental time-series analysis in contrast to GEO2R, which will be explored in this report.\n\n\nExperimental setup\n\nThe human induced pluripotent stem cell (hiPSC) GibcoTM Episomal line (A18945) was purchased from Thermo Fisher Scientific (Waltham, MA, USA). The hiPSC line was derived from cord blood CD34+ progenitors using seven episomally expressed factors (Oct4, Sox2, Klf4, Myc, Nanog, Lin28, and SV40 T) and adapted to feeder-free, serum-free conditions. This line is indistinguishable from human embryonic stem cells and can be robustly differentiated into cardiac lineages.12\n\nhiPSCs were maintained according to the manufacturer’s recommendations. Cells were cultured on Vitronectin (VTN-N) Recombinant Human Protein, Truncated-coated 6-well tissue culture plates (A14700, Thermo Fisher Scientific) using Gibco StemFlex™ Medium (A1517001, Thermo Fisher Scientific) maintained under normoxic conditions in 5.0% CO2. hiPSCs were maintained and renewed and passaged at least twice per weekusing Versene clump dissociation reagent(15040, Thermo Fisher Scientific) at multiple split ratios. The weekend-free Stemflex media passaging protocol was completed as described below. On day 1 cell passaging occurred as described below. VTN-N-coated 6-well plate were prepared by diluting 60-μL of the VTN stock solution (0.5 mg/mL) in 6 mL 1X Dulbecco’s Phosphate-Buffered Saline (DPBS) without calcium or magnesium (Thermo Fisher Scientific, 14190) to a final concentration of 0.5 μg/mL, adding 1 mL of diluted solution to each well, incubating the plate at room temperature for one hour, aspirating the solution, and then adding 1 mL of StemFlex Medium. Clump dissociation was performed by rinsing each well with 2 mL of DPBS, adding 1 mL of 1X Versene clump dissociation reagent(15040, Thermo Fisher Scientific) for 3-5 mins at room temperature, aspirating the Versene solution, and then removing cell clumps from the surface by gentle pipetting in 2 mL StemFlex Medium and transfer to a sterile 15 mL conical tube. The split ratios varied from 1:4 to 1:10 (0.5 to 0.2 mL) depending on the confluency and density of the hPSC colonies. The appropriate cell suspension volume was transferred to a new 15 mL conical tube, Stemflex media added to a final volume of 1 mL, mixed gently by pipetting, and then transferred into a well containing 1 mL of media. On day 2, wells were renewed with 2 mLs of Stemflex medium. On day 4, cells were Versene clump dissociated, passaged as described above. On day 5, cells were renewed with 4 mL StemFlex Medium. On day 8, cells were then passaged as described above.\n\nAliquots of cells were cryopreserved using the Gibco PSC Cryopreservation Kit (A2644601, Thermo Fisher Scientific) and recovered in stemflex media supplemented with 1X RevitaCellTM supplement (A2644501, Thermo Fisher Scientific) according to the manufacturer’s recommendations. For cryopreservation, an ~80% confluency well containing hiPSCs were Versene clump dissociated as described above except the entire cell suspension was centrifuged at 200 × g for 4 mins using an Eppendorf Centrifuge 5810 (Hamburg, Germany) followed by media aspiration. 2 mL of chilled PSC Cryomedia was then added to the cell pellet dropwise, gently mixed with 1 mL of cryo suspension aliquoted to cryovials (430488, CorningTM, New York, New York). Vials were then transferred to a Mr. Frosty™ freezing container and slowly frozen overnight at -80°C and then cryopreserved in the vapor phase of liquid nitrogen for long-term storage. For cryopreserved hiPSCs recovery, a vial was floated in a 37°C water bath until thawed and then transferred into a 15-mL conical tube. 10 mL of Stemflex media was added dropwise and then centrifuged. The cell pellet was then resuspended in 1 mL of Stemflex media supplemented 1X RevitaCell and transferred to one VTN-N-coated well of a 6-well plate containing 1 mL of Stemflex media supplemented with 1X RevitaCell. The next morning the well was renewed with 2 mL of Stemflex media and cultured as described above. Cell imaging was performed using an Olympus CKX41 Inverted Phase Contrast Microscope with a DP23M digital camera system and CellSens software (Evident, Tokyo, Japan). Micrographs were collected at 100× using the automatic settings.\n\nGibco Episomal hiPSCs were differentiated using the Gibco PSC Cardiomyocyte Differentiation Kit (A29212-01, Thermo Fisher Scientific) according to the manufacturer’s recommendations. Briefly, 70-85% confluent hiPSC cultures were dissociated into single cells usingTrypLETM Select Enzyme reagent (12563029, ThermoFisher Scientific), triturated, and resuspended in Stemflex media supplemented with 1X RevitaCell. Each well of a 6-well plate containing hiPSCs is rinsed with 2 mL of DPBS, 1 mL of TrypLETM Select Enzyme reagent (12563029, ThermoFisher Scientific) solution is added to each plate, incubated at 37°C for approximately 5 minutes until cells have detached from the well, and inactivated by adding 1 mL of Stemflex media. Cell suspensions are combined into a single 50-mL conical tube, pelleted by centrifuged at 100 × g for 5 minutes, and resuspended with 6 mL of Stemflex media supplemented with 1X RevitaCell. A 500 μL aliquot of cell suspension was removed to determine live cell counts and cell viability using the Bio-RAD TC20 automated cell counter and cell counting kit with trypan blue (Hercules, CA, USA). 20 μL of this suspension was combined with 20 μL of trypan blue solution with 10 μL transferred into one well of the counting slide. All cell counts were completed in duplicate. A cell suspension of 6 × 104 cells/mL was prepared in Stemflex media supplemented with 1X RevitaCell. One mL of cell suspension per well (6 × 104 cells/well) was plated onto a 12-well tissue plate coated with GeltrexTM LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix (A14133, Thermo Fisher Scientific) after aspiration of the Geltrex solution. Geltrex-coated plates were prepared according to manufacturer’s recommendation. First, the concentrated Geltrex stock solution (15 mg/mL) was diluted in an equal volume of Dulbecco’s Modified Eagle Medium (DMEM) (11965092, Thermo Fisher Scientific) on ice to prevent gelling. This 180 μL of this solution was then added to a cold 15 mL conical containing 9 mL of DMEM on ice and mixed gently. 750 μL of this solution was added to each well of a 12-well plate and incubated at 37°C for 1 hour prior to aspiration and plating of the cells.\n\nTwelve well plates were renewed with 1 mL of StemFlex medium each day until they density approached 60-80% confluency. Upon reaching the appropriate density (day 0), the wells were renewed with 1 mL of Cardiomyocyte Differentiation Medium A incubated for two days. On day 2, the wells were renewed with 1mL of Cardiomyocyte Differentiation Medium B. On days 6 and 8, the wells were renewed with 1 mL of Cardiomyocyte Maintenance Medium every two days. Small areas of beating cardiomyocytes were observed on day 6. Two days later (day 8), the cultures appeared to have undergone extensive remodeling.\n\nTotal RNA was isolated on the day of cardiomyocyte differentiation (day 0) and subsequently on days 2, 4, and 8. For each cardiomyocyte differentiation time point, three separate wells were harvested so that downstream gene expression analysis could be performed in triplicate. Cells were directly lysed by adding 0.3 mL TRIzol RNA isolation reagent (15596016, Thermo Fisher Scientific) to each well, vigorously rocking the plate for 5 minutes, and then freezing the lysate at -80.0 °C. Total RNA was isolated using the Direct-ZolTM RNA MicroPrep Kit (R2061, Zymo Research, Irvine, CA) according to the manufacturer’s recommendations, which included in-column DNase I treatment to remove genomic DNA. Total RNA was eluted in 10 μL of RNase/DNase-free water. One microliter was used to quantify the total RNA concentration and quality using a ThermoFisher Scientific NanoDrop™ One Microvolume UV-Vis Spectrophotometer. cDNA was prepared using the SuperScriptTM IV VILOTM Master Mix with ezDNaseTM Kit (11756050, Thermo Fisher Scientific) using 0.2 μg of total RNA according to the manufacturer’s recommendations, including ezDNaseTM pre-treatment to remove genomic DNA. cDNA synthesis reactions (20 μL) were diluted 1:10 to a final volume of 200 μL using RNase/DNase-free water to obtain a concentration of 1 ng/μL total RNA.\n\nRT-qPCR was used to quantify the relative transcript expression between cardiomyocyte differentiation time points. Oligonucleotide primers were designed using Primer3 with standard parameters and amplicon product sizes ranging from 75 to 300 nucleotides, ensuring that each primer spanned at least one intron to ensure cDNA-specific application, and were produced by Integrated DNA Technologies using standard synthesis procedures (IDT, Coralville, IA).19 Table 1 lists the design and sequence information of each primer set. qPCR was performed using the PowerUpTM SYBRTM Green Master Mix (100029283, Thermo Fisher Scientific) system in an Applied BiosystemsTM QuantStudioTM 3 Real-Time PCR System (Thermo Fisher Scientific). qPCR reactions (10 μL qPCR reactions containing 2 μL (2 ng) of the reverse-transcribed total RNA, 1 pmol each of the relevant forward and reverse primers, and 5 μL of the 2X master mix PowerUpTM SYBRTM Green Master Mix (100029283, Thermo Fisher Scientific). qPCR reactions were performed in technical triplicates to evaluate the reproducibility of the quantification cycle (Cq) for each amplified condition. QuantStudioTM Design and Analysis Software VERSION 1.4.3 (Thermo Fisher Scientific) was used to run the experimental method, analyze, and determine the Cq values. This software is downloadable from https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/quantstudio-3-5-real-time-pcr-systems.html. The manufacturer’s standard cycling method consisted of a UDG activation step at 50.0 °C for 2 min, DNA polymerase activation step at 95.0 °C for 2 min, PCR amplification stage (40 cycles × 95.0 °C for 15 s, 58.0 °C, 72.0 °C for 1 min), and a dissociation curve stage (60.0–95.0° C at 0.1 °C/s) was used for all qPCR reactions. The qPCR experimental parameters utilized the standard curve experimental type setting, which determined the Cq value using both Auto-Threshold and Auto-Baseline analysis functions. The qPCR results were exported to MicrosoftTM ExcelTM for relative gene expression quantification. Relative gene expression was calculated using the 2-ΔΔCT method as described previously.20 The average standard deviation for all samples for the qPCR triplicate reactions was 0.159 Cq; the range between triplicate reactions for each sample varied from 0.003 to 0.544, demonstrating reproducibility near a standard deviation of 0.5 Cq. At least three No Template Controls (NTC) qPCR for each primer set were included in each experiment, validating the absence of template-independent amplification or template contamination. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a reference gene to normalize targets because it demonstrated a low Cq variance of 20.19 ± 0.73 (Mean ±).20,21\n\nThis table provides gene information, oligonucleotide sequences, and amplicon lengths for each gene-specific RT-qPCR experiment.\n\nFigures 1 and 2 describe the small-molecule-directed cardiomyocyte differentiation used in these experiments11,13 our own study. Here, we highlight the key genes involved in developing our list of key marker genes and their expression patterns. First, the procedure involves seeding, recovering, and growing hiPSCs dissociated into single cells in pluripotency culture media.\n\nThe initial time point (day 0) of these cells in pluripotency culture media prior to subsequent media changes represents proliferative hiPSCs expressing the expected pluripotency markers POU Class 5 Homeobox 1 (POU5F1, also known as OCT4) and Nanog Homeobox (NANOG).22–24 On day 0, hiPSC media was replaced with cardiomyocyte differentiation media containing a GSK3 inhibitor, such as CHIR99021, which activates the canonical WNT signaling pathway and initiates mesodermal specification, as identified by T-Box Transcription Factor T (TBXT, also known as BRACHYURY [T]) and the early cardiac marker GATA Binding Protein 4 (GATA4).25,26 GATA4 is necessary for mesoendodermal development during gastrulation and is then expressed within the mesoderm and later in the cardiac lineage, in which it directs cardiac development and postnatal cardiac function.27–29 The divergence of day 2 induction of TBXT and GATA4 gene expression signatures enabled the classification of transient mesodermal expression from early cardiomyocyte gene signatures because GATA4 is robustly activated during mesodermal differentiation and then persists throughout cardiomyocyte differentiation (Figures 1B and 2B). Therefore, TBXT expression identifies transient mesodermal expression describing the mesodermal gene signature, whereas GATA4 represents the earliest state of cardiomyocyte gene induction, describing the early cardiomyocyte gene signature (Figure 1).\n\nAfter 48-72 hours of incubation (days 2 or 3), the GSK3 inhibitor-containing media was replaced with media containing canonical WNT signaling inhibitors, such as IWP2 or IWP4 (Figure 1B). Canonical WNT inhibition induces the expression of several important progenitor genes that mark the cardiac lineages of early embryos.12,13 The cardiac progenitor markers ISL LIM Homeobox 1 (ISL1), Myocyte Enhancer Factor 2C (MEF2C), NK2 Homeobox 5 (NKX2-5), and T-Box Transcription Factor 5 (TBX5) exhibit unique expression profiles during later cardiomyocyte differentiation stages (Figure 1 and 2).30–33 Although these four genes are robustly expressed at high levels at the end of differentiation (days 8, 15, or 30, see Figure 1), the initial detection of transcripts occurs earlier in differentiation at lower levels.12,13 For example, while ISL1 transcripts in the GSE85331 (Liu et al., 2017) experiment demonstrated the greatest change in expression from day 2 to day 4, NKX2-5, MEF2C, and TBX5 genes were not maximally expressed until day 30 (Figure 6). A similar result was identified via RT-qPCR analysis of Gibco hiPSC cardiomyocyte differentiation (Figure 2B). Therefore, these progenitor markers represent two different gene expression signatures: a mid-cardiomyocyte gene expression signature with a maximum change in expression at day 4 (ISL1) or a late-cardiomyocyte gene expression signature on day 8 (MEF2C, NKX2-5, and TBX5) (Figures 1 and 2).\n\nMedian gene expression patterns of the five cardiomyocyte gene expression signatures were determined by LOESS, median, and basic analysis for GSE122380 (Strober et al., 2019) and GSE85331 (Liu et al., 2017). Each graph plots the median expression values and the 95% confidence interval error bars for pluripotency, mesodermal, early-cardiomyocyte, mid-cardiomyocyte, and late-cardiomyocyte-grouped genes.\n\nRT-qPCR analysis of candidate gene expression signatures during directed cardiomyocyte differentiation in Gibco hiPSCs. The plots are from the present study, with samples taken on Days 0, 2, 4, and 8. The grouping of genes/plots was based on the basic/descriptive gene analysis of the GSE85331 dataset (i.e., CABLES1 is listed under mesodermal because it was identified using the basic/descriptive analysis of GSE85331). RT-qPCR profiling approximates the expected gene expression signature for each stage of differentiation in this single analysis. However, discrepancies in these signature calls exist when these results are compared to those of some of the classification methods discussed in the article.\n\nComparison of correlation curve fitting models for GSE122380 and GSE85331 to RT-qPCR analysis of ACTN2 (a late-cardiomyocyte signature call) and ZEB2 (an early cardiomyocyte signature call). These two genes have been used as examples in the text to describe our classification methods. To evaluate the LOESS (left panel) and median curve-fitting correlation methods (middle panel), the log2 expression values for each time point were plotted for both datasets, and the line overlay identified the respective curve-fitting model. The additional time points located within GSE122380 (16 time points) enhanced the gene expression curve compared with GSE85331 (four time points). Although both methods generated similar curves for each gene, the LOESS function provided additional smoothing to the plot. The right panel shows log2 relative gene expression changes during cardiomyocyte differentiation of GIBCO hiPSCs using RT-qPCR. Note the gene expression signature similarities among the three analytical methods.\n\nGraphs of day 0, 2, 4, and 30 log2 expression values for ISL1, MEF2C, NKX2-5, and TBX5. Each line represents an individual cell line and replicates. Note that ISL1 and TBX5 demonstrated marked expression at day 4, whereas MEF2C and NXK2-5 exhibited baseline expression until day 30. Therefore, ISL1 and TBX5 were the best candidates for representing the mid-cardiomyocyte gene expression signature.\n\nAfter 48 h of cardiomyocyte progenitor induction (day 4-5), a cardiomyocyte-maintenance medium containing B-27 supplement and insulin was added, which supports cardiomyocyte differentiation and viability. Subsequently, key contractile cardiomyocyte markers, such as MYH6, MYH7, and TNNT2, are highly expressed.24,34 After the onset of contraction on approximately day 6-7 (Figures 1 and 2), the differentiated cardiomyocytes underwent remodeling into syncytia, with rhythmic contraction apparent at the gross level (Figure 2A). The expression patterns of the genes described above were utilized as key cardiac gene expression signatures for the classification of differentially expressed genes during cardiomyocyte differentiation in the preceding experiments (Figures 1 and 2).\n\n\nMethods\n\nHere, we describe the main features and workflow of devGEA. We look at these features in more detail in the Results and Discussion section where we use the software to analyze the prior datasets (Refs. 17 and 18).\n\ndevGEA is a shiny web application written completely in the R programming language. We also provide a self-contained R markdown file with the analysis that is contained in the Results and Discussion section.\n\nData import, normalization, and plots. The devGEA shiny web application can import data as raw counts or already normalized. Data files can be imported by uploading a file or specifying a GEO ID. The web application allows for normalization using limma. Data can be scaled by taking the logarithm of the data or scaling it to have a mean of 0 and standard deviation of 1. Data can be filtered based on a raw count threshold and whether the gene information is missing. The data and results can be viewed in an interactive table format so that the user can verify the data import, analytical methods, and results. The table can be searched using gene symbols or identifiers, or by setting ranges for columns. Gene selection by mouse clicks provides a basic gene expression plot.\n\nAdditional metadata for the samples (e.g., time point, cell line) can be specified by importing a csv/tsv file, using a regular expression based on the column headings, or manually entered within the app. Once the sample metadata have been imported, the sample groupings used for analysis are specified (e.g., groups based on time point or cell line). Additional metadata for genes (e.g., gene symbols or names) can be imported automatically from Ensembl BioMart35 through the app.\n\nAdditional data normalization plots were provided to evaluate the quality of the dataset. Gene expression box plots or histograms for each sample were used to identify outliers. The PCA of the samples or groups provides a linear representation of variation within the data set. Samples identified as outliers or with poor gene expression preparation can then be marked for exclusion, and the data can be reanalyzed.\n\nAnalysis. Once a dataset is loaded, the user can choose to add an analysis. For a basic analysis, the software computes for each gene – medians of each time point, maximum and minimum time points based on expression, and other simple descriptive statistics of the data. These results are displayed within a table and can be exported; results can be filtered based on fold change, maximum/minimum time point, or time point of maximum change. For a correlation analysis, the user specifies either a set of marker genes or a set of gene expression patterns. For each gene in the dataset, the software computes the correlation of the gene with each marker gene (or given gene expression pattern) and then classifies each gene based on the highest correlation. The results of this analysis are the correlations and classifications for each of the genes. We discuss this analysis technique further in the Results and Discussion section. For an ANOVA analysis, the user specifies a sample property (e.g., time point or sample group) to define a linear model, and the software computes adjusted p values for each gene based on this property. The results of the analysis are the adjusted p values for each gene. For a subset analysis, the software combines results from previous analyses within the app (i.e., by taking intersections or unions of result sets). By default, the software takes the intersection of each successive analysis (i.e., first filtering based on fold change with basic analysis, and then filtering based on adjusted p values with ANOVA analysis, and so forth).\n\nSaving and exporting results. The entire project can be saved as an R data file and then later loaded into the software again. Result sets can be exported in csv format. Plots can be exported as svg files.\n\nWe note that the main novelty in devGEA is the correlation analysis, which is a novel form of analysis in this setting (as far as we are aware). We have built the standard steps of differential gene expression analysis around the correlation analysis so that users with little or no programming experience can use this form of analysis themselves.\n\ndevGEA is written completely within the R programming. The code has been tested on macOS 13.4, Windows 10, and Ubuntu Linux.\n\nThe shiny web application can be downloaded and run locally or can be run from our server. To run locally, the user runs the file app. R that is within the shiny_app directory of our gitlab repository (https://gitlab.com/jkinne/devgea).\n\nWhen the shiny web application is run from our server (https://cs.indstate.edu/devgea), the user does not require to install any software on their own system. We note that we use ShinyProxy36 as the backend on our server; we provide example configuration files within the shinyproxy directory of our gitlab repository.\n\nTo run the R markdown file that contains the analysis in this paper, the user should knit the file devGEA. Rmd that is in the gitlab repository.\n\n\nResults and discussion\n\nHere, we describe our analysis of the prior datasets (Refs. 17 and 18). We focus our discussion on the analysis provided within the Rmd. After describing our analysis, we discuss validation with our study results.\n\nMany researchers argue for using transcripts per kilobase million (TPM) as the preferred normalization for RNA seq count data (see Ref. 37 which introduced the term, and more recently38 which evaluated different normalization methods). The National Center for Biotechnology Information (NCBI) has recently begun to provide both raw counts and normalized files for all GEO datasets. We used the TPM-normalized data available from NCBI as the input for our analysis. The NCBI database also provides supporting gene annotations.\n\nWe filtered the data so that we only considered protein-coding genes, and we also only considered genes that were non-zero in at least two samples and had a total TPM sum of at least 10.\n\nWe extracted metadata about the samples using series matrix files that can be downloaded from the NCBI GEO. The design matrix contains the following for each sample: cell line, time point (day #), replicate #, sample ID, whether to exclude the sample from analysis, and sample name for use on plots.\n\nAs is standard for biological data, we take the logarithm (base 2) and use these values for further analysis.\n\nEvaluating cell lines - Ref. 18 used a Gaussian process model to identify clusters of cell lines that share gene clusters. One of the cell line clusters was noted to have less robust expression of cardiac troponin. Thus, we removed these cell lines from the analysis. Many approaches can be used to cluster cell lines and identify outliers. We considered an approach similar to Ref. 39, but decided to stick with the clustering of cell lines identified in Ref. 18.\n\nCombined analysis - We considered whether the two datasets could be combined and analyzed together.40 lists a number of potential problems when attempting to combine datasets from separate experiments or laboratories. In this case, it was determined that the datasets should not be combined. As can be seen from the principal components analysis (PCA) plot in Figure 7, the samples from the datasets are well separated on the PCA plot. Notably, Refs. 18 and 17 used different laboratory methods to filter out ribosomal RNA -17 used rRNA depletion, while18 used poly(A)+ selection. This is one of the potential inconsistencies that Ref. 40 warns.\n\nA principal component analysis plot combining the datasets GSE122380 and GSE85331. We considered whether the two datasets could be combined in a single analysis. On the left, each sample is colored by day. Note that the samples are clustered by day, going from top to bottom and left to right. On the right, each sample is colored according to the experiment, and we see that GSE122380 and GSE85331 are clearly separated on the PCA plot.\n\nWe identify and cluster significant genes using a variety of methods.\n\n• Linear model ANOVA was performed using a linear model over the key time points to obtain adjusted p-values.\n\n• Basic/descriptive statistical analysis - using simple conditions related to the highest time points of expression and the largest change in expression.\n\n• Correlation analysis using the correlation of each gene with key marker genes or expression patterns of interest.\n\nWe suggest that our basic analysis and correlation analysis as types of analysis should be considered when known patterns of interest or marker genes are known. Our precise method of using correlation to cluster is novel (to our knowledge at the time of writing), although it is well known that using correlation is preferred for computing distances with biological data (see e.g., Ref. 41). These methods are discussed in detail in the following sections.\n\nSome parts of our analysis looked at gene expression at only the key time points as described earlier: days 0, 2, 4, and 30 in Ref. 17 and days 0, 3, 5, and 15 in Ref. 18. Other parts of the analysis are time-series methods that use all the available time points.\n\nFor each gene, we used a linear model over the four key time points. The resulting adjusted p-values were used to indicate if a gene had a statistically significant difference between at least two of the key time points. This is the standard step in the analysis process.\n\nDifferential gene expression analysis described above with standard cutoff for adjusted p value of 0.05 and log2 fold change of at least 1 identified 8634 genes within the GSE85331 dataset and 7117 genes within the GSE122380 dataset that had a significant difference among the four key time points, with a total of 5241 genes common between both lists. We will further filter by requiring that each gene has a correlation of at least 0.75, one of our key marker genes (POU5F1 (pluripotency), TBXT (mesodermal), GATA4 (early-cardiomyocyte), TBX5 (mid-cardiomyocyte), and TNNT2 (late-cardiomyocyte)), using the correlation analysis that is described later. This provided a list of 3259 genes for further investigation.\n\nTable 2 and Figure 5 present the main analysis results for two example genes: ZEB2 and ACTN2. As indicated in the table, the adjusted p-values for both genes were 0 for both datasets. Both genes also passed the log2 fold change criteria for both datasets, and had a correlation of at least 0.75 for their closest matches, for the correlation analysis. Therefore, both genes were in the 3259 gene set.\n\nA summary of the analysis of the two genes is provided.\n\nThe expected classification for ZEB2 is early, and each analysis method (in bold) classifies ZEB2 as early. The expected classification for ACTN2 is late, but some classification methods classify ACTN2 as mid-cardiac.\n\nThe class (descriptive) is based on the time points of the maximum expression and the time point at which there is a maximum change. For gse122380, the major time points used for descriptive analysis were days 0, 3, 5, and 15; for gse85331, the major time points were days 0, 2, 4, and 30. ZEB2 is classified as early because it has the maximum change going into the second major time point and its maximum expression in one of the last two time points. ACTN2 is classified as late because it has the maximum change at the last major time point and has the maximum expression at the last major time point.\n\nThe loess class was based on the correlation of the loess fit of the gene with the loess fits of the marker genes for each class (pluri - POU5F1, meso-TBXT, early - GATA4, mid - TBX5, late - TNNT2). The median class is based on the correlation of the day median of the gene with the day median of the marker genes. ZEB2 was classified as early in each of these methods with both datasets because its correlation was closer to GATA4 than to the other marker genes. For example, for gse122380 and the loess fit, the loess fit of ZEB2 was 0.96 with GATA4, and the second highest correlation was with the mid-cardiac marker gene TBX5 (0.75). ACTN2 is classified as late according to the loess and day median fit for gse122380, but it is classified as mid-cardiac for both fits for gse85331. For example, for gse85331 and the median fit, ACTN2 had a correlation of 0.99 with the mid-cardiac gene GATA4, while it had a correlation of 0.95 with the late marker gene TNNT2. Note that ACTN2 has a high correlation with both, and this is also the case for many genes that are classified as either mid- or late-cardiac.\n\nSmall-molecule cardiomyocyte differentiation is an easy and effective procedure involving three media changes that allows transcriptomic profiling throughout differentiation. Coinciding with each medium change, subsequent gene expression changes should proceed in a straightforward manner, representing the four major stages of cardiomyocyte differentiation. Therefore, the following rules can classify the major gene expression signatures according to the day of maximum expression (DayMax) and the day of maximum difference in the time series (DayMax-difference) (Figures 1 and 2).\n\n• Pluripotency – DayMax occurring on day 0 similar to POU5F1 and NANOG expression.\n\n• Mesodermal – DayMax at day 2/3 and maximum difference centered on day 2/3 (either positive DayMax-difference occurring on day 2/3, or negative DayMax-difference occurring on day 4/5), similar to TBXT and MIXL1 expression.\n\n• Early-cardiomyocyte – DayMax occurred later in differentiation on days 4/5 or 8/15/30 since expression persisted throughout cardiomyocyte differentiation and a positive DayMax-difference on day 2/3, similar to GATA4 expression.\n\n• Mid-cardiomyocyte – DayMax occurred on days 4/5 or 8/15/30 and a positive DayMax-difference was observed on day 4/5, similar to ISL1 expression.\n\n• Late-cardiomyocyte – DayMax occurring on days 8/15/30 and positive DayMax-difference on day 8/15/30 gene, similar to TNNT2 expression.\n\nConsider the example genes, ZEB2 and ACTN2. The middle plots in Figure 5 show the median values at each time point. For GSE85331, ZEB2 had its maximum value on day 4 and the maximum difference in expression on day 2. ZEB2 was thus classified as an early cardiomyocyte in GSE85331. For GSE122380, we analyzed a subset of time points: days 0, 3, 5, and 15. Among these time points, the maximum expression of ZEB2 was at day 15, and the maximum difference in expression increased from day 0 to day 3. ZEB2 was thus classified as an early cardiomyocyte for GSE122380. For ACTN2 in GSE85331, the maximum expression was observed at day 30, with the maximum difference in expression occurring at day 30. In GSE122380, considering only days 0, 3, 5, and 15, the maximum expression of ACTN2 was on day 15, with the maximum difference going up from day 5 to day 30. ACTN2 was classified as a late cardio for both datasets. Table 2 contains a summary of the analysis for ZEB2 and ACTN2, with the “class (descriptive)” given for each matching our discussion here (early for ZEB2 and late for ACTN2).\n\nClassification using simple descriptive statistical rules is understandable. If a gene of interest is misclassified via user-defined rules, it is easy to determine the cause. In contrast, sophisticated unsupervised clustering methods may generate unexpected gene cluster patterns that require additional filtering or parameter modifications to generate results usable by the investigator. We propose that the simple basic analysis described here may aid investigators in data-exploration tasks.\n\nThe basic descriptive analysis of GSE85331 and GSE122380 datasets identified 1711 genes within the 3259 gene list that possessed identical signature calls for this basic/descriptive analysis for the POU5F1 (pluripotency), TBXT (mesodermal), GATA4 (early-cardiomyocyte), TBX5 (mid-cardiomyocyte), and TNNT2 (late-cardiomyocyte) classifications in this basic analysis. As indicated in Table 2, the example genes ZEB2 and ACTN2 are given the same “class (descriptive)” for both datasets (early for ZEB2 and late for ACTN2); therefore, both are on the 1711 gene list. The median expression patterns of each gene signature classification for descriptive analysis of both datasets are shown in Figure 3. These cardiac gene signatures approximate previous investigations of cardiomyocyte differentiation, demonstrating a robust method for precisely classifying gene expression patterns in a developmental system.12,13,15\n\ndevGEA shiny web application: The shiny web application computes the basic statistical properties of a dataset and allows the user to define clustering groups and rules for the clustering groups. The shiny web application can thus be used to easily perform the basic/descriptive analysis discussed here, as well as filtering based on p values and fold changes without requiring any programming or software installed locally.\n\nAn independent experimental analysis of cardiomyocyte differentiation using a commercially available hiPSC cell line was performed to evaluate the success of gene expression signature calls and to validate the candidate cardiac genes identified in this analysis. The episomal GIBCO hiPSC line was obtained, expanded, and differentiated into cardiomyocytes using commercially available reagents. As expected, hiPSC differentiation proceeded as expected: on day 0, independent hiPSC colonies were visible; from days 2 to 4, differentiating cells had proliferated to confluency with detaching and dead cells visible in the culture dish; on day 6, small contracting areas within the cellular lawn were identifiable and proceeded to undergo remodeling to large rhythmically contracting web-like syncytia (Figure 2A). At equivalent time points to the GSE85331 experiment, total RNA was extracted, and RT-qPCR was used to validate relative gene expression across the experiment. The relative expression of each gene was determined by the 2-ΔΔCT method using Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) expression for normalization. The set of 32 genes tested in this way are listed in Figures 2 and 3 (RT-qPCR results) and Table 3 (summary of our analysis of these genes in the prior datasets). We now describe the set of 32 genes, their RT-qPCR results, and the analysis of the prior datasets.\n\nSummary of the analysis of the 32 genes for which we performed qPCR measurements. The results are given for each of the two datasets under which we analyzed the genes. First, the expected classification of the gene, gene id, and gene symbol are given. Then, for each dataset (gse122380, gse85311), the following are given: adjusted p values, log2 fold change between the highest and lowest major time point, classification by basic/descriptive analysis, classification by loess fit, correlation of loess fit to classified marker gene (pluri - POU5F1, meso-TBXT, early - GATA4, mid - TBX5, late - TNNT2), classification by day median correlation, and correlation of day median correlation classification.\n\nPOU5F1 and NANOG expression was identified to verify pluripotency and the subsequent downregulation of pluripotency factors during differentiation (Figures 1 and 2B). Ten key cardiomyocyte differentiation markers were selected for evaluation and compared with the 1711 gene descriptive analysis results (Figure 2B). All ten differentiation markers were identified in the 3259 descriptive analysis list, while all but three (ISL1, MEF2C, TBX5) were present in the 1711 gene list. While pluripotency and mesodermal and early cardiomyocyte expression patterns were comparable between the RT-qPCR and descriptive analysis results, several discrepancies were identified within the mid-cardiomyocyte and late-cardiomyocyte expression pattern groups. For example, ISL1 demonstrated robust activation at day 4 (a mid-cardiomyocyte signature) in the RT-qPCR data but was absent from the 1711 gene list, indicating variable expression between the two prior datasets. Interestingly, MEF2C and NKX2-5 levels determined via RT-qPCR were extremely low or undetectable until day 8, which is consistent with a late cardiomyocyte signature rather than a mid-cardiac signature (Figure 2B). Within the 3259 gene list, NKX2-5 was classified as a late-cardiomyocyte signature in both datasets, while the MEF2C classification was mismatched between mid- and late-cardiomyocyte signatures in the prior data sets. The mid-cardiac genes ISL1, MEF2C, and NKX2-5 are important cardiac regulatory genes necessary for cardiac lineage development, cardiomyocyte differentiation, and proliferation. This inconsistency may result from the delayed induction of key cardiac genetic regulatory genes during cardiomyocyte differentiation. Additionally, biological variation or experimental differences between hiPSC lines and/or experimental methods may be responsible for these discrepancies. Therefore, these expected mid-cardiomyocyte genes possess similar expression profiles to late-cardiomyocyte genes, such as sarcomeric TNNT2 which is highly expressed prior to contraction. Interestingly, NKX2-5 expression marks the cardiac mesoderm, which later gives rise to a linear heart tube in early mouse embryonic heart development.11,30,33,42 The later-than-expected expression of these genes may represent a lagging entrance of differentiating cells into the cardiac progenitor phase or alterations to the overall cardiogenic program.\n\nNext, twenty genes with previously unvalidated gene expression patterns in hiPSC cardiomyocyte differentiation representing various cardiomyocyte differentiation signatures as called by the GSE85331 basic/descriptive analysis were selected (six mesodermal genes, four early-cardiomyocyte genes, two mid-cardiomyocyte genes, and eight late-cardiac genes) and investigated for reproducibility using RT-qPCR (Figure 3). RT-qPCR was performed on each gene to establish the gene expression signature pattern in the GIBCO hiPSC line. The RT-qPCR expression patterns for the 20 genes were classified according to the descriptive signature call in the GSE85331 dataset (Figure 3). RT-qPCR expression patterns approximately matched the descriptive signature classifications within the RNA-seq data sequence.\n\nTo increase the rigor of this analysis, the 32 RT-qPCR genes investigated were filtered, requiring descriptive signature calls to match the GSE85331 and GSE122380 analyses. 29 of the 32 genes possessed the same descriptive signature classification between the two data sets. Interestingly, CABLES, ISL1, MEF2C, and TBX5 did not meet these criteria, indicating variability between the datasets. The expected mid-cardiomyocyte genes, ISL1 and TBX5, were not successfully replicated in these datasets, indicating potential difficulty in distinguishing mid- and late-cardiomyocyte genes because of their similarity in gene expression, perhaps due to differences in the activation of the cardiomyocyte differentiation program. Although discrepancies exist between the datasets, this stringent approach demonstrates the advantages of utilizing the descriptive analysis method to identify gene expression patterns.\n\nWhereas gene signature classification utilizing hierarchical clustering, k-means clustering, and self-organizing maps relies on classification techniques that randomly sample the dataset, we utilized a method that classifies genes based on correlation with user-specified gene or expression profiles that model the gene signature patterns of interest. This method enables the user to utilize a priori knowledge of gene expression or to explore gene expression patterns of interest based on their analyses. It also provides reproducibility between analyses and flexibility in selecting genes based on the extent of correlation with a gene model. In correlation analysis of cardiac signatures during differentiation, specific gene models can be selected within the dataset based on prior knowledge.\n\nKey marker genes - The following results were obtained from using the following cardiac marker gene signatures represented by a specific cardiomyocyte differentiation gene: POU5F1 (pluripotency), TBXT (mesodermal), GATA4 (early-cardiomyocyte), TBX5 (mid-cardiomyocyte), and TNNT2 (late-cardiomyocyte). Although ISL1 is a potential mid-cardiomyocyte signature due to its expression during early cardiac progenitor development, ISL1 was not considered a gene signature because the signature calls using our basic/descriptive statistical analysis did not match between the GSE85331 and GSE122380data sets (and thus ISL1 is not on the 1711 gene list). Instead, we arbitrarily selected TBX5 as the mid-cardiomyocyte gene expression signature for the following correlation analyses because it demonstrated moderate upregulation on day 4 or 5 within the RNA-seq and RT-qPCR data sets compared to later upregulation of the late-cardiomyocyte marker TNNT2 after this time point (Figure 5). Within the RT-qPCR data, TBX5 relative expression is moderately increased from day 2 (0.45) to day 4 (7.68); however, this expression was upregulated nearly 50 times on day 8 (49.12), whereas TNNT2 demonstrated several magnitudes of upregulation from day 4 (0.88) to day 8 (1899.00).\n\nLOESS and medians correlation: Two different methods were used to determine correlations between each gene and the cardiac marker genes within the 3259 priority cardiomyocyte gene list (see above). The LOESS smoothing technique uses a model to fit each gene to the cardiomyocyte differentiation marker gene and then computes the correlation between the fit of each gene and the fit of each cardiac marker gene. The second method computes a median value for each time point for each gene, and then correlates the results with the medians of each cardiac marker gene. After computing the correlations (using either LOESS fit or medians), each gene was classified according to the cardiac marker gene with the highest correlations. Each gene was correlated to a specific gene model, with the highest correlation selected for a cardiac expression signature.\n\ndevGEA shiny web application: We note that the shiny web application includes gene clustering based on median correlation but does not yet (at the time of writing) contain LOESS correlation clustering.\n\nExample genes: Consider example genes ZEB2 and ACTN2. The LOESS fits are given in the plots on the left side of Figure 5, and the median values are given in the middle plots. Table 2 shows the correlation between these values and those of each of the key marker genes. For example, ZEB2’s LOESS model fit for GSE122380 was 0.966721808 with the model fit of the early marker gene (GATA4), with the second-highest correlation being 0.745102698 with the model fit of the mid-cardiac marker gene (TBX5). ACTN2 was assigned a different classification using the LOESS fit for the two datasets (late-cardiomyocytes for GSE122380 and mid-cardiomyocytes for GSE85331). For GSE85331 and LOESS fit, the LOESS fit for ACTN2 had a correlation of 0.987544522 with the mid-cardiomyocyte marker gene (TBX5), with the second highest correlation of 0.95867473 with the late-cardiomyocyte marker gene (TNNT2). Note that both mid- and late-cardiomyocyte signatures are reasonably good fits for ACTN2 in the correlation analysis, while the drop-off in correlation with the other marker genes is much larger.\n\nFiltering: A minimum correlation value of 0.75 was selected as an arbitrary cut-off to further filter the differentially expressed genes (the LOESS fit and median values should have a correlation of at least 0.75, assigned to least one of the key marker genes). The mean correlation factor for this gene list was 0.931 with a standard deviation of 0.057, demonstrating the combined effectiveness of this filtering and classification strategy. The mean expression patterns of all genes in a particular signature classification reflected the corresponding model in both the datasets (Figure 4).\n\nComparisons: The comparison of the LOESS and median correlation methods within each dataset was surprisingly robust. 93% of the 3259 genes within the GSE85331 dataset were classified into the same signature classification (same classification using LOESS correlation and using median correlation), while 91% of the genes in the GSE122380 dataset were similarly classified using LOESS and median correlation. The comparison between GSE85331 and GSE122380 datasets was less robust. Using the LOESS method, 58% of the 3259 genes were successfully classified into the same signature using the LOESS method between the GSE85331 and GSE122380, while 59% of the genes were successfully classified using the median correlation method in the two data sets. Consider two example genes: ZEB2 and ACTN2. As indicated in Table 2, ZEB2 has the same correlation classification using both methods and both datasets, so ZEB2 is among the genes counted for all these percentages. ACTN2 has the same classification using LOESS and medians fit for GSE122380 (so is among the 91%) and has the same LOESS and median classifications for GSE85331 (so is among the 93%). ACTN2 has different classifications for both datasets for median correlation (not among the 59% mentioned) and has different classifications between the two datasets for LOESS correlation (not among the 58% mentioned).\n\nThe median gene expression signatures of each method and RNA-seq dataset are shown in Figure 4. Discrepancies may reflect a combination of biological and technical variations and analysis limitations due to differing numbers of time points between the RNA-seq experiments of the differentiation procedures. Further contrast of these analyses requiring both datasets to give the same classification for both methods (GSE122380 provides the same classification for both LOESS and medians, and GSE85331 provides the same classification for both LOESS and medians) identifies a total of 1704 of the 3259 gene lists reproducibly assigned to the same signature.\n\nNext, we compared our RT-qPCR results with the LOESS and median correlation results of the inter-RNA-seq dataset comparisons. A summary of the analysis of these 32 genes is provided in Table 3. Of the 32 genes investigated, 27 RT-qPCR genes were identified in 3259 genes. Interestingly, 13 passed all filters and were classified the same using all six of our classification methods (basic/descriptive on both datasets, loess correlation on both datasets, and medians correlation on both datasets). Of these, TNNT2 was the only gene with an expected classification as mid or late. Most of the other mid/late genes were not classified consistently or, as expected, in GSE85331. This points to the difficulty in distinguishing the later time points in the experiment, although we expect that we can obtain a higher degree of matching by either selecting different key marker genes or using constructed gene patterns rather than the model fits of the marker genes. We report the results based on our initial plans to avoid simply selecting the parameters that yield the best results. Even so, most of the 32 genes in the mid/late phase that do not have 6-way agreement have high correlation values for both mid and late marker genes, meaning that we should consider not only the marker gene with the highest correlation, but also the second highest correlation and group.\n\nFinally, we considered which of the 3259 genes were classified as the same using all six methods. Of the 3259 genes, 840 were classified as the same using all six methods.\n\nOverall, this investigation demonstrates the unique analytical methods that devGEA provides to classify gene expression signatures in order to organize and study high-throughput developmental time-series gene expression studies. In addition, these studies suggest that caution must be taken when interpreting these analyses because of the inherent variability between experiments. Multiple methodological approaches may be necessary to evaluate the biological processes that are investigated to obtain the best representation of gene expression data. Because of the inherent gene expression similarity between the later cardiomyocyte differentiation time points, further investigation is warranted to determine whether the different key marker genes or the constructed gene expression patterns would better differentiate these time points in all datasets.\n\n\nConclusion\n\nDifferential gene expression analysis of high-throughput RNA-seq gene expression data represents a challenge, as datasets grow to several time points or conditions containing many biological replicates. We have developed a devGEA bioinformatics software suite that combines basic statistical analysis techniques, data visualization, and novel gene expression signature classification methods to improve the analysis of developmental time series. Additionally, we demonstrated the effective use of our methods in classifying developmental signatures that represent key stages of cardiomyocyte differentiation by filtering genes based on statistical descriptions and correlation to specific gene signatures. The robustness of the software and analysis was validated via RT-qPCR analysis of gene expression using the commercially available Gibco hiPSC cardiomyocyte differentiation procedure.\n\nThe devGEA analysis of directed hiPSC-cardiomyocyte differentiation provides an effective methodology for identifying and exploring gene expression signatures that characterize cardiac development, which is applicable to other domains of research. Three different classification methods used either basic statistics or correlations to identify similarly expressed genes. Additional experiments can be used to enhance or validate data analysis.\n\nThe GSE85331 and GSE122380 datasets offer a means to robustly identify gene expression signatures across cardiomyocyte differentiation and to explore the effectiveness of each method. To validate these findings, 32 genes comprising differentiation markers and understudied genes of the 3259 priority gene list were evaluated using RT-qPCR profiling of the cardiomyocyte differentiation of the GIBCO hiPSC line when using stringent criteria requiring the same gene signatures to be called in all three datasets across both experiments. Thirteen of the 32 genes were validated in this manner, indicating the reliability of signature identification between these diverse methods. Of the remaining genes on the 32 gene list, most were mid or late-cardiac genes, where at least one of the six classifications placed the gene in an adjacent cluster (i.e., classifying mid genes as late or late genes as mid). The discrepancies between these experiments may be due to the biological nature of cardiomyocyte differentiation or the technical challenges of discriminating unique developmental expression signatures characterizing a differentiating subpopulation from a heterogeneous population of cells. Nevertheless, our RT-qPCR investigation of important developmental cardiac markers from the correlation analysis demonstrated the robust classification of differentially expressed genes into specific cardiac developmental signatures.\n\nFurthermore, these experiments identified unique gene expression patterns occurring during human cardiomyocyte differentiation, with several of these genes associated with mammalian heart development or congenital cardiovascular defects.\n\nThe earliest cell state transition involves specification of the mesodermal lineage from the pluripotency state. The mesodermal signature genes were transiently upregulated on day 2 and then repressed during the remainder of cardiomyocyte differentiation. The cadual-type homeobox genes CDX1 and CDX2, are early embryonic genes that control the anterior-posterior patterning of the developing embryo.43,44 Recent studies in mice have identified important roles for CDX genes in early embryonic fate decisions that drive differentiating cells to the cardiac lineage and in epicardial development.45,46 Additional genes associated with the mesodermal signature include msh homeobox MSX1 and doublesex and mab-3 related DMRT1 transcription factors. MSX1 and MSX2 double homozygous null mutant mice developed abnormalities in the atrioventricular valves and myocardium.47 Two additional genes include the CDK/ABL kinase interaction protein CABLES1 and the interleukin 17 receptor IL17RD which are yet to be investigated in heart development.\n\nThe early cardiomyocyte signature is characterized by transcriptional upregulation at day 2, with persistent or increasing gene expression persisting throughout the entire cardiomyocyte differentiation process. Examples of genes classified as early cardiomyocyte signatures include the Wnt cargo receptor WLS, YY1-associated factor YAF2, and transcriptional regulators ZEB2 and ZNF503. WLS encodes a conserved protein necessary for WNT secretion, which is required for early embryonic axis and heart field formation.48–50 While developmental functions for YAF2, ZEB2, and ZNF503 have been identified in mice, embryonic cardiac developmental roles for these genes are yet to be reported.51–53\n\nMid-cardiomyocyte genes represent the induction of gene expression on day four of cardiomyocyte differentiation. The protein kinase PKDCC gene and frizzled-class WNT receptor FZD4 are examples of candidate genes that have yet to be investigated for cardiac developmental functions. PKDCC is an essential mesenchymal regulator of lung development.54,55 FZD4 is expressed within the embryonic vasculature, and mutations are responsible for the incomplete vascularization of the retina occurring in human exudative vitreoretinopathy I disorder.56,57 Furthermore, FZD4 was recently found to be a marker of the lateral plate mesoderm and to contribute to cardiomyocytes and other cardiac cell lineages.58,59\n\nLate-cardiomyocyte signature candidates are associated with later stages of differentiation involving myofibril organization and contractility. The actinin ACTN2, cardiomyopathy-associated protein CMYA5, sarcomeric protein CSRP3, nuclear lamin-interacting protein MLIP, sarcomeric protein MYOM1, and actin-binding protein NEXN were markedly enriched at the endpoint of the developmental series. Interestingly, each of these genes is associated with a human cardiomyopathy disorder, produces cardiomyopathy in a mouse model, or localizes to the cardiac myofibrils.60–64 Additionally, protein kinase HIPK3 and protein phosphatase regulatory subunit PPP1R12B were classified as late-cardiac signature genes. HIPK3 is expressed in the early developing heart; however, the function of the gene may be dispensable because homozygous null adult mice survive into adulthood and develop impaired insulin secretion and glucose tolerance.65,66 The PPP1R12B gene encodes a subunit of MYPT2, a muscle phosphatase that regulates cardiac myosin within contractile myofibrils.67\n\nOverall, devGEA provides an effective analysis tool that enables the reproducible identification of unique cardiac signatures occurring throughout hiPSC-cardiomyocyte differentiation. Given the reproducibility of several genes across multiple experiments and cell lines, these genes may represent important regulatory nodes in the human developmental cardiac network, warranting further investigations. The study of heart development is of critical importance to biomedical, clinical, and translational research, as it allows us to understand and intervene in human cardiovascular disease. Directed cardiomyocyte differentiation from hiPSCs allows researchers to answer important biological questions regarding the differentiation of these specialized cells, the pathogenesis underlying the disease, and their potential therapeutic treatment for human cardiovascular disease. Since differential gene expression during hiPSC-directed cardiomyocyte differentiation recapitulates the in vivo cardiogenic program of the embryo, this experimental system allows us to advance and expand our knowledge of gene regulation in human cardiogenesis from other model organisms such as mice. The translational medicine effectiveness of this technique is already being realized by the generation and differentiation of hiPSCs into cardiomyocytes from patients with congenital cardiovascular disease, which allows the determination of the molecular, cellular, developmental, and physiological dysfunction underlying gene mutations.68,69 Additionally, hiPSCs can be genetically modified using RNAi, homologous recombination, or Crispr/Cas9 techniques to inactivate gene function during cardiomyocyte differentiation, allowing the study of gene function in the human developmental context. High-throughput gene expression profiling of hiPSC differentiation allows the classification of discrete gene expression patterns during cardiomyocyte differentiation, which may prove useful for the analysis of genetically modified hiPSCs and patient-derived hiPSCs that disrupt normal cardiac regulatory gene function.\n\nThis research did not involve human subjects or animals.", "appendix": "Data availability\n\nThe data and full results of this study are available in the Gitlab repository https://gitlab.com/jkinne/devgea with DOI https://doi.org/10.5281/zenodo.13118760. 70 The analysis code and shiny web app are also included in this repository. The entire repository, including the dataset, was provided using Apache License Version 2.0. The following data and result files were included:\n\n• data/GIBCO_qPCR_cardiac_genes.csv – RT-qPCR measurements for genes studied across four timepoints.\n\n• results/all_results.xlsx - analysis results for all genes within the previous datasets studied.\n\n• results/results_pass_filters.csv - analysis results for all genes that passed the filters used in our study (p value, log2 fold change, correlation to one of the marker genes).\n\n• results/results_6way_agreement.csv - analysis results for all genes that passed all filters and also produced the same classification under all of the methods used in the study.\n\nAll analyses were performed using R Statistical Software (v4.4.1 (2024-06-14)). 71 Packages used for computations and analysis were matrixStats, 72 ClassComparison, 73 and base R packages. 71\n\nTables are available as extended data via the above repository link.https://doi.org/10.5281/zenodo.13118760\n\n\nAcknowledgements\n\nWe thank the following for useful discussions, technical assistance, and/or preliminary work related to this project: Dwayne Tally, Andrew Williamson, Mirian Alvarez-Dubon, Ishmeet Kaur, Joseph Dalloul, Danielle Muse, Basundhara Raj, Josh Soto, Laura Cochran, Michaela Ward, Hayden Fell, Garett Oxford, Om Dalal, AJ Farmer, Shaad Ahmad, and Rusty Gonser.\n\n\nReferences\n\nSmith CM, Hayamizu TF, Finger JH, et al.: The mouse Gene Expression Database (GXD): 2019 update. Nucleic Acids Res. 2019; 47(D1): D774–D779. Epub 2018/10/20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVisel A, Thaller C, Eichele G: GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 2004; 32(Database issue): D552–6. Epub 2003/12/19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConsortium GT: Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015; 348(6235): 648–60. Epub 2015/05/09. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBult CJ, Blake JA, Smith CL, et al.: Mouse Genome Database G. Mouse Genome Database (MGD) 2019. Nucleic Acids Res. 2019; 47(D1): D801–6. Epub 2018/11/09. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarrett T, Wilhite SE, Ledoux P, et al.: NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013; 41(Database issue): D991–5. Epub 2012/11/30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTakahashi K, Yamanaka S: Induced pluripotent stem cells in medicine and biology. Development. 2013; 140(12): 2457–2461. PubMed Abstract \| Publisher Full Text\n\nShi Y, Inoue H, Wu JC, et al.: Induced pluripotent stem cell technology: a decade of progress. Nat. Rev. Drug Discov. 2017; 16(2): 115–30. Epub 2016/12/16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMummery CL, Zhang J, Ng ES, et al.: Differentiation of human embryonic stem cells and induced pluripotent stem cells to cardiomyocytes: a methods overview. Circ. Res. 2012; 111(3): 344–58. Epub 2012/07/24. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDoyle MJ, Lohr JL, Chapman CS, et al.: Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes as a Model for Heart Development and Congenital Heart Disease. Stem Cell Rev. Rep. 2015; 11(5): 710–27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu Z, Huangfu D: Human pluripotent stem cells: an emerging model in developmental biology. Development. 2013; 140(4): 705–17. Epub 2013/01/31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurridge PW, Keller G, Gold JD, et al.: Production of de novo cardiomyocytes: human pluripotent stem cell differentiation and direct reprogramming. Cell Stem Cell. 2012; 10(1): 16–28. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurridge PW, Thompson S, Millrod MA, et al.: A universal system for highly efficient cardiac differentiation of human induced pluripotent stem cells that eliminates interline variability. PLoS One. 2011; 6(4): e18293. Epub 2011/04/16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLian X, Hsiao C, Wilson G, et al.: Robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling. Proc. Natl. Acad. Sci. USA. 2012; 109(27): E1848–57. Epub 2012/05/31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKattman SJ, Witty AD, Gagliardi M, et al.: Stage-specific optimization of activin/nodal and BMP signaling promotes cardiac differentiation of mouse and human pluripotent stem cell lines. Cell Stem Cell. 2011; 8(2): 228–40. PubMed Abstract \| Publisher Full Text\n\nBurridge PW, Matsa E, Shukla P, et al.: Chemically defined generation of human cardiomyocytes. Nat. Methods. 2014; 11(8): 855–60. Epub 2014/06/15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLian X, Zhang J, Azarin SM, et al.: Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/beta-catenin signaling under fully defined conditions. Nat. Protoc. 2013; 8(1): 162–75. Epub 2012/12/20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu Q, Jiang C, Xu J, et al.: Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circ. Res. 2017; 121(4): 376–91. Epub 2017/07/01. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrober BJ, Elorbany R, Rhodes K, et al.: Dynamic genetic regulation of gene expression during cellular differentiation. Science. 2019; 364(6447): 1287–90. Epub 2019/06/30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKoressaar T, Remm M: Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007; 23(10): 1289–91. Epub 2007/03/22. PubMed Abstract \| Publisher Full Text\n\nLivak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001; 25(4): 402–8. PubMed Abstract \| Publisher Full Text\n\nBustin SA, Benes V, Garson JA, et al.: The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009; 55(4): 611–22. Epub 2009/02/26. PubMed Abstract \| Publisher Full Text\n\nTakahashi K, Yamanaka S: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126(4): 663–76. Epub 2006/08/15. PubMed Abstract \| Publisher Full Text\n\nOkita K, Ichisaka T, Yamanaka S: Generation of germline-competent induced pluripotent stem cells. Nature. 2007; 448(7151): 313–7. Epub 2007/06/08. PubMed Abstract \| Publisher Full Text\n\nYu J, Vodyanik MA, Smuga-Otto K, et al.: Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007; 318(5858): 1917–20. Epub 2007/11/20. PubMed Abstract \| Publisher Full Text\n\nKouskoff V, Lacaud G, Schwantz S, et al.: Sequential development of hematopoietic and cardiac mesoderm during embryonic stem cell differentiation. Proc. Natl. Acad. Sci. USA. 2005; 102(37): 13170–5. Epub 2005/09/02. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDavid R, Jarsch VB, Schwarz F, et al.: Induction of MesP1 by Brachyury(T) generates the common multipotent cardiovascular stem cell. Cardiovasc. Res. 2011; 92(1): 115–22. Epub 2011/06/01. PubMed Abstract \| Publisher Full Text\n\nKuo CT, Morrisey EE, Anandappa R, et al.: GATA4 transcription factor is required for ventral morphogenesis and heart tube formation. Genes Dev. 1997; 11(8): 1048–60. PubMed Abstract \| Publisher Full Text\n\nvan Berlo JH , Elrod JW, van den Hoogenhof MM , et al.: The transcription factor GATA-6 regulates pathological cardiac hypertrophy. Circ. Res. 2010; 107(8): 1032–40. Epub 2010/08/12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMolkentin JD, Lin Q, Duncan SA, et al.: Requirement of the transcription factor GATA4 for heart tube formation and ventral morphogenesis. Genes Dev. 1997; 11(8): 1061–72. PubMed Abstract \| Publisher Full Text\n\nLints TJ, Parsons LM, Hartley L, et al.: Nkx-2.5: a novel murine homeobox gene expressed in early heart progenitor cells and their myogenic descendants. Development. 1993; 119(2): 419–31. PubMed Abstract \| Publisher Full Text\n\nEdmondson DG, Lyons GE, Martin JF, et al.: Mef2 gene expression marks the cardiac and skeletal muscle lineages during mouse embryogenesis. Development. 1994; 120(5): 1251–63. PubMed Abstract \| Publisher Full Text\n\nBu L, Jiang X, Martin-Puig S, et al.: Human ISL1 heart progenitors generate diverse multipotent cardiovascular cell lineages. Nature. 2009; 460(7251): 113–7. PubMed Abstract \| Publisher Full Text\n\nBruneau BG, Logan M, Davis N, et al.: Chamber-specific cardiac expression of Tbx5 and heart defects in Holt-Oram syndrome. Dev. Biol. 1999; 211(1): 100–8. PubMed Abstract \| Publisher Full Text\n\nHe X, Liu Y, Sharma V, et al.: ASK1 associates with troponin T and induces troponin T phosphorylation and contractile dysfunction in cardiomyocytes. Am. J. Pathol. 2003; 163(1): 243–51. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartin FJ, Amode MR, Aneja A, et al.: Ensembl 2023. Nucleic Acids Res. 2023; 51(D1): D933–41. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNV OA: ShinyProxy.2024.\n\nWagner GP, Kin K, Lynch VJ: Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012; 131(4): 281–5. Epub 2012/08/08. PubMed Abstract \| Publisher Full Text\n\nAbrams ZB, Johnson TS, Huang K, et al.: A protocol to evaluate RNA sequencing normalization methods. BMC Bioinformatics. 2019; 20(Suppl 24): 679. Epub 2019/12/20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCoombes KR, Fritsche HA Jr, Clarke C, et al.: Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin. Chem. 2003; 49(10): 1615–23. PubMed Abstract \| Publisher Full Text\n\nZhao S, Ye Z, Stanton R: Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols. RNA. 2020; 26(8): 903–9. Epub 2020/04/13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNakamura T, Fidler IJ, Coombes KR: Gene expression profile of metastatic human pancreatic cancer cells depends on the organ microenvironment. Cancer Res. 2007; 67(1): 139–48. PubMed Abstract \| Publisher Full Text\n\nLyons I, Parsons LM, Hartley L, et al.: Myogenic and morphogenetic defects in the heart tubes of murine embryos lacking the homeo box gene Nkx2-5. Genes Dev. 1995; 9(13): 1654–66. Epub 1995/07/01. PubMed Abstract \| Publisher Full Text\n\nSavory JG, Bouchard N, Pierre V, et al.: Cdx2 regulation of posterior development through non-Hox targets. Development. 2009; 136(24): 4099–110. Epub 2009/11/11. PubMed Abstract \| Publisher Full Text\n\nSavory JG, Pilon N, Grainger S, et al.: Cdx1 and Cdx2 are functionally equivalent in vertebral patterning. Dev. Biol. 2009; 330(1): 114–22. Epub 2009/03/27. PubMed Abstract \| Publisher Full Text\n\nChu M, Wang L, Wang H, et al.: A novel role of CDX1 in embryonic epicardial development. PLoS One. 2014; 9(7): e103271. Epub 2014/07/28. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFoley TE, Hess B, Savory JGA, et al.: Role of Cdx factors in early mesodermal fate decisions. Development. 2019; 146(7). Epub 2019/04/01. PubMed Abstract \| Publisher Full Text\n\nChen YH, Ishii M, Sucov HM, et al.: Msx1 and Msx2 are required for endothelial-mesenchymal transformation of the atrioventricular cushions and patterning of the atrioventricular myocardium. BMC Dev. Biol. 2008; 8: 75. Epub 2008/07/30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFu J, Jiang M, Mirando AJ, et al.: Reciprocal regulation of Wnt and Gpr177/mouse Wntless is required for embryonic axis formation. Proc. Natl. Acad. Sci. USA. 2009; 106(44): 18598–603. Epub 2009/10/19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBanziger C, Soldini D, Schutt C, et al.: Wntless, a conserved membrane protein dedicated to the secretion of Wnt proteins from signaling cells. Cell. 2006; 125(3): 509–22. PubMed Abstract \| Publisher Full Text\n\nMiyamoto M, Kannan S, Anderson MJ, et al.: Cardiac progenitors instruct second heart field fate through Wnts. Proc. Natl. Acad. Sci. USA. 2023; 120(4): e2217687120. Epub 2023/01/17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan de Putte T, Maruhashi M, Francis A, et al.: Mice lacking ZFHX1B, the gene that codes for Smad-interacting protein-1, reveal a role for multiple neural crest cell defects in the etiology of Hirschsprung disease-mental retardation syndrome. Am. J. Hum. Genet. 2003; 72(2): 465–70. Epub 2003/01/09. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEid A, Torres-Padilla ME: Characterization of non-canonical Polycomb Repressive Complex 1 subunits during early mouse embryogenesis. Epigenetics. 2016; 11(6): 389–97. Epub 2016/04/15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen SY, Liu FC: The Fgf9-Nolz1-Wnt2 axis regulates morphogenesis of the lung. Development. 2023; 150(16). Epub 2023/08/17. PubMed Abstract \| Publisher Full Text\n\nKinoshita M, Era T, Jakt LM, et al.: The novel protein kinase Vlk is essential for stromal function of mesenchymal cells. Development. 2009; 136(12): 2069–79. PubMed Abstract \| Publisher Full Text\n\nBrutsch SM, Madzharova E, Pantasis S, et al.: Mesenchyme-derived vertebrate lonesome kinase controls lung organogenesis by altering the matrisome. Cell. Mol. Life Sci. 2023; 80(4): 89. Epub 2023/03/15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXu Q, Wang Y, Dabdoub A, et al.: Vascular development in the retina and inner ear: control by Norrin and Frizzled-4, a high-affinity ligand-receptor pair. Cell. 2004; 116(6): 883–895. PubMed Abstract \| Publisher Full Text\n\nSummerhurst K, Stark M, Sharpe J, et al.: 3D representation of Wnt and Frizzled gene expression patterns in the mouse embryo at embryonic day 11.5 (Ts19). Gene Expr. Patterns. 2008; 8(5): 331–48. Epub 2008/02/13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen Q, Zhang H, Liu Y, et al.: Endothelial cells are progenitors of cardiac pericytes and vascular smooth muscle cells. Nat. Commun. 2016; 7: 12422. Epub 2016/08/12. PubMed Abstract \| Free Full Text Publisher Full Text \|\n\nYoon C, Song H, Yin T, et al.: FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors. Stem Cell Reports. 2018; 10(1): 87–100. Epub 2017/12/14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu C, Spinozzi S, Chen JY, et al.: Nexilin Is a New Component of Junctional Membrane Complexes Required for Cardiac T-Tubule Formation. Circulation. 2019; 140(1): 55–66. Epub 2019/04/15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu T, Xu Y, Zhang L, et al.: Filamin C is Essential for mammalian myocardial integrity. PLoS Genet. 2023; 19(1): e1010630. Epub 2023/01/27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuang ZP, Kataoka M, Chen J, et al.: Cardiomyocyte-enriched protein CIP protects against pathophysiological stresses and regulates cardiac homeostasis. J. Clin. Invest. 2015; 125(11): 4122–34. Epub 2015/10/05. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTsoupri E, Kostavasili I, Kloukina I, et al.: Myospryn deficiency leads to impaired cardiac structure and function and schizophrenia-associated symptoms. Cell Tissue Res. 2021; 385(3): 675–96. Epub 2021/05/26. PubMed Abstract \| Publisher Full Text\n\nBroadway-Stringer S, Jiang H, Wadmore K, et al.: Insights into the Role of a Cardiomyopathy-Causing Genetic Variant in ACTN2. Cells. 2023; 12(5). Epub 2023/02/24. PubMed Abstract \| Free Full Text Publisher Full Text \|\n\nShojima N, Hara K, Fujita H, et al.: Depletion of homeodomain-interacting protein kinase 3 impairs insulin secretion and glucose tolerance in mice. Diabetologia. 2012; 55(12): 3318–30. Epub 2012/09/16. PubMed Abstract \| Publisher Full Text\n\nIsono K, Nemoto K, Li Y, et al.: Overlapping roles for homeodomain-interacting protein kinases hipk1 and hipk2 in the mediation of cell growth in response to morphogenetic and genotoxic signals. Mol. Cell. Biol. 2006; 26(7): 2758–2771. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee E, May H, Kazmierczak K, et al.: The MYPT2-regulated striated muscle-specific myosin light chain phosphatase limits cardiac myosin phosphorylation in vivo. J. Biol. Chem. 2024; 300(2): 105652. Epub 2024/01/13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSun RH, Hu BC, Li Q: Stress-induced cardiomyopathy complicated by multiple organ failure following cephalosporin-induced anaphylaxis. Intern. Med. 2012; 51(8): 895–9. Epub 2012/04/17. PubMed Abstract \| Publisher Full Text\n\nAng YS, Rivas RN, Ribeiro AJS, et al.: Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis. Cell. 2016; 167(7): 1734–1749.e22. Epub 2016/12/17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIsaiah Bartlett JK, Martin G, Coombes K, et al.: devGEA 1.0.1 - source code and dataset.2024. Publisher Full Text\n\nTeam RC: R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2024.\n\nBengtsson H: matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors).2024. Publisher Full Text\n\nCoombes KR: ClassComparison: Classes and Methods for “Class Comparison” Problems on Microarrays.2019. ClassComparison. Publisher Full Text" }	[ { "id": "327630", "date": "12 Oct 2024", "name": "Qing Liu", "expertise": [ "Reviewer Expertise Stem cell biology", "genomics", "cardiovascular" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 \"A high-throughput gene expression analysis software tool for developmental time series and gene signature analysis of human cardiomyocyte differentiation\" by Bartlett et al. developed a novel bioinformatic tool named Developmental Gene Expression Analysis (devGEA), which can be be implemented locally or via web browsers to analyze gene expression for developmental biology study, such as developmental time series profiling, identification of differentially expressed genes and markers. Overall this study is promising for those scientists who is focusing on stem cell biology or developmental biology but with limited expertise in bioinformatics. However, the manuscript has some pitsfalls in some parts that the author need to be clarified or revised.\n1. Datasets used for this study is limited to stem-cell-based differentiation. If the authors state that this tool can be used for analyzing gene expression of the developmental biology, the dataset from in-vivo studies should be included. Otherwise, this will downgrade the significance and importance of tool.\n\n2. Can this tool be used for single-cell RNA-seq? Or just for the bulk RNA-seq? One of major challenges of studying cell differentiation is the heterogeneity of the cell population. For instance, despite of using monolayer cardiomyocyte differentiation, the whole cell populations still include various cell types, such as ventricle-like, atrial-like, endothelial, epithelial cells, etc. The authors need to state of challenge or potential pitfall of this tool\n3. Choosing the markers are kind of arbitrary. For example, on page 16, I don't think it is a good idea to use GATA4 as the major marker for early cardiac stage. Actually, GATA4, TBX5 and TNTT2 can be detected from the early beating cardiomyocytes to late stages. This issue is also seen in using ZEB2 as a marker. Based on Liu's study (2017), those genes showed highly weight in the network analysis, but they are not used as typical makers for early stages. In addition, using only one marker for filtration has very low power. Usually, for mesoderm, TBXT, EMOS, TBX6, et al, For early cardiac lineage/cardiac progenitors, MESP1, NKX2.5, For cardiac markers: GATA4, TNNT2, TBX5, MYL7, et al Reference: https://www.rndsystems.com/research-area/mesodermal-lineage-markers https://www.rndsystems.com/research-area/cardiac-stem-cell-markers\n4. If this tool can provide GO enrichment analysis or KEGG analysis, it will be a plus to increase the significance of this tool.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] }, { "id": "345653", "date": "28 Dec 2024", "name": "Stephanie Agioti", "expertise": [ "Reviewer Expertise Cancer Genetics", "Computational Biology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nHigh-throughput gene expression analysis is very important in the investigation of developmental time series of human hi- PSC cardiomyocyte differentiation and can be performed using various bioinformatic tools. Despite this, there are still several difficulties and gaps in the procedure of analysis of combined sample groups. The Developmental Gene Expression Analysis (devGEA) tool was developed by the team to provide an effective method for classifying cardiac signatures during hi-PSC cardiomyocyte differentiation. Enhancing gene expression and gene signature analysis is an important goal in cardiomyocyte differentiation, where the identification of key developmental markers is stimulated to disrupt cardiac regulatory gene function. The manuscript is highly informative and presents a promising tool for bioinformaticians studying developmental biology. It is well-designed, cites relevant literature, and presents accurate results with significant academic merit. However, there are still some shortcomings that need to be addressed, and the authors must revise the manuscript accordingly:\n1. Figures 1 and 2 would be more appropriately presented in the results section, as they depict the research findings. I can understand that the reason researchers add figure 1 in background is because it has results from the previous studies by Liu et. al., 2017 and Strober et al., 2019, but for me you cannot present your results’ as a background. A good idea would be to leave only the diagrams of differentiation stage and developmental markers with the results from previous studies at the background section and the rest of the results move in the results’ section. Additionally, Figures 3, 4, 5, and 6 also present results from the study and should be moved to the results section. The datasets and experimental setup sections are part of the methodology and should be relocated accordingly. Results section must be re-organized with the figures 1-6 in order to present accurately only the research’s’ results and discussion part must be a different section. Furthermore, the analysis overview should be moved to the methodology section, clearly outlining the three methods used: linear model ANOVA, basic descriptive statistical analysis, and correlation analysis. Finally, overall results – all methods of classification must be used as a discussion of the study and last paragraph must be categorized as the conclusions of the study.\n2. On page 5 (datasets section), the authors refer to the original procedure without explaining it in sufficient detail, leaving gaps in the readers' understanding. Also, authors don’t mention the multiple hPSC lines which they referred to (line 8). Moreover, the manuscript does not clearly explain why day 8 was selected as the 4th time point, while other studies used day 15 and day 30 as corresponding time points.\nOn page 21, paragraph 2, authors refer to twenty genes without mentioned them name by name, while figure 4 must be referred to paragraph 3 since it describes its results. In page 23, paragraph 2 (the devGA…), authors did not refer which are the three different classification methods were used for basic statistics or correlation. Finally, they are not clear in the manuscript the criteria used in the developmental markers for each stage as well as how the markers that are between two different development stages can be used.\n3. The environment plays a critical role in influencing developmental processes, including the differentiation of human pluripotent stem cells (hPSCs) into cardiomyocytes. Given that gene expression and signaling are key environmental factors that influence the expression of other factors and molecules, it would be valuable for the authors to experimentally study how the overexpression and/or inhibition of these genes in the environment affects cardiomyocyte differentiation, and at which stages or levels this impact occurs.\n4. A future perspectives section should be added to discuss the potential role of devGEA in identifying differentially expressed genes in cardiomyocyte differentiation in humans as a predictive tool. Additionally, its applicability to other developmental processes should be explored to highlight the broader value of the tool. Team presents very clear the methodology used in their study, allowing the replication of analyses by others with very easy access to the source data used for the results to ensure full reproducibility. In addition, they provide a very clear guidance about devGA and how they designed it in order to give to the readers clear instructions how to use it. In addition, interpretation of the statistical analysis of the results was very appropriate and it is clear how statistically significant results were ‘’extracted’’ from the study.\nTeam presents very clear the methodology used in their study, allowing the replication of analyses by others with very easy access to the source data used for the results to ensure full reproducibility. In addition, they provide a very clear guidance about devGA and how they designed it in order to give to the readers clear instructions how to use it. In addition, interpretation of the statistical analysis of the results was very appropriate and it is clear how statistically significant results were ‘’extracted’’ from the study.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1097
https://f1000research.com/articles/12-1084/v1	01 Sep 23	{ "type": "Study Protocol", "title": "Comparative Evaluation of Mechanical Properties and Bond Strength of Glass Ionomer Cement reinforced with three different concentrations of Silver Nanoparticles as against Conventional Glass Ionomer Cement in Primary Teeth.", "authors": [ "Harikishan Kanani", "Monika Khubchandani", "Monika Khubchandani" ], "abstract": "Introduction:\nRestorative dental materials are defined as substances that are used to repair, replace, or enhance a patient's teeth. Various materials used in paediatric dentistry are zinc oxide eugenol, glass ionomer cement, resin composite, calcium hydroxide, silver amalgam, giomers etc. GIC is a biocompatible material having a low thermal expansion coefficient and fluoride release property. There are still a few drawbacks of GIC due of their poor mechanical properties therefore addition of Silver Nanoparticles demonstrated improved mechanical and bactericidal capabilities. There hasn't been much study on the quality of the bond contact between silver nanoparticles and dentin, as well as the color's durability. Aim: To evaluate and compare the mechanical properties and bond strength of Glass ionomer cement reinforced with three different concentrations of silver nanoparticle as against conventional glass ionomer cement in primary Teeth. Materials and Method: Silver nanoparticles will be prepared using three chemicals namely, silver nitrate, sodium citrate and tannic acid. Traditional GIC (GC Fuji II, GC Corporation, Tokyo, Japan) will be purchased. Three different concentrations of silver nanoparticles will be prepared i.e., 0.2, 0.4, and 0.6%. The GIC specimens will then be divided into 4 groups: GIC without silver nanoparticles (AgNPs),0.2%,0.4% and 0.6% AgNPs. Mechanical properties will be checked such as compressive, tensile, and bond strength using Universal Testing Machine. Expected Results:\nGIC reinforced with silver nano particles is expected to have better mechanical strength, less microleakage and wear resistance, greater fracture resistance and adhesive bond strength. Conclusion: GIC reinforced with silver nano particles will be expected to have better mechanical and physical properties than conventional Type II GICs and is expected to be a promising material for restoration in primary teeth.", "keywords": [ "Restorative material", "Glass ionomer cement", "silver nano particles." ], "content": "Introduction\n\nRestorative dental materials are defined as substances that are mostly used to repair, replace, or enhance a patient’s carious teeth. Dental caries experienced a sharp drop around the turn of the 20th century, and dental enhancement and health became more popular.1 Properties of ideal restorative materials would be: fracture resistance, compressive strength, tensile strength, no microleakage, hardness, adhesion, higher bond strength, ease of clinical use, good clinical performance, economical, bio-compatible and cost-effectiveness.2 However, the appropriate restorative material that meets all the properties has yet to be formed.3\n\nThe glass ionomer cement (GIC) was invented by Wilson & Kent (1972).4 This material offers plenty of applications in paediatric dentistry such as restorations, core build-up, pit and fissure sealants, liners and bases, luting materials, and orthodontic bracket adhesives. GIC is a biocompatible material with a low coefficient of thermal expansion and fluoride releasing property.5\n\nGIC still has significant downsides, though, because of its poor mechanical qualities, which include low resistance to fracture, poor resistance to wear, and formal disintegration on water sorption.6 Secondary caries and restoration failures are caused by these mechanical defects, which encourage the formation of bacterial colonies, especially Streptococcus mutans.7 Fluoride release underlies the majority of GIC’s antibacterial activity.8 To boost antibacterial and mechanical qualities without compromising their bond strength and reduce the development of secondary caries, fillers including silicates and fluorides were added to GIC.9\n\nNanotechnology is the study of making high-quality structures and materials made of particle substances with sizes ranging from 1–100 nm.10 Among all the materials used in nanotechnology silver has been employed in its ionised forms as nanoparticles. A metal reinforced GIC that is stronger and tougher was previously made with the use of silver alloy powder.11 How effective silver or its compounds are against bacteria, viruses and fungus is determined by the silver ions amount created and their ability to interact with microorganism cell membranes.12\n\nSilver powder is sintered to glass after being heated to a high temperature. Silver-sintered powder has the potential to increase abrasion resistance and durability.12\n\nWhen contrasted, Dentin’s mechanical attributes (compressive strength of 297 MPa, tensile strength of 44.4 MPa, and hardness of 52 to 64 KHN) outweigh those of GIC (fracture toughness of 0.72 MPa m1/2, compressive strength of 196-251 MPa, tensile strength of 18 to 26 MPa, and hardness of 87 to 177 KHN).12 According to previous study, tiny silver nanoparticles may occupy the crevices between the bigger glass particles and give an additional bonding site for the polyacrylic polymer, reducing the possibility of the cement dissolution.5 As when silver nanopowder were incorporated into GIC it is revealed that when the concentration of silver nanopowder raised, bacterial colonies are reduced.5 Higher concentration of silver nanoparticles showed a significant improvement in mechanical properties in relation to dentin.\n\nThere has not been enough research on the strength of the binding contact between dentin and silver nanoparticles, as well as the colour stability. Hence, objective of this study is to assess and compare mechanical characteristics, colour stability, and bond strength of primary teeth filled with GIC reinforced with various concentration of silver nanoparticles.\n\nIn this study we aim to evaluate and compare the mechanical properties of GIC reinforced with three different concentrations of silver nanoparticles as against traditional GIC.16\n\nTrial design: An in vitro study.\n\nStudy setting\n\nThis is an in vitro study and will be conducted at the Department of Paediatric and Preventive Dentistry, Sharad Pawar Dental College in collaboration with Research and development house, DMIHER, Sawangi (Meghe), Wardha.\n\nInclusion criteria\n\n• Silver nanoparticle liquid (AgNPs) <100 nm particle size.\n\n• Conventional GIC (GC Fuji II, GC Corporation, Tokyo, Japan).\n\n• Primary molars close to their shedding time, affected by gross caries or the tooth that are over-retained will be extracted and included in this study.\n\nExclusion criteria\n\n• Extracted tooth with enamel cracks, fracture, malformation, erosion, restoration will be excluded in the study.\n\n• Permanent teeth shall not be taken into consideration.\n\n• Primary anterior teeth will be excluded from the study.\n\n\nMethods\n\nMaterials used\n\nTraditional GIC (GC Fuji II, GC Corporation, Tokyo, Japan) shall be procured and\n\nThree chemicals:\n\nA. silver nitrate\n\nB. sodium citrate\n\nC. tannic acid\n\nSynthesis of silver nanoparticles\n\nSilver nitrate, sodium citrate, and tannic acid will be used to prepare silver nanoparticles for this in vitro investigation. Three different concentrations of silver nanoparticles 0.2, 0.4, and 0.6% will be synthesized by chemical reduction of reducing agents i.e. sodium citrate is used for reduction of silver ions (Ag+) in aqueous or non-aqueous solutions of silver nitrate. This reducing chemical cause the reduction of Ag+ to metallic silver (Ag0), which then aggregates into oligomeric clusters. In the end, these clusters result in the emergence of metallic colloidal silver particles.\n\nFollowing that, the GIC samples will be split into four groups:\n\nGROUP 1: GIC without silver nanoparticles (AgNPs) (n=26)\n\nGROUP 2: GIC with 0.2% silver nanoparticles (AgNPs) (n=26)\n\nGROUP 3: GIC with 0.4% silver nanoparticles (AgNPs) (n=26)\n\nGROUP 4: GIC with 0.6% silver nanoparticles (AgNPs) (n=26)\n\nThe extracted teeth will be collected from an operating room and dental clinic. The teeth will be carefully examined, which will be included in the criteria. For 1 month, the teeth will be stored in a 0.1% thymol solution with 0.9% isotonic sodium chloride (5°C) until the beginning of the experiment. We will use a diamond bur at a slow-speed handpiece with continuous water cooling, perpendicular to the tooth’s long axis, and cavity preparation will be done from approx 2.0 mm of the tissue along with the cusps without exposing the pulp. The 104 teeth will be categorized into four groups with an equal distribution, which will include group 1 (applying GIC on dentin as the control group), group 2 (applying GIC with silver nanoparticles (AgNPs) (0.2%) on dentin), group 3 (applying GIC with silver nanoparticles (AgNPs) (0.4%) on dentin), and group 4 (applying GIC with silver nanoparticles (AgNPs) (0.6%) on dentin). For the preparation of the control group, the ratio of powder and liquid will be taken as per the manufacturers’ instructions, and they will be mixed on a glossy paper pad.\n\nThen, utilising a universal testing equipment (Instron universal testing machine), mechanical qualities including compressive strength, tensile strength, and bond strength will be examined. Utilising universal hardness testing equipment, the hardness will be evaluated.\n\nIn comparison to standard Type II GIC, GIC reinforced with silver nanoparticles is anticipated to have improved mechanical and physical qualities, less microleakage, and fewer risks of secondary caries due to the antibacterial ability of silver nanoparticles. A potential restorative material for primary teeth is GIC enhanced with silver nanoparticles.\n\nSample size is determined using the following formula,\n\nProportion of outcome (p1) = 0.58\n\nProportion of outcome (p2) = 0.65\n\nLevel of significance (α) = 0.05\n\nPower (1- β) = 0.80\n\nZ alpha value = 1.96\n\nZ beta value = 0.85\n\nInput: Effect size f = 0.34\n\nα error probability = 0.05\n\nPower (1-β error probability) = 0.85\n\nNumerator df = 10\n\nNumber of covariates = 1\n\nOutput: Noncentrality parameter λ = 25.0000000\n\nCritical F = 1.759\n\nDenominator df = 76\n\nTotal sample size = 104\n\nActual power = 0.9125\n\nSample size = 104\n\nTotal Sample size = 104\n\nAs per Wassefy et al.13\n\nAll the results will be calculated using SPSS version 27 software (IBM Corp, 2020) (RRID:SCR_002865). Data for outcome variables will be tested for normality using kalmogorov-smirlov. Comparative analysis over the outcome of functional occlusion in different malocclusion will be evaluated and measurement of depth of curve of Spee and Wilson in millimetres respectively. ANOVA will be used to find significant difference in mean in comparison of four groups. The Tukey test will be used for comparative evaluation of measurement in between two groups pairwise. P-value≤0.05 will be considered significant with a 5% level of significance and 95% confidence of interval.\n\nArticle will be published in indexed journal/findings will be shared in conferences.\n\nThe study is not yet started. However, we are planning to begin the research in August 2023 and complete in around six months.\n\n\nDiscussion\n\nAnti-bio adhesion coatings, antibiotic coatings, and silver inclusion are some of the ways proposed to inhibit bacterial attachment to bare material surfaces; the latter has attracted the curiosity of many researchers.\n\nNoha A. El-Wassefy et al., investigated adding silver nanoparticles to GIC. This showed that this can prevent the establishment of S. Aureus biofilms while having just a minor impact on mechanical properties.13\n\nFaisal Mohammed Abed et al., conducted an in vitro investigation and found that GIC added with AgNPs positively affected the bond quality in dentin interaction at concentrations more than 0.4%.5\n\nA broad-spectrum antibiofilm effect of silver has been found, with little to no bacterial resistance. According to literature on the antibiofilm actions of silver compounds, silver can be used in bone cement and wound dressings.14,15 Thus, data from past studies indicate the advantages of inserting silver nanoparticles, which show increased mechanical and antibacterial properties. There is still not enough research on the strength of the bond contact between dentin and silver nanoparticles as well as durability of colour. As a result, the goal of this work is to evaluate and compare the mechanical properties, colour stability, and bond strength of primary teeth filled with glass ionomer cement at varying concentrations of silver nanoparticles.\n\nEthical approval received from Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha\n\nIEC reference number - DMIHER (DU)/IEC/2023/566", "appendix": "Data availability\n\nZenodo: Spirit _checklist Harry, https://doi.org/10.5281/zenodo.7788338. 16\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nZafar MS, Amin F, Fareed MA, et al.: Biomimetic Aspects of Restorative Dentistry Biomaterials. Biomimetics. 2020 Jul 15; 5(3): 34. Publisher Full Text\n\nRekow ED, Bayne SC, Carvalho RM, et al.: What constitutes an ideal dental restorative material? Adv. Dent. Res. 2013 Nov; 25(1): 18–23. PubMed Abstract \| Publisher Full Text\n\nRekow ED, Bayne SC, Carvalho RM, et al.: What Constitutes an Ideal Dental Restorative Material? Adv. Dent. Res. 2013. [cited 2023 Apr 11]. Publisher Full Text\n\nWilson AD, Kent BE: A new translucent cement for dentistry. The glass ionomer cement. Br. Dent. J. 1972 Feb 15; 132(4): 133–135. PubMed Abstract \| Publisher Full Text\n\nAbed FM, Kotha SB, AlShukairi H, et al.: Effect of Different Concentrations of Silver Nanoparticles on the Quality of the Chemical Bond of Glass Ionomer Cement Dentine in Primary Teeth. Front. Bioeng. Biotechnol. 2022 [cited 2023 Apr 11]; 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcLean JW, Wilson AD: The clinical development of the glass-ionomer cement. II. Some clinical applications. Aust. Dent. J. 1977 Apr; 22(2): 120–127. Publisher Full Text\n\nHu J, Du X, Huang C, et al.: Antibacterial and physical properties of EGCG-containing glass ionomer cements. J. Dent. 2013 Oct; 41(10): 927–934. PubMed Abstract \| Publisher Full Text\n\nGarcia-Contreras R, Scougall-Vilchis RJ, Contreras-Bulnes R, et al.: Mechanical, antibacterial and bond strength properties of nano-titanium-enriched glass ionomer cement. J. Appl. Oral Sci. 2015; 23(3): 321–328. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan I, Saeed K, Khan I: Nanoparticles: Properties, applications and toxicities. Arab. J. Chem. 2019 Nov 1; 12(7): 908–931. Publisher Full Text\n\nMonteiro DR, Gorup LF, Takamiya AS, et al.: The growing importance of materials that prevent microbial adhesion: antimicrobial effect of medical devices containing silver. Int. J. Antimicrob. Agents. 2009 Aug; 34(2): 103–110. PubMed Abstract \| Publisher Full Text\n\nLansdown ABG: Silver. I: Its antibacterial properties and mechanism of action. J. Wound Care. 2002 Apr; 11(4): 125–130. PubMed Abstract \| Publisher Full Text\n\nAnusavice KJ, Phillips RW, Shen C, et al.: Phillips’ science of dental materials. 12th ed.St. Louis, Mo.: Elsevier/Saunders; 2013 [cited 2023 Apr 16]; 29. Reference Source\n\nEl-Wassefy NA, El-Mahdy RH, El-Kholany NR: The impact of silver nanoparticles integration on biofilm formation and mechanical properties of glass ionomer cement. J. Esthet. Restor. Dent. Off. Publ. Am. Acad. Esthet. Dent. Al. 2018 Mar; 30(2): 146–152. PubMed Abstract \| Publisher Full Text\n\nAlt V, Bechert T, Steinrücke P, et al.: An in vitro assessment of the antibacterial properties and cytotoxicity of nanoparticulate silver bone cement. Biomaterials. 2004 Aug; 25(18): 4383–4391. PubMed Abstract \| Publisher Full Text\n\nBjarnsholt T, Kirketerp-Møller K, Kristiansen S, et al.: Silver against Pseudomonas aeruginosa biofilms. APMIS Acta Pathol. Microbiol. Immunol. Scand. 2007 Aug; 115(8): 921–928. Publisher Full Text\n\nKanani H, Khubchandani M: Spirit _checklist Harry (Version V1). [Guidelines]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "229250", "date": "22 Dec 2023", "name": "Dr.Anushka Deoghare", "expertise": [ "Reviewer Expertise Dental materials.. Oral habits" ], "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 article evaluates the most commonly used dental material which is Glass ionomer cement in pediatric dentistry. This modification with silver nanoparticles will improve the strength of the material and improves the quality of the material. This paper will contribute in the literature. It will provide a base for the further in vivo studies which will give a new modified way to use GIC covering its drawback\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": "250686", "date": "11 Sep 2024", "name": "Tamer M Hamdy", "expertise": [ "Reviewer Expertise Dental materials", "nanotechnology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 comments to Editor I would like to express my deepest appreciation to the editor for the invitation to review the manuscript. The current article investigates and compares the mechanical properties and bond strength of Glass ionomer cement reinforced with three different concentrations of silver nanoparticles as against conventional glass. The following comments and minor corrections provided to the author are given below.\nReviewer comments to Author According to this manuscript, I would like to express my thanks to the authors for their great efforts. In my opinion, the paper is found interesting. I would like to get attention to the following simple comments.\nThe null hypothesis should be mentioned in the introduction In the introduction, you should mention other studied modifications performed in G.I. as \"Evaluation of compressive strength, surface microhardness, solubility and antimicrobial effect of glass ionomer dental cement reinforced with silver doped carbon nanotube fillers\" as they added silver-doped carbon CNT into conventional G.I. ( Hamdy TM. et al., 2023)[Ref 1]. Also, in the discussion, you should compare it with your results. In the introduction, you should address the advantages and benefits of adding nanosilver to dental restorations. You should mention in the methodology the causes of using the selected percentages of nanosilver.\n- Limitations of the study and recommendations should be added to the end of the manuscript.\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": "318291", "date": "14 Sep 2024", "name": "Ana Ivanišević Malčić", "expertise": [ "Reviewer Expertise Endodontics", "endodontic surgery", "restorative materials" ], "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\nPlease consider the following:\nAbstract After you establish that much of the previous research with the addition of silver particles to GIC has dealt with the mechanical properties, you want to introduce the purpose of your study and that is determining how the addition of the silver particles affects the bond strength of the modified material to dentine and color stability of the GIC modified with silver nano particles, (rather than „the quality of the bond contact between the silver particles and, as well as the color's durability.'') However, if determining the color stability is not the aim of the study and is not mentioned in the expected results and methods, maybe this part can be omitted from this introductory section of the Abstract as well.\n''Three different concentrations of silver nanoparticles will be prepared i.e., 0.2, 0.4, and 0.6%.'' Here you should be more precise. If you are talking about weight or volume percentage than it would be better to write wt%, or vol%\nIntroduction Similarly as in abstract, authors state at the end of the introduction ''There has not been enough research on the strength of the binding contact between dentin and silver nanoparticles, as well as the cooler stability.'' But, the bond between particular particles is not the objective rather the bond strength of the modified material to the dentin of primary teeth. So, a sentence describing objective should be clear: instead ''… bond strength of primary teeth filled with GIC reinforced ….'' It should say ''…bond strength of GIC reinforced with various concentration of silver nanoparticles to primary teeth…''\n\nObjective It is not compatible with the last sentence in the Introduction. It is not clear whether the color stability will be determined or not.\nMethods It is important to carefully chose storage solutions. It is also important to properly describe concentration of storage solutions. Was it W/V % of chloramine and thymol? It was shown that storage in thymol (up to 6 months) does not affect the bond strength of dental resins to dentin, but PBS would be better choice than saline. For testing mechanical properties, material specimens should be prepared. Please consult ISO 9917-1:2007, ISO 9917-2:2017 (CS and TS cylinders 4x6mm, and for FS rods 25 x2x2 mm). Also, The ISO 9917-1:2007 is relevant to micro tensile bond strength measurement for water-based cements.\nStatistical method The choice of statistical tests will depend on the dana distribution which you cannot predict. In case you get normal distribution, the suggested tests can be performed.\nDiscussion You discuss antibacterial effect of silver, jet it is not your objective of the proposed study.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1084
https://f1000research.com/articles/13-664/v1	20 Jun 24	{ "type": "Systematic Review", "title": "(Semi)automated approaches to data extraction for systematic reviews and meta-analyses in social sciences: A living review", "authors": [ "Amanda Legate", "Kim Nimon", "Ashlee Noblin", "Kim Nimon", "Ashlee Noblin" ], "abstract": "Background An abundance of rapidly accumulating scientific evidence presents novel opportunities for researchers and practitioners alike, yet such advantages are often overshadowed by resource demands associated with finding and aggregating a continually expanding body of scientific information. Data extraction activities associated with evidence synthesis have been described as time-consuming to the point of critically limiting the usefulness of research. Across social science disciplines, the use of automation technologies for timely and accurate knowledge synthesis can enhance research translation value, better inform key policy development, and expand the current understanding of human interactions, organizations, and systems. Ongoing developments surrounding automation are highly concentrated in research for evidence-based medicine with limited evidence surrounding tools and techniques applied outside of the clinical research community. The goal of the present study is to extend the automation knowledge base by synthesizing current trends in the application of extraction technologies of key data elements of interest for social scientists.\n\nMethods We report the baseline results of a living systematic review of automated data extraction techniques supporting systematic reviews and meta-analyses in the social sciences. This review follows PRISMA standards for reporting systematic reviews.\n\nResults The baseline review of social science research yielded 23 relevant studies.\n\nConclusions When considering the process of automating systematic review and meta-analysis information extraction, social science research falls short as compared to clinical research that focuses on automatic processing of information related to the PICO framework. With a few exceptions, most tools were either in the infancy stage and not accessible to applied researchers, were domain specific, or required substantial manual coding of articles before automation could occur. Additionally, few solutions considered extraction of data from tables which is where key data elements reside that social and behavioral scientists analyze.", "keywords": [ "Automated data extraction", "systematic review", "meta-analysis", "evidence synthesis", "social science research", "APA Journal Article Reporting Standards (JARS)" ], "content": "Introduction\n\nAcross disciplines, systematic reviews and meta-analyses are integral to exploring and explaining phenomena, discovering causal inferences, and supporting evidence-based decision making. The concept of metascience represents an array of evidence synthesis approaches which support combining existing research results to summarize what is known about a specific topic (Davis et al., 2014; Gough et al., 2020). Researchers use a variety of systematic review methodologies to synthesize evidence within their domains or to integrate extant knowledge bases spanning multiple disciplines and contexts. When engaging in quantitative evidence synthesis, researchers often supplement the systematic review with meta-analysis (a principled statistical process for grouping and summarizing quantitative information reported across studies within a research domain). As technology advances, in addition to greater access to data, researchers are presented with new forms and sources of data to support evidence synthesis (Bosco et al., 2017; Ip et al., 2012; Wagner et al., 2022).\n\nSystematic reviews and meta-analyses are fundamental to supporting reproducibility and generalizability of research surrounding social and cultural aspects of human behavior, however, the process of extracting data from primary research is a labor-intensive effort, fraught with the potential for human error (see Pigott & Polanin, 2020; Yu et al., 2018). Comprehensive data extraction activities associated with evidence synthesis have been described as time-consuming to the point of critically limiting the usefulness of existing approaches (Holub et al., 2021). Moreover, research indicates that it can take several years for original studies to be included in a new review due to the rapid pace of new evidence generation (Jonnalagadda et al., 2015).\n\nIn the clinical research domain, particularly in Randomized Control Trials (RCTs), automation technologies for data extraction are evolving rapidly (see Schmidt et al., 2023). In contrast with the more defined standards that have evolved throughout clinical research domains, within and across social sciences, substantial variation exists in research designs, reporting protocols, and even publication outlet standards (Davis et al., 2014; Short et al., 2018; Wagner et al., 2022). In health intervention research, targeted data elements generally include Population (or Problem), Intervention, Control, and Outcome (i.e., PICO; see Eriksen and Frandsen, 2018; Tsafnat et al., 2014). While experimental designs are considered a gold-standard for translational value, many phenomena examined across the social sciences occur within contexts which necessitate research pragmatism in both design and methodological considerations (Davis et al., 2014).\n\nConsider, for example, the field of Human Resource Development (HRD). In HRD, a primary focal hub for research includes outcomes of workplace interventions intended to inform and improve areas such as learning, training, organizational development, and performance improvement (Shirmohammadi et al., 2021). While measuring intervention outcomes is a substantial area of discourse, HRD researchers have predominantly relied on cross-sectional survey data and the most commonly employed quantitative method is Structural Equation Modeling (Park et al., 2021). Thus, meta-analyses are increasingly essential for supporting reproducibility and generalizability of research. In these fields, data elements targeted for extraction would rarely align with the PICO framework, but rather, meta-analytic endeavors would entail extraction of measures such as effect sizes, model fit indices, or instrument psychometric properties (Appelbaum et al., 2018).\n\nServing as a model for the present study, Schmidt et al. (2023) are conducting a living systematic review (LSR) of tools and techniques available for (semi)automated extraction of data elements pertinent to synthesizing the effects of healthcare interventions (see Higgins et al., 2022). Exploring a range of data-mining and text classification methods for systematic reviews, the authors uncovered that early often employed approaches (e.g., rule-based extraction) gave way to classical machine-learning (e.g., naïve Bayes and support vector machine classifiers), and more recently, trends indicate increased application of deep learning architectures such as neural networks and word embeddings (for yearly trends in reported systems architectures, see Schmidt et al., 2021, p. 8).\n\nIn social sciences and related disciplines, several related reviews of tools and techniques for automating tasks associated with systematic reviews and meta-analyses have been conducted. Table 1 provides a summary of related research.\n\nBased on extant reviews analyzing trends in Artificial Intelligence (AI) technologies for automating Systematic Literature Review (SLR) efforts outside of clinical domains, we noted several trends. First, techniques to facilitate abstraction, generalization, and grouping of primary studies represent the majority of (semi)automated approaches. Second, extant reviews highlight a predominant focus on supporting search and study selection stages, with significant gaps in (semi)automating data extraction. Third, evaluation concerns underscore the importance of performance metrics, validation procedures, benchmark datasets and improved transparency and reporting standards to ensure the reliability and effectiveness of AI techniques. Finally, challenges in cross-discipline transferability illuminate the need for domain-specific adaptations and infrastructures.\n\nExisting reviews evidence the widespread application of techniques such as topic modeling, clustering, and classification to support abstraction, generalization, and grouping of primary research studies. Topic modeling, particularly Latent Dirichlet Allocation (LDA), is commonly applied to (semi)automate content analysis, facilitating the distillation of complex information into meaningful insights and identification of overarching trends and patterns across a literature corpus (Antons et al., 2020; Dridi et al., 2021; Roldan-Baluis et al., 2022; Yang et al., 2023). Additionally, classification and clustering techniques are commonly applied for tasks such as mining article metadata and automatically grouping papers by relevance to SLR research questions are (Feng et al., 2017; Sundaram & Berleant, 2023; Wagner et al., 2022).\n\n(Semi)automation efforts in social sciences and related disciplines have primarily addressed supporting the search and study selection stages of SLRs (Cairo et al., 2019; Feng et al., 2017), with significant gaps in automation techniques for tasks such as data extraction (Göpfert et al., 2022; Sundaram & Berleant, 2023). Further, available software tools lack functionality to support activities beyond study selection (Kohl et al., 2018). Key findings across these reviews underscore the need for more comprehensive automation solutions, particularly for quantitative data extraction (Göpfert et al., 2022).\n\nAdditionally, researchers express transparency concerns regarding AI’s reliance on black box models (Wagner et al., 2022) and limited visibility into underlying processes and algorithms in proprietary software solutions (Antons et al., 2020). Adding to these considerations, Antons et al. (2020) identified substantial reporting gaps, including 35 of 140 articles omitting details about software used. Since metrics alone may not be sufficient to objectively assess AI performance (Dridi et al., 2021), strategies for mitigating bias and ensuring transparency and fairness represent a substantial topic of automation discourse.\n\nOngoing research of AI tools for clinical studies (Sundaram & Berleant, 2023) and the extraction of PICO data elements from RCTs (Wagner et al., 2022) underscore the success of domain-specific adaptation efforts. While the promise of adopting AI-based techniques and tools in social science domains is evident (Cairo et al., 2019; Feng et al., 2017), extant research reveals challenges in transferring existing technologies across disciplines. Further, many SLR software applications are tailored specifically for health and medical science research (Kohl et al., 2018). Literature suggests that overcoming global obstacles can be facilitated by concentrated efforts to develop domain-specific knowledge representations, such as standardized construct taxonomies and vocabularies (Feng et al., 2017; Göpfert et al., 2022; Wagner et al., 2022).\n\nIn the present study, we conduct a baseline review of existing and emergent techniques for the (semi)automated data extraction which focus on target data entities and elements relevant to evidence synthesis across social sciences research domains. We report findings that supplement the growing body of research dedicated to the automatic extraction of data from clinical and medical research.\n\n\nMethods\n\nThis LSR was conducted following a pre-registered and published protocol (Legate & Nimon, 2023b). For additional details and project repositories, see ‘Data availability’ section.\n\nWe adopted the LSR methodology for this study primarily due to the pace of emerging evidence, particularly in light of ongoing technological advancements. The ongoing nature of an LSR allows for continuous surveillance, ensuring timely presentation of new information that may influence findings (Elliott et al., 2014, 2017; Khamis et al., 2019). This baseline review was initiated upon peer approval of the associated protocol (Legate & Nimon, 2023b). It remains our intent for the review to be continually updated via living methodological surveys of published research (Khamis et al., 2019) following the workflow schedule as previously published in the protocol (see Figure 1; Legate & Nimon, 2023b). Necessary adjustments to the workflow will be detailed within each subsequent update.\n\nThis image is reproduced under the terms of a Creative Commons Attribution 4.0 International license (CC-BY 4.0) from Legate and Nimon (2023b).\n\nNote. Arrows represent stages involved in a static systematic review; the dotted line (from “Publish Report” to “Search”) represents the stage at which the review process is repeated from the beginning while the review remains in living status.\n\nAs in prior reviews, English language reports, published 2005 or later were considered for inclusion (Jonnalagadda et al., 2015; O’Mara-Eves et al., 2015; Schmidt et al., 2020). Eligible studies utilized, presented, and/or evaluated semi-automated approaches to support evidence-synthesis research methods (e.g., systematic reviews, psychometric meta-analyses, meta-analyses of effect sizes, etc.). Studies may have reported on any automated approach to data extraction, given that at least one entity was extracted semi-automatically from the abstracts or full-text of a literature corpus and sufficient detail was reported for:\n\na) entity(ies) or data element(s) extracted;\n\nb) location of the extracted entities (e.g., abstract, methods, results sections); and\n\nc) the automation tool and/or technique used to support extraction.\n\nWe excluded studies labeled as editorials, briefs, or opinion pieces and/or engaged in narrative discussion without applying automation tools or technologies to extract data from research literature. Per the protocol, we also excluded studies that applied tools/techniques to:\n\na) extract data exclusively from medical, biomedical, clinical (e.g., RCTs), or natural science research;\n\nb) extract metadata only (i.e., citation details) from research articles; or\n\nc) extract data from alternative (i.e., non-research literature) sources (e.g., web scraping, electronic communications, transcripts, etc.).\n\nThe search strategy for this review was developed by adapting the search strategy from a related LSR of clinical research (Schmidt et al., 2020). We initially intended to conduct searches in the same databases used by Schmidt et al. (2020, 2021), excluding medical research sources. Because IEEE content is indexed in Web of Science (Young, 2023), we did not include IEEE Xplore as a separate source. We added two additional databases (ACL and ArXiv) and conducted a search for data extraction tools in the Systematic Review Toolbox (Marshall et al., 2022) to capture associated articles. Our final source list of sources for this baseline review included: (1) ACL, (2) ArXiv, (3) DBLP Computer Science Bibliography, (4) Web of Science Core Collection, and (5) SR Toolbox. The Web of Science search and deduplication followed procedures stated in the protocol (Legate & Nimon, 2023b). We adapted source code developed by Schmidt et al. (2021) for automating search, retrieval, and deduplication functions on full database dumps for ACL, ArXiv, and DBLP platforms. Search syntax and adapted source code are available in the project repository (see ‘Data availability’ section).\n\nTitle, abstract, and full-text screening was conducted using Rayyan (Ouzzani et al., 2016; free and subscription accounts available at https://www.rayyan.ai/). Three researchers (1000 abstracts per week) screened all titles and abstracts. Researchers met weekly to review, resolve conflicts, and further develop the codebook for this LSR. All conflicts that arose during the title and abstract screening (n=103/N=10,644) were resolved on a weekly basis. Where disagreements arose, they were related to methods for abstractive text summarization and transferability of methods applied to clinical research studies (i.e., RCTs). In cases where level of abstraction and potential for transferability could not be determined from the abstract alone, full text articles were reviewed and discussed by all three researchers until consensus was reached.\n\nFor the data extraction stage, a Google form was developed following items of interest as described in the protocol. All data extraction tasks were performed independently in triplicate. Researchers met weekly to review and reach a consensus on coding of extracted items of interest. The extraction form was updated over the course of data extraction to better fit project goals and promote reliability of future updates.\n\nWe originally intended to conduct Inter-Rater Reliability (IRR) assessments to provide reliability estimates following each stage of the baseline review (Belur et al., 2018; Zhao et al., 2022). Given the nascency of our research and scope of our items of interest, coding forms allowed for input of “other” responses (e.g., APA data elements) that were not included in extant reviews that focus on medical and clinical data extraction (e.g., PICO elements). Further, data extraction presented opportunities to develop reporting structure for methods and items of interest that were not reported in prior literature (e.g., NER, open-source tools). A weekly review meeting was used to continually develop the project codebook to promote continuity, structure, and develop an IRR framework for future iterations of this review.\n\n\nResults\n\nSearch results are presented in the PRISMA flowchart (see Figure 2). A total of 11,336 records were identified through all search sources, including databases and publications available through the SRToolbox (Marshall et al., 2022). After deduplication, 10,644 articles were included in the title and abstract screening stage. We retrieved 46 articles for full-text screening. One duplicate print was detected during full text screening and was removed. This iteration of the LSR includes 23 articles. Detailed description of deduplication and preliminary screening procedures are available in the OSF project repository (see ‘Data availability’ section).\n\nNote. ACL=ACL Anthology (https://aclanthology.org/), arXiv=arXiv Research-Sharing Platform (https://arxiv.org/), DBLP=DBLP Computer Science Bibliography (https://dblp.org/), WOS=Web of Science Core Collection, SRTool=Systematic Review Toolbox (http://systematicreviewtools.com/).\n\nThe following sections describe the rationale for exclusions, followed by a brief overview of studies included in the baseline review. These results are presented in Figures 3 and 4, respectively. An overview of included studies is presented in Table 2.\n\nNote. Domain = exclusively medical, biomedical, clinical, or natural science (n=2); Target entities = Lack of detail in reporting extracted entities (n=7); Application = no application, testing, or extraction conducted manually (n=6); Lack of Detail in Reporting Corpus or Wrong Corpus (n=7).\n\nNote. Presented Tool = Describe/demonstrated a software tool, system, or application for data extraction (n=12), Developed Method = Developed techniques and/or methods for automated data extraction (n=9); Evaluated Techniques = Tested or evaluated the performance of existing tools, techniques, or methods (n=2); Applied Tool = Applied automation tools to conduct secondary research (n=0).\n\nMost studies were excluded due to lack of detail in extracted data entities (n=7) and wrong corpus or data source (n=7). Carrión-Toro et al. (2022), for example, developed a method and software tool supporting researchers with selection of relevant key criteria in a field of study based on term frequencies. While text summarization has proven valuable for evidence synthesis tasks, the primary focus of this LSR involves efforts to extract specific data points from primary research (O’Connor et al., 2019). We also excluded extraction techniques that were not applied to abstracts or full text of research articles. Ochoa-Hernández et al. (2018), for instance, presented a method to automatically extract concepts from web blog articles.\n\nThe second most common exclusion category were articles that presented techniques or systems utilizing pre-extracted data (n=4). Ali and Gravino (2018), for example, proposed an ontology-based SLR system with semantic web technologies; however, the data (derived from a prior review conducted by the authors) were added to the ontology system after the manual extraction stage. Finally, articles were excluded due to exclusive application in medical/clinical research (n=2), or the proposed tool had not yet been implemented (n=2). Goswami et al. (2019), for example, described and evaluated a supervised ML framework to identify and extract anxiety outcome measures from clinical trial articles. Zhitomirsky-Geffet et al. (2020) presented a conceptual description of a network-based data model capable of mining quantitative results from social sciences articles, but the system had not been implemented at the time of publication.\n\nThe majority of included studies (n=12) presented or described a software tool, system, or application to support researchers extracting data from research literature. The second most common inclusion category focused on the development of specialized techniques or methods for automating data extraction tasks (n=9). We identified two studies that evaluated or tested the performance of existing tools or methods for (semi)automated data extraction. Unlike related reviews of data extraction methods for healthcare interviews (see Schmidt et al., 2023), we did not identify social science studies applying existing automated data extraction tools to conduct secondary research.\n\nTo report approaches identified, we organized the extracted data under four overarching categories, including: (1) data preprocessing and feature engineering, (2) model architectures and components, (3) rule-bases, and (4) evaluation metrics. See ‘Data Availability’ section for labeling and additional descriptions of techniques. We opted to extract and report rule-based techniques separately because the approaches we identified intertwined with various aspects of the data processing and extraction pipeline, spanning data preprocessing to the model architecture itself. This distinction allows for more discussion about the prevalence, scope and utility of these techniques.\n\nThe data preprocessing category encompasses methods and techniques used to preprocess raw text and data before it is fed into ML/NLP models. This includes tasks such as tokenization, stemming, lemmatization, stop word removal, and other steps necessary to clean and prepare the text data for analysis. Figure 5 plots the aggregate results of preprocessing techniques identified.\n\nNearly all studies applied tokenization and/or segmentation (83%, n=19) for breaking down text into manageable units. Similarly, PDF parsing/extraction techniques were applied in 65% (n=15) of studies, the remaining studies applied extraction to other document formats (e.g., journal articles available online in HTML format; see Diaz-Elsayed & Zhang, 2020). While similar methods, which additionally take into account syntactic structure, including chunking and dependency parsing were less frequently applied (Angrosh et al., 2014; Li et al., 2022; Nayak et al., 2021; Pertsas & Constantopoulos, 2018). Tagging methods, including PoS tagging (assigning grammatical categories, e.g., noun, verb), followed by concept tagging (e.g., semantic annotation), or sequence tagging, where labels were assigned based on order of appearance, were used in 43% (n=15) of studies. Nine studies used manual annotation for training and/or evaluation.\n\nAmong noise reduction approaches, stop-word removal was the most common, stemming, normalization, and lemmatization were applied, though less frequently. For stemming approaches, the Porter stemmer (Porter, 1980), including its extensions (e.g., Porter2, S-stemmer, snowball stemmer), were as commonly reported as traditional stemmers (see Aumiller et al., 2020; Bayatmakou et al., 2022; Shahid & Afzal, 2018). Optical Character Recognition (OCR) appeared in three studies, however, Iwatsuki et al. (2017) used OCR only as a benchmark for evaluating their CRF method for detecting math expressions.\n\nFeature engineering (e.g., ranking functions, representation learning and feature extraction techniques) covers a range of methods essential for transforming raw text data into structured, machine-readable representations to facilitate downstream ML/NLP tasks (Kowsari et al., 2019). See Figure 6.\n\nWord embeddings were the most frequently used techniques. We grouped ELMo (word embeddings from language models) with traditional word embeddings such as Word2Vec and Glove (Kowsari et al., 2019; Young et al., 2018, Chapter 6). Of these, GloVe was used in four studies (Chen et al., 2021; Goldfarb-Tarrant et al., 2020; Nowak & Kunstman, 2019; Anisienia et al., 2021) and ELMo in two (Nowak & Kunstman, 2019; Anisienia et al., 2021). The most common frequency-based feature representation approaches were Bag-of-Words (BoW, n=5) and Term frequency-Inverse Document Frequency (TF-IDF, n=4). Although less frequently applied in the corpus, methods for representing words or documents as vectors based on semantic properties such as Vector Space Models (VSM) and sentence embeddings were used as early as 2007. Other less commonly reported methods included synonym aggregation/expansion, best match ranking (BM25), shingling, and subject-verb pairings.\n\nThe model architecture category focuses on the architectures and components of ML/NLP models used for data extraction. Results are shown in Figure 7. Some approaches overlapped across applications – e.g., semantic web or semantic indexing structures and ontology-pipeline approaches – we grouped these techniques into categories to facilitate reporting. Likewise, all transformer-based approaches were grouped into a single category, however, specific architectures and components are discussed in the sections below, and detailed coding of extracted data is available in the supplemental data files (see ‘Underlying Data’ section). Where ruled-based approaches were considered a part of the system architecture, they are reported under the ‘Rule-bases’ section.\n\nOverall, approaches ranged from straightforward implementations to complex layered architectures. Examples of more straightforward approaches included architectures based entirely on rule-bases (e.g., Diaz-Elsayed & Zhang, 2020), applications based one classification method (e.g., naïve Bayes; Neppalli et al., 2016), or those utilizing a single type of probabilistic model (Angrosh et al., 2014; Iwatsuki et al., 2017). At the other end of the complexity continuum, Nowak and Kunstman (2019) presented an end-to-end deep learning model based on a BI-LSTM-CRF architecture with interleaved alternating LSTM layers and highway connections. In the following sections, we further elaborate on various approaches identified.\n\nOntology-based and Semantic Web. These pipelines involve leveraging ontologies and semantic web technologies for semantic annotation or knowledge representation. Among included studies, ontology and semantic web capabilities were explored as early as 2014, but the preliminary results from this baseline review suggest an upward trend in recent years. Angrosh et al. (2014), for example, developed a Sentence Context Ontology (SENTCON) for modeling the contexts of information extracted from research documents. Piroi et al. (2015) developed and presented an annotation system for populating ontologies in domains lacking adequate dictionaries. Some work focused on automatically mapping structures of research documents. For example, using an open source lexical database to develop a canonical model of structure, Aliyu et al. (2018) were able to automatically identify and extract target paper sections from research documents. Shahid and Afzal (2018) utilized specialized ontologies to automatically tag content in research papers by logical sections. Chen et al. (2020) presented a novel framework for text summarization, including ontology-based topic identification and user-focused summarization modules.\n\nTransformer-based Approaches. Our results suggested that transformer-based approaches have experienced rapid growth since 2020. Bidirectional Encoder Representations from Transformers (BERT) and other BERT-based language models made up the majority of transformer-based approaches. Specifically BERT (Aumiller et al., 2020; Shen et al., 2022) and SciBERT (Goldfarb-Tarrant et al., 2020; Li et al., 2022) were the most utilized for tasks relevant to extracting data from research in social sciences. Others language models included BioBERT (Chen et al., 2020) and distilBERT (Goldfarb-Tarrant et al., 2020). We identified a recent application of the Hugging Face LED model (Li et al., 2022), a pre-trained longformer model developed to address length limitations associated with other transformer-based approaches (see Beltagy et al., 2020).\n\nNamed Entity Recognition (NER). Six of the included studies applied Named Entity Recognition (NER) techniques. Increasing availability of tools to support the entire SLR pipeline, including data extraction efforts, may be partially to credit for upward trends in NER applications. Based on applications we identified, NER would best be described as versatile. Some studies incorporated NER as an integral component embedded throughout a larger ML/NLP pipeline (e.g., Goldfarb-Tarrant et al., 2020), others included NER subcomponents leveraged primarily for preprocessing and feature representation tasks (e.g., Pertsas & Constantopoulos, 2018), and in one study, authors took advantage of open source NER tools that could be easily integrated into a highly modifiable artifact serving as platform for future development of holistic approaches to scaling SLR tasks (e.g., Denzler et al., 2021).\n\nExtractive Questing-Answering Models. Extractive questing-answering models involve tasks where a model generates answers to questions based on a given context. Question-answering models appeared in our dataset as early as 2007 (Liu et al., 2007), with the remaining applications published in 2020 or later. Question answering techniques have a range of applications that most readers are likely familiar with, like chatbots and intelligent assistants (e.g., Alexa, Google Assistant, Siri). However, state-of-the-art approaches for question-answering over knowledge bases are also being put to use in the data extraction arena. The study by Bayatmakou et al. (2022), for example, introduced new methods for interactive multi-document text summarization that allow users to specify summary compositions and interactively refine queries after reviewing complete sentences automatically extracted from documents.\n\nClassifiers. For classification approaches, we followed Schmidt et al. (2021) in reporting instances of Support Vector Machines (SVM) separately from other binary classifiers and likewise found a high prevalence of SVM usage, accounting for 50% of all binary classifiers identified (Goldfarb-Tarrant et al., 2020; Shahid & Afzal, 2018; Shen et al., 2022; Zielinski & Mutschke, 2017). Among classifiers that use a linear combination of inputs (Jurafsky & Martin, 2024), naïve Bayes was the most frequent (Neppalli et al., 2016; Shahid & Afzal, 2018; Torres et al., 2012; Zielinski & Mutschke, 2017). One study used a Perceptron classifier; however, it was extended (i.e., OvR) to handle multiclass problems (Aumiller et al., 2020). Multi-class classifiers were less common with one instance each of k-Nearest Neighbors (aka KNN/kLog; Zielinski & Mutschke, 2017) and the J48 classifier (C4.5 Decision Trees; Piroi et al., 2015).\n\nNeural Networks. Overall, there were a variety of neural network applications across the included studies. Most used Long Short-term Memory (LSTM), more specifically, Bidirectional LSTM (BiLSTM). We also identified one application Bidirectional Gated Recurrent Unit (BiGRU; Shen et al., 2022). Convolutional Neural Network (CNN) architectures (Goldfarb-Tarrant et al., 2020; Nowak & Kunstman, 2019; Anisienia et al., 2021) were also present. Several studies evaluated state-of-the-art deep learning methods. For example, Shen et al. (2022) compared the performance of deep learning models (TextCNN and BERT) for sentence classification in social sciences abstracts. In another comparative study, Anisienia et al. (2021) compared methods for pretraining deep contextualized word representations for cutting-edge transfer learning techniques based on CNN and LSTM architectures in addition to classifier models (e.g., SVM).\n\nProbabilistic Models. Among probabilistic models, Conditional Random Field (CRF) applications were predominant in our dataset. CRF was often applied for sequence labeling tasks, such as named entity recognition (e.g., Nayak et al., 2021), or for classification tasks (e.g., Angrosh et al. 2014). Overall, included studies provided evidence that CRF can form a powerful architecture when combined with RNNs (e.g., bi-GRU-CRF, bi-LSTM-CRF; see Nowak & Kunstman, 2019; Shen et al., 2022). We found a single application of the Maximum Entropy Markov Model (MEMM), however, based on experimental results the authors ultimately selected CRF for identifying sentence context for extraction from research publications (Angrosh et al., 2014).\n\nRule-based techniques involve the application of predefined rules or patterns to extract specific features from the text. Versatile and widely applicable, they offer a robust framework for automating data extraction or for capturing relevant information from large volumes of text. See Figure 8 for rule-based approaches reported across included studies.\n\nOverall, 70% (n=16) of included studies utilized rule- or heuristic-based approaches to support a variety of tasks for data extraction. Of these, nearly half (n=7) reported using Regular Expressions (RegEx). For example, based on rules developed from manual inspection, RegEx was used by Torres et al. (2012) to construct patterns for identifying specific types of sentences (e.g., objective, results, conclusions) and by Goldfarb-Tarrant et al. (2020) for splitting papers into specific sections (e.g., abstract, introduction, methods). Alternatively, Pertsas and Constantopoulos (2018) used RegEx to exploit lexico-syntactic patterns derived from an ontology knowledge base (Activities, Goals, and Propositions). Other RegEx uses included modifying datasets to incorporate patterns related to citation mentions (Anisienia et al., 2021) or application of rule-based chunking and processing to identify and extract relevant chunks from text (Nayak et al., 2021). The remaining six studies described custom rule-based algorithms or other heuristic approaches. Li et al. (2022), for example, applied rule-based algorithms PrefixSpan and Gap-Bide for the extraction of frequent discourse sequences. RAKE (Rapid Automatic Keyword Extraction) was applied by Bayatmakou et al. (2022) to extract keywords which served as representations of a document’s content. And Aliyu et al. (2018) described a rule-based algorithm developed for processing full-text documents to identify and extract section headings.\n\nEvaluation metrics are presented in Figure 9. Precision, recall, F-scores, and accuracy were predominantly reported across studies, including the earliest published articles. For assessment of model performance, six studies used cross-validation (CV), a process of “averaging several hold-out estimators of the risk corresponding to different data splits” (Arlot & Celisse, 2010, p. 53). K-fold CV (5 or 10 folds) was predominantly applied (Angrosh et al., 2014; Iwatsuki et al., 2017; Neppalli et al., 2016; Shen et al., 2022, with one application of leave-one-out or LOOCV (Piroi et al.; 2015) and one application of document level CV used as a supplemental technique to k-fold (Neppalli et al., 2016). Five studies provided description of user feedback and other ratings. User feedback (among other metrics) was reported by Li et al. (2022) who conducted expert human comparative assessment to assess fluency, relevance, coherence, and overall quality of model citation span/sentence generation outputs. This category also included evaluation metrics not listed in the sources we adapted when developing our protocol (see O’Mara-Eaves et al., 2015, p. 3, Table 1; Schmidt et al., 2021, pp. 8-9). For example, in assessing their system on values returned for queries of interest, Nayak et al. (2021) reported suitably, adaptability, relevance scores, and data-dependencies. As another example, Denzler et al. (2021, p. 5) evaluated their artifact based on design science aspects (i.e., validity, efficacy, and utility).\n\nGiven the rapid growth of domain-specific ontologies and pre-trained language models, it is not surprising to find Kappa statistics reported for tasks such as evaluating agreement between human annotators when creating gold standard datasets for training and evaluation (Cohen’s Kappa, see Pertsas & Constantopoulos, 2018; Mezzich’s Kappa or Gwet’s AC1, see Anisienia et al., 2021). Semantic similarity scores, which can be used to compare model generated responses against ground truth responses in query-based or question-answering based applications, were reported in two studies (Jaccard Index, Bayatmakou et al., 2022; DKPro Similarity, Zielinski & Mutschke, 2017).\n\nWhile only one study we reviewed presented an existing tool that was accessible to users through an online application (sysrev.com; Bozada et al., 2021) at the time of conducting this baseline review, two other studies were either being prepared or were available through other means. These included the Holistic Modifiable Literature Review tool (Denzler et al., 2021), which was listed as, “currently being prepared” (available at https://holimolirev.github.io/HoliMoLiRev/) and HypothesisReader (Chen et al., 2021), which was available to users through an Rshiny application. SysRev (Bozada et al., 2021) was also the only tool cataloged in the SR Toolbox (Marshall et al., 2022). Six of the twenty-three studies (26%) made source code openly available (Chen et al., 2021; Denzler et al., 2021; Diaz-Elsayed & Zhang, 2020; Goldfarb-Tarrant et al., 2020; Iwatsuki et al., 2017; Li et al. 2022). Article references and corresponding repositories are detailed in Table 3. GitHub stood out as the most popular repository for code and data sharing, and one study made source code available online through an open access publisher.\n\nIn the evolving landscape of systematic reviews and meta-analyses, the adaptability of tools and technologies to new research domains emerged as a critical factor for enhancing research efficiency and scope. The insights provided by many of the authors working towards automation of data extraction illuminate the transferability of various tools and technologies for research targeting the extraction of data elements beyond PICO.\n\nSeveral authors of reviewed studies specifically addressed transferability in describing the development of their tools, and further subjected these tools to rigorous testing aimed at validating transferable capabilities (Chen et al., 2020; Goldfarb-Tarrant et al., 2020; Neppalli et al., 2016). For instance, Neppalli et al. (2016) created MetaSeer.STEM with a focus on extraction of data across a range of research domains, including education, management, and health informatics. Chen et al. (2020) highlighted the adaptability of OATS, showcasing its broader application potential to fields beyond the authors’ COVID-19 specific demonstration. Finally, Goldfarb-Tarrant et al. (2020) affirmed the domain-independent nature of their framework, suggesting its suitability for various systematic reviews.\n\nAdditionally, other studies highlighted the need for transferability and discussed the potential for their research tools and technologies to be extended and adapted across varying domains, stressing the importance of flexible design principles in the development of these tools (Angrosh et al., 2014; Diaz-Elsayed & Zhang, 2020). Angrosh et al. (2014) explained how SENTCON’s preliminary design was applied to a specific set of articles in computer science but emphasized that the tool was flexible enough to be applied to other domains through the use of the Web Ontology Language (OWL). Diaz-Elsayed & Zhang (2020) presented methods that were initially applied to wastewater-based resource recovery, but likewise emphasized that the tool was capable of evaluating other engineered systems and retrieving different types of data than those initially extracted.\n\nAs noted by Chen et al. (2021), while efforts are being made to assist the process of conducting systematic reviews there is often limited generalizability of domain-specific pre-trained language models. Many studies included in our review dedicated discussion points toward addressing the critical issue of generalizability and transferability of tools developed to support the broader research community in (semi)automated data extraction tasks. Collectively, these studies suggest a positive trend toward the development of adaptable, transferable research tools and technologies. However, they also underscore the need for ongoing effort across and between diverse domains to make continued progress toward broader research applications.\n\nAn outcome we did not anticipate was the substantial number of open source tools, toolkits, and frameworks utilized by our relatively small corpus of articles. Because we were unsure what to expect, we made every effort to capture evidence that might prove useful to social science researchers. We identified 50 different open source technologies including platforms, software, software suites, packages/libraries, algorithms, pre-trained models, controlled vocabularies/thesauri, lexical databases, knowledge representations, and more. Open source tools identified are reported in Figure 10. Of the open source resources available to researchers, the overwhelming majority were Python tools (n=16; see Python Package Index, https://pypi.org/) and 8 of 23 (35%) studies used the Python Natural Language Toolkit (NLTK). The full list of open-source tools and license details are available in the OSF repository (see ‘Underlying Data’ section).\n\nThis section discusses potential for extraction of key data elements of interest, as well as locations (i.e., paper sections), structures, and review tasks addressed by the studies reviewed. We limited this section to reporting tools that users could theoretically access and use to support their own research projects. There were 12 studies that presented systems or artifacts designed to facilitate various tasks associated with identifying and extracting data from published literature. To avoid speculating as to the future availability of these tools, we included all studies which presented tools or systems where authors incorporated user interfaces (UIs), regardless of availability at the time of conducting this base review.\n\nTable 4 provides an overview of data elements targeted as outlined by JARS (Appelbaum et al., 2018, p. 6). Each tool was assessed for potential to extract specific data elements by manuscript section (i.e., methods and results reporting elements pertinent to meta-analytic research; see Legate & Nimon, 2023b). Where the authors did not state a tool name, we used the description of the tool as presented in the paper (e.g., Bayatmakou et al., 2022; Nayak et al., 2021).\n\nUnlike ongoing research that focuses on data extraction from clinical literature (e.g., PICO elements/RCTs; see Schmidt et al., 2023), specific reporting guidelines were not a primary focus of the studies we identified. However, authors described target entities and/or research methods of interest with high levels of specificity. For instance, extracting descriptive statistics, sample size, and Likert scale points (Neppalli et al., 2016) and extracting research hypotheses from published literature in organizational sciences (Chen et al., 2021). Despite the lack of discourse surrounding specific reporting guidelines, many of the tools reviewed incorporated some form of user-prompted, annotation- or query-based approach to (semi)automated data extraction. Thus, the collective body of work lends optimism surrounding customizable state-of-the art methods that can support extraction for a wide range of disciplines, research designs, and entities or data elements of interest to social science researchers.\n\nOne example of a highly flexible approach is extractive question-answering based on pre-trained Transformer models. Extractive question-answering models are able to generate direct answers from knowledge base in response to natural language questions posed by users (Kwiatkowski et al. 2019). These tools typically offer enhanced flexibility through user-defined prompts and mechanisms for interactive query refinement. Example tools that incorporated question answering techniques included CIRRA (Piroi et al., 2015), the Interactive Text Summarization System for Scientific Documents (Bayatmakou et al., 2022), and OATS (Chen et al., 2021).\n\nOther types of flexible systems allow users to view excerpts related to specific keywords or queries, supporting expedited identification and labeling of target data elements. For example several tools supported user labeling of data, followed by predictive classification based on user annotations. Although these tools do not automatically extract data for users, they do augment human effort by (semi)automating time consuming tasks associated with data annotation and extraction. For instance, Sysrev (Bozada et al., 2021) supports researchers in labeling and extracting data by leveraging active learning models developed to replicate user decisions across various review tasks. Likewise, MetaSeer (Neppalli et al., 2016) developed ML techniques to identify and extract numbers from documents, which were then presented to users for manual annotation. Unlike question-answering models, human-computer interactions in these examples are not based on natural language queries, however, human expertise can be used to ‘train’ ML models to predict future annotation decisions. Similarly, to overcome the time-constraints of open-ended annotation in fields that lack domain-specific dictionaries, DASyR (Piroi et al., 2015) utilized a combination of user annotations, classification models, and contextual information for populating ontologies. They reported substantial reduction in annotation time, stating that through the DASyR UI “five experts added approximately 30,000 annotations at a speed of 4s/annotation” (p. 595).\n\nLastly, we note the utility of NER for the advancement of (semi)automated extraction of APA defined data elements. NER methodologies can be leveraged alongside classification models (Nayak et al., 2021), linked to domain specific ontologies or other knowledge bases (Piroi et al., 2015), or incorporated as stand-alone modules integrated into larger modifiable frameworks (Denzler et al. 2021). In addition to pre-trained NER models for identification and extraction of named entities, Research Spotlight (Pertsas & Constantopoulos, 2018) also exploited lexico-syntactic patterns in the scholarly ontology to identify and extract non-named entities. The Semi-automatic Data Extraction System for Heterogeneous Data Sources (Nayak et al., 2021) combined features of NER and rule-based chunking to identify and extract phrases on regular expressions as well as named entities contained in the documents. Further, NER can be implemented through open source tools as demonstrated by Denzler et al. (2021) and Nayak et al. (2021).\n\nTable 5 provides an overview of structure and location of extracted data elements, followed by review tasks supported by tools identified. The majority developed approaches for (semi)automating extraction of data from any section of full text research articles. Two studies tested the proposed techniques on specific article sections, including titles and abstracts (Bayatmakou et al., 2022) and introduction and background sections (Li et al., 2022). Regarding structure from which data were extracted, all except one extracted from unstructured text, two extracted from both tabular structures (i.e., tables) and text (Nayak et al., 2021; Pertsas & Constantopoulos, 2018), and one was designed specifically to extract elements from tables (TableSeer; Liu et al., 2007).\n\nAll tools focused heavily on tasks related to data extraction (e.g., identification, labeling/annotation, ontology population), which was anticipated based on our search strategy and inclusion criteria. However, several studies advanced solutions for supporting other SLR tasks or stages (see Tsafnat et al., 2014). The most common task (excluding data extraction) was literature search (Bayatmakou et al., 2022; Bozada et al., 2021; Chen et al., 2020; Denzler et al., 2021; Liu et al., 2007; Pertsas & Constantopoulos, 2018). Many tasks listed are likely supported by a range of computational tools and techniques (e.g., synthesize and meta-analyze results); readers interested in (semi)automating other SLR stages are referred to the Systematic Review Toolbox for an extensive catalogue of tools and methods (Marshall et al., 2022).\n\nThroughout the corpus a number of challenges were presented. These challenges included difficulties in identifying functional structures within unstructured texts (Shen et al., 2022), extracting data from PDF file sources (Nayak et al., 2021; Goldfarb-Tarrant et al., 2020; Iwatsuki et al., 2017), and accurately detecting in-line mathematical expressions (Iwatsuki et al., 2017). Computational complexity created another significant obstacle for researchers, with issues arising from text vectorization methods, optimization problems, and the computational resources required by neural network frameworks (Bayatmakou et al., 2022; Anisienia et al., 2021). Furthermore, challenges associated with annotation, particularly biases introduced through the automated processes and limitations of available datasets, were a topic of discourse (Li et al., 2022; Nowak & Kunstman, 2019; Torres et al., 2012).\n\nCompared to the medical field, domain-specific challenges, particularly those in social sciences and related fields, necessitated tailored approaches, which can become time-consuming as researchers often lack sufficient training data to develop robust classifiers (Chen et al., 2021; Aumiller et al., 2020; Zielinski & Mutschke, 2017). Additionally, meta-analytic methods often face hurdles related to data representation variability, which has significant limitations in the use of data extraction tools, and class imbalance in the development of classification tasks (Aumiller et al., 2020; Neppalli et al., 2016; Goldfarb-Tarrant et al., 2020).\n\n\nConclusions\n\nThe findings of the baseline review indicate that when considering the process of automating systematic review and meta-analysis information extraction, social science research falls short as compared to clinical research that focuses on automatic processing of information related to the PICO framework (i.e., Population, Intervention, Control, and Outcome; Eriksenand Frandsen, 2018; Tsafnat et al., 2014). For example, while an LSR focusing on clinical research that is based on the PICO framework yielded 53 studies that included original data extraction (Schmidt et al., 2021), the present review of social science research yielded only 23 relevant studies. This is not necessarily surprising when considering the breadth of social science research and the lack of unifying frameworks and domain specific ontologies (Göpfert et al., 2022; Wagner et al., 2022).\n\nWith a few exceptions, most tools we identified were either in the infancy stage and not accessible to applied researchers, were domain specific, or require substantial manual coding of articles before automation can occur. Additionally, few solutions considered extraction of data from tables, which is where many elements (e.g., effect sizes) reside that social and behavioral scientists analyze. Further, development appears to have ceased for many of the tools identified.\n\nWe found no evidence indicating hesitation on the part of social science researchers to adopt data extraction tools, on the contrary, abstractive text summarization approaches continue to gain traction across social science domains (Cairo et al., 2019; Feng et al., 2017). While these methods aid researchers in distilling complex information into meaningful insights, there remains a gap in technologies developed to augment human capabilities in the extraction of key data entities of interest for secondary data collection from quantitative empirical reports.\n\nThe impact of time-intensive research activities on translational value is not a new concern for the SLR research community. In many social sciences, emphasis is often placed on practical application and translational value, underscoring the importance of efficient research methodologies (Githens, 2015). Further development of the identified systems and techniques could mitigate time delays that often result in outdated information as researchers cannot feasibly include all new evidence that may be released throughout the lifetime of a given project (Marshall & Wallace, 2019).\n\nAs with any method that involves subjectivity, results can be influenced by a variety of factors (e.g., study design, publication bias, researcher judgment, etc.). We worked diligently to conduct this review and document our procedures in a systematic and transparent manner; however, efforts to replicate our search strategy or screening processes may not result in the same corpus or reach the same conclusions (Belur et al., 2018). This baseline review presented an opportunity to better develop our search and screening strategy, methodological procedures, and research goals. Moving forward, we have developed a codebook and assessment procedures to increase the transparency and reliability of our research.\n\nA second limitation of this study was the omission of snowballing as a search strategy. Though we did not uncover applied secondary research articles utilizing automation tools, several potentially useable tools and systems were discovered in the course of this review. For future iterations of this LSR, we plan to incorporate forward snowballing from relevant articles in previous searches as part of our formalized search strategy (see Wohlin et al., 2022).\n\nFinally, in this baseline review, we did not capture techniques used for optimization, training, or fine-tuning on specific datasets or tasks. Several techniques surfaced while conducting this review, such as class modifiers (e.g., OvR; Aumiller et al., 2020), genetic algorithms (Bayatmakou et al., 2022; Torres et al. (2012), Adam optimizer (Nowak & Kunstman, 2019); Shen et al., 2022), cross entropy loss (Chen et al., 2020; Li et al., 2022), Universal Language Model Fine-tuning (e.g., ULMFiT; Anisienia et al., 2021), and back-propagation optimizers (Chen et al., 2020; Anisienia et al., 2021). With increasing applications of pre-trained language models that can be fine-tuned for specific applications (Jurafsky & Martin, 2024), inclusion of training and optimization approaches would provide a more comprehensive framework for reporting findings on ML/NLP approaches to data extraction. We plan to supplement future iterations of this review by capturing various optimization and training methods.\n\n\nEthics and consent\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nOSF: (Semi)Automated Approaches to Data Extraction for Systematic Reviews and Meta-Analyses in Social Sciences: A Living Review (Legate & Nimon, 2024). Open Science Framework: https://doi.org/10.17605/OSF.IO/C7NSA (Legate & Nimon, 2024).\n\nThis project contains the following underlying data:\n\n• Baseline Review Underlying Data\n\n○ Baseline Review Results.xlsx\n\n○ Baseline Search Results Folder (a folder containing results by each search source)\n\n○ Open Source Tools.xlsx\n\n• Baseline Review Extended Data\n\n○ Baseline Review Deduplication and Screening.docx\n\n○ Baseline Review Search Strategy.docx\n\n○ Baseline Review PRISMA Checklist.docx\n\n○ LSR Codebook.docx\n\n○ Regex to Boolean Sytnax.xlsx\n\n• Baseline Review Code\n\n○ Adapted code files and results for automated search and screening for ACL, ArXIV, and DBLP full database dumps.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0).\n\nOpen Science Framework: https://doi.org/10.17605/OSF.IO/C7NSA(Legate & Nimon, 2023a).\n\nThis project contains the following extended data:\n\n• Extraction Techniques Revised.docx – categories and descriptions of data extraction techniques, architecture components, and evaluation metrics of interest\n\n• Review Classifications.docx – review tasks and stages of interest\n\n• Target Data Elements.docx – key elements of interest for targeted data elements\n\n• Comprehensive List of Eligible Data Elements.xlsx – comprehensive list of elements with extraction potential per APA JARS\n\n• Search Strategy.docx – search syntax for preliminary search in Web of Science\n\n• APA & Cochrane Data Elements.xlsx – tabled data elements for Cochrane reviews, APA Module C (clinical trials), and APA (all study designs)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0).\n\nThis study follows PRISMA reporting guidelines (Page et al., 2021).\n\nOpen Science Framework: PRISMA checklist for ‘Open Science Framework: (Semi)Automated Approaches to Data Extraction for Systematic Reviews and Meta-Analyses in Social Sciences: A Living Review’. https://doi.org/10.17605/OSF.IO/C7NSA (Legate & Nimon, 2024).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0).\n\n\nReferences\n\nAliyu MB, Iqbal R, James A: The canonical model of structure for data extraction in systematic reviews of scientific research articles. 2018 Fifth International Conference on Social Networks Analysis, Management and Security (SNAMS). IEEE; 2018, October; pp. 264–271. Publisher Full Text\n\nAngrosh MA, Cranefield S, Stanger N: Contextual information retrieval in research articles: Semantic publishing tools for the research community. Semantic Web. 2014; 5(4): 261–293. Publisher Full Text\n\nAnisienia A, Mueller RM, Kupfer A, et al.: Research method classification with deep transfer learning for semi-automatic meta-analysis of information systems papers. Proceedings of the 54th Hawaii International Conference on System Sciences. 2021; pp. 6099–6108. Reference Source\n\nAntons D, Grünwald E, Cichy P, et al.: The application of text mining methods in innovation research: Current state, evolution patterns, and development priorities. R&D Manag. 2020; 50(3): 329–351. Publisher Full Text\n\nAli A, Gravino C: An ontology-based approach to semi-automate systematic literature reviews. 2018 12th International Conference on Open Source Systems and Technologies (ICOSST). IEEE; 2018, December; pp. 09–16. Publisher Full Text\n\nArlot S, Celisse A: A survey of cross-validation procedures for model selection. Stat. Surv. 2010; 4: 40–79. Publisher Full Text\n\nAumiller D, Almasian S, Hausner P, et al.: UniHD@CL-SciSumm 2020: Citation extraction as search. Proceedings of the First Workshop on Scholarly Document Processing. 2020, November; pp. 261–269. Publisher Full Text\n\nAppelbaum M, Cooper H, Kline RB, et al.: Journal Article Reporting Standards for Quantitative Research in Psychology: The APA Publications and Communications Board Task Force report. Am. Psychol. 2018; 73(1): 3–25. PubMed Abstract \| Publisher Full Text\n\nBayatmakou F, Mohebi A, Ahmadi A: An interactive query-based approach for summarizing scientific documents. Inf. Discov. Deliv. 2022; 50(2): 176–191. Publisher Full Text\n\nBelur J, Tompson L, Thornton A, et al.: Interrater reliability in systematic review methodology: Exploring variation in coder decision-making. Sociol. Methods Res. 2018; 50(2): 837–865. Publisher Full Text\n\nBeltagy I, Peters ME, Cohan A: Longformer: The long-document transformer. arXiv, abs/2004.05150. 2020. Publisher Full Text\n\nBosco F, Uggerslev K, Steel P: MetaBUS as a vehicle for facilitating meta-analysis. Hum. Resour. Manag. Rev. 2017; 27(1): 237–254. Publisher Full Text\n\nBozada T Jr, Borden J, Workman J, et al.: Sysrev: A FAIR platform for data curation and systematic evidence review. Front. Artif. Intell. 2021; 4: 1–18. Article 685298. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCairo LS, de Figueiredo Carneiro G , da Silva BC : Adoption of machine learning techniques to perform secondary studies: A systematic mapping study for the computer science field. ICEIS. 2019; 2: 351–356. Publisher Full Text\n\nCarrión-Toro M, Aguilar J, Santórum M, et al.: iKeyCriteria: A qualitative and quantitative analysis method to infer key criteria since a systematic literature review for the computing domain. Data. 2022; 7(6): 70. Publisher Full Text\n\nChen PHA, Leibrand A, Vasko J, et al.: Ontology-based and user-focused automatic text summarization (OATS): Using COVID-19 risk factors as an example. arXiv preprint arXiv:2012.02028. 2020. Publisher Full Text\n\nChen VZ, Montano-Campos F, Zadrozny W, et al.: Machine reading of hypotheses for organizational research reviews and pre-trained models via R Shiny app for non-programmers.2021. Publisher Full Text Reference Source\n\nDavis J, Mengersen K, Bennett S, et al.: Viewing systematic reviews and meta-analysis in social research through different lenses. Springerplus. 2014; 3(1): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDenzler T, Enders MR, Akello P: Towards a semi-automated approach for systematic literature reviews. Twenty-Seventh Americas Conference on Information Systems (AMCIS). 2021; Vol. 4: pp. 1–10. Reference Source\n\nDiaz-Elsayed N, Zhang Q: Extracting the characteristics of Life Cycle Assessments via data mining. MethodsX. 2020; 7(101004): 1–6. Publisher Full Text\n\nDridi A, Gaber MM, Azad RMA, et al.: Scholarly data mining: A systematic review of its applications. Wiley Interdiscip. Rev.: Data Min. Knowl. Discov. 2021; 11(2): 1–23. Publisher Full Text\n\nElliott J, Turner T, Clavisi O, et al.: Living systematic reviews: An emerging opportunity to narrow the evidence-practice gap. PLoS Med. 2014; 11(2): E1001603. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElliott J, Synnot A, Turner T, et al.: Living systematic review: 1. Introduction—the why, what, when, and how. J. Clin. Epidemiol. 2017; 91: 23–30. PubMed Abstract \| Publisher Full Text\n\nEriksen MB, Frandsen TF: The impact of patient, intervention, comparison, outcome (PICO) as a search strategy tool on literature search quality: a systematic review. J. Med. Libr. Assoc. 2018; 106(4): 420–431. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeng L, Chiam YK, Lo SK: Text-mining techniques and tools for systematic literature reviews: A systematic literature review. 2017 24th Asia-Pacific Software Engineering Conference (APSEC) 2017, December; pp. 41–50. Publisher Full Text\n\nGithens RP: Critical action research in human resource development. Hum. Resour. Dev. Rev. 2015; 14(2): 185–204. Publisher Full Text\n\nGoldfarb-Tarrant S, Robertson A, Lazic J, et al.: Scaling systematic literature reviews with machine learning pipelines. arXiv preprint arXiv:2010.04665. 2020. Publisher Full Text\n\nGöpfert J, Kuckertz P, Weinand J, et al.: Measurement extraction with natural language processing: A review. Findings of the Association for Computational Linguistics: EMNLP 2022. 2022; 2191–2215. Publisher Full Text\n\nGoswami S, Pal S, Goldsworthy S, et al.: An effective machine learning framework for data elements extraction from the literature of anxiety outcome measures to build systematic review.Abramowicz W, Corchuelo R, editors. Business Information Systems. BIS 2019. Lecture Notes in Business Information Processing. Vol. 353. . Cham: Springer; 2019; pp. 265–277. Publisher Full Text\n\nGough D, Davies P, Jamtvedt G, et al.: Evidence Synthesis International (ESI): Position statement. Syst. Rev. 2020; 9(1): 155. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHiggins JPT, Thomas J, Chandler J, et al.: Cochrane Handbook for Systematic Reviews of Interventions version 6.3 (updated February 2022). Cochrane; 2022; 2022. Reference Source\n\nHolub K, Hardy N, Kallmes K: Toward automated data extraction according to tabular data structure: Cross-sectional pilot survey of the comparative clinical literature. JMIR Form. Res. 2021; 5(11): E33124. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIp S, Hadar N, Keefe S, et al.: A web-based archive of systematic review data. Syst. Rev. 2012; 1(1): 15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIwatsuki K, Sagara T, Hara T, et al.: Detecting in-line mathematical expressions in scientific documents. Proceedings of the 2017 ACM Symposium on Document Engineering. 2017, August; pp. 141–144. Publisher Full Text\n\nJonnalagadda S, Goyal P, Huffman M: Automating data extraction in systematic reviews: A systematic review. Syst. Rev. 2015; 4(1): 78. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJurafsky D, Martin JH: Speech and language processing [Feb 2024 release].2024. Reference Source\n\nKhamis A, Kahale L, Pardo-Hernandez H, et al.: Methods of conduct and reporting of living systematic reviews: A protocol for a living methodological survey [version 1; peer review: 2 approved]. F1000 Res. 2019; 8: 221. Publisher Full Text\n\nKohl C, McIntosh EJ, Unger S, et al.: Online tools supporting the conduct and reporting of systematic reviews and systematic maps: A case study on CADIMA and review of existing tools. Environ. Evid. 2018; 7(1): 1–17. Publisher Full Text\n\nKowsari K, Meimandi K, Heidarysafa M, et al.: Text classification algorithms: A survey. arXiv, abs/1904.08067. 2019. Publisher Full Text\n\nKwiatkowski T, Palomaki J, Redfield O, et al.: Natural questions: A benchmark for question answering research. Trans. Assoc. Comput. Linguist. 2019; 7: 453–466. Publisher Full Text\n\nLegate A, Nimon K: Updated supplemental files: (Semi)automated approaches to data extraction for systematic reviews and meta-analyses in social sciences: A living review protocol.2023a, January 12. Publisher Full Text\n\nLegate A, Nimon K: (Semi)automated approaches to data extraction for systematic reviews and meta-analyses in social sciences: A living review protocol [version 2; peer review: 2 approved, 1 approved with reservations]. F1000Res. 2023b; 11: 1036. Publisher Full Text\n\nLegate A, Nimon K: (Semi) Automated Approaches to Data Extraction for Systematic Reviews and Meta-Analyses in Social Sciences: A Living Review. [Dataset]. OSF. 2024, May 5. Publisher Full Text\n\nLi X, Mandal B, Ouyang J: CORWA: A citation-oriented related work annotation dataset. arXiv preprint arXiv:2205.03512. 2022. Publisher Full Text\n\nLiu Y, Bai K, Mitra P, et al.: Searching for tables in digital documents. Ninth International Conference on Document Analysis and Recognition (ICDAR 2007). IEEE; 2007, September; Vol. 2: pp. 934–938. Publisher Full Text\n\nMarshall C, Sutton A, O’Keefe H, et al., editors. The Systematic Review Toolbox.2022. Reference Source\n\nMarshall I, Wallace B: Toward systematic review automation: A practical guide to using machine learning tools in research synthesis. Syst. Rev. 2019; 8(1): 110–163. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcGuinness LA, Schmidt L: mcguinlu/COVID_suicide_living: Initial Release (v1.0.0). [Data set]. Zenodo. 2020. Publisher Full Text\n\nNayak R, Balasubramaniam T, Kutty S, et al.: A Semi-automatic Data Extraction System for Heterogeneous Data Sources: A Case Study from Cotton Industry. Data Mining: 19th Australasian Conference on Data Mining, AusDM 2021. Singapore: Springer; 2021, December; pp. 209–222. Publisher Full Text\n\nNeppalli K, Caragea C, Mayes R, et al.: MetaSeer. STEM: Towards automating meta-analyses. Proc. AAAI Conf. Artif. Intell. 2016, February; 30(2): 4035–4040. Publisher Full Text\n\nNowak A, Kunstman P: Team EP at TAC 2018: Automating data extraction in systematic reviews of environmental agents. arXiv preprint arXiv:1901.02081. 2019. Publisher Full Text\n\nOchoa-Hernández JL, Barcelo-Valenzuela M, Sanchez-Smitz G, et al.: Concept identification from single-documents.Valencia-García R, Alcaraz-Mármol G, Del Cioppo-Morstadt J , et al., editors. Technologies and Innovation. CITI 2018. Communications in Computer and Information Science. Vol. 883. . Cham: Springer; 2018; pp. 141–152. Publisher Full Text\n\nO’Connor A, Tsafnat G, Thomas J, et al.: A question of trust: Can we build an evidence base to gain trust in systematic review automation technologies? Syst. Rev. 2019; 8(1): 143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nO’Mara-Eves A, Thomas J, McNaught J, et al.: Using text mining for study identification in systematic reviews: A systematic review of current approaches. Syst. Rev. 2015; 4(1): 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOuzzani M, Hammady H, Fedorowicz Z, et al.: Rayyan-a web and mobile app for systematic reviews. Syst. Rev. 2016; 5(1): 210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPage M, McKenzie J, Bossuyt P, et al.: The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. J. Clin. Epidemiol. 2021; 88: 105189–105906. PubMed Abstract \| Publisher Full Text\n\nPark JJ, Kim Y, Han H: Research method trends in the field of human resource development [Refereed Extended Abstract]. 2021 AHRD Virtual Conference. 2021, February 17-19. Reference Source\n\nPertsas V, Constantopoulos P: Ontology-driven information extraction from research publications.Aalberg T, Papatheodorou C, Dobreva M, et al., editors. Digital Libraries for Open Knowledge: 22nd International Conference on Theory and Practice of Digital Libraries, (TPDL 2018). Springer International Publishing; 2018; pp. 241–253. Publisher Full Text\n\nPigott T, Polanin J: Methodological guidance paper: High-quality meta-analysis in a systematic review. Rev. Educ. Res. 2020; 90(1): 24–46. Publisher Full Text\n\nPiroi F, Lipani A, Lupu M, et al.: DASyR (IR)-document analysis system for systematic reviews (in Information Retrieval). 2015 13th International Conference on Document Analysis and Recognition (ICDAR). IEEE; 2015, August; pp. 591–595. Publisher Full Text\n\nPorter MF: An algorithm for suffix stripping. Program: Electronic Library and Information Systems. 1980; 14(3): 130–137. Publisher Full Text\n\nRoldan-Baluis WL, Zapata NA, Vasquez MSM: The effect of natural language processing on the analysis of unstructured text: A systematic review. Int. J. Adv. Comput. Sci. Appl. 2022; 13(5): 43–51. Publisher Full Text\n\nSchmidt L, Olorisade BK, McGuinness LA, et al.: Data extraction methods for systematic review (semi)automation: A living systematic review [version 1; peer review: 3 approved]. F1000Res. 2021; 10: 401. Publisher Full Text\n\nSchmidt L, Olorisade BK, McGuinness LA, et al.: Data extraction methods for systematic review (semi)automation: A living review protocol (Version 2; peer review: 2 approved). F1000Res. 2020; 9: 210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmidt L, Finnerty Mutlu AN, Elmore R, et al.: Data extraction methods for systematic review (semi)automation: Update of a living systematic review (Version 2; peer review: 3 approved). F1000Res. 2023; 10: 401. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShahid A, Afzal MT: Section-wise indexing and retrieval of research articles. Clust. Comput. 2018; 21(1): 481–492. Publisher Full Text\n\nShen S, Jiang C, Hu H, et al.: A model for the identification of the functional structures of unstructured abstracts in the social sciences. Electron. Libr. 2022; 40(6): 680–697. Publisher Full Text\n\nShirmohammadi M, Mehdiabadi A, Beigi M, et al.: Mapping human resource development: Visualizing the past, bridging the gaps, and moving toward the future. Hum. Resour. Dev. Q. 2021; 32(2): 197–224. Publisher Full Text\n\nSundaram G, Berleant D: Automating systematic literature reviews with natural language processing and text mining: A systematic literature review. Eighth International Congress on Information and Communication Technology (ICICT). Singapore: Springer; 2023; pp. 73–92. Publisher Full Text\n\nShort JC, McKenny AF, Reid, et al.: More than words? Computer-aided text analysis in organizational behavior and psychology research. Annu. Rev. Organ. Psych. Organ. Behav. 2018; 5(1): 415–435. Publisher Full Text\n\nTorres JAS, Cruzes DS, do Nascimento Salvador L : Automatic results identification in software engineering papers. Is it possible? 2012 12th International Conference on Computational Science and Its Applications. IEEE; 2012, June; pp. 108–112. Publisher Full Text\n\nTsafnat G, Glasziou P, Choong M, et al.: Systematic review automation technologies. Syst. Rev. 2014; 3(1): 74. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWagner G, Lukyanenko R, Paré G: Artificial intelligence and the conduct of literature reviews. J. Inf. Technol. 2022; 37(2): 209–226. Publisher Full Text\n\nWohlin C, Kalinowski M, Felizardo KR, et al.: Successful combination of database search and snowballing for identification of primary studies in systematic literature studies. Inf. Softw. Technol. 2022; 147: 106908. Publisher Full Text\n\nYu Z, Kraft N, Menzies T: Finding better active learners for faster literature reviews. Empir. Softw. Eng. 2018; 23(6): 3161–3186. Publisher Full Text\n\nYang J, Kinshuk, An Y: A survey of the literature: how scholars use text mining in Educational Studies? Educ. Inf. Technol. 2023; 28(2): 2071–2090. Publisher Full Text\n\nYoung S: Abstract and Index and Web Discovery Services IEEE Partners. IEEE Xplore; 2023, January. Reference Source\n\nYoung T, Hazarika D, Poria S, et al.: Recent trends in deep learning based natural language processing.2018. Reference Source\n\nZhao X, Feng GC, Ao SH, et al.: Interrater reliability estimators tested against true interrater reliabilities. BMC Med. Res. Methodol. 2022; 22: 232. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhitomirsky-Geffet M, Bergman O, Hilel S: Towards a wider perspective in the social sciences using a network of variables based on thousands of results. Scientometrics. 2020; 123: 1385–1406. Publisher Full Text\n\nZielinski A, Mutschke P: Mining social science publications for survey variables. Proceedings of the Second Workshop on NLP and Computational Social Science. 2017, August; pp. 47–52. Publisher Full Text" }	[ { "id": "298396", "date": "16 Jul 2024", "name": "Fred Oswald", "expertise": [], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this paper is an excellent review of automated data-extraction methods for the purposes of synthetic reviews and meta-analysis. To my knowledge, there is no such review in the literature, and yet given the rise in AI-based technologies, there is a rising need for researchers to have a single resource identifying these extraction methods. This review nicely summarizes the types of tools that are out there, but it might further tie the tools more closely to a checklist that reflects must be typically must be accomplished when conducting meta-analysis (e.g., identifying literature, extracting sample sizes and effect sizes, converting effect sizes when necessary, coding effect sizes into variables, associated moderators, associated reliability coefficients, dealing with missing data). This would give the reader a better sense of what* gets automated and serves their purposes (e.g., you can take the ‘model architectures and components’ section and populate the checklist/framework with these AI tools/functions) . Also, though it is certainly useful to document when and how humans are compared to automated systems, the level of accuracy reported (e.g., errors of commission and omission by automated systems) would be useful as well (i.e., are these automated systems any good? when systems agree with humans, when are they agreeing in an accurate way vs. a biased way?)\nThank you for the opportunity to review – again, this will be a valuable paper to readers.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [ { "c_id": "12499", "date": "26 Sep 2024", "name": "Amanda Legate", "role": "Author Response", "response": "Comment 1 Also, though it is certainly useful to document when and how humans are compared to automated systems, the level of accuracy reported (e.g., errors of commission and omission by automated systems) would be useful as well (i.e., are these automated systems any good? when systems agree with humans, when are they agreeing in an accurate way vs. a biased way?) Thank you for the opportunity to review – again, this will be a valuable paper to readers. Comment 1: Response Thank you for this insightful suggestion. We agree that evaluating the accuracy of automated systems compared to human assessments, particularly regarding errors of commission and omission, would provide valuable insights into their effectiveness and potential biases. Understanding when automated systems align with human judgments accurately is indeed crucial for advancing the field. Given the \"living\" nature of our review, we see this as an important focus for future updates. Although additional technical expertise may be required to conduct a comprehensive comparative assessment of these accuracy measures, we hope to expand our team to include experts in areas of data science and AI evaluation. This addition will enhance the rigor of our review and address critical questions surrounding the reliability of automated tools. We appreciate your valuable feedback and are committed to integrating these considerations in future versions of our living review." } ] }, { "id": "298402", "date": "19 Aug 2024", "name": "Biljana Macura", "expertise": [ "Reviewer Expertise Systematic Evidence Synthesis Methodology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 represents an important contribution to the evidence synthesis methodology. Given the rise of AI technology, a living evidence base on approaches to data extraction will be very useful. However, the manuscript could benefit from improved clarity. Below are my comments:\nTitle:\nClarify the type of data being extracted (qualitative, quantitative, or mixed). Since this review does not include any qualitative or quantitative synthesis per se, but rather provides an overview of the field (methods for semi-automated data extraction), I suggest removing \"living systematic review\" and adding \"living systematic map.\"\n\nAbstract:\nThe summary of methods could include more detailed information on searches, screening, critical appraisal, and synthesis. Please specify which standards for review conduct were followed. The summary of results could provide more information (briefly) about the included studies.\n\nKeywords:\nAvoid repeating terms already present in the title\n\nIntroduction:\nThe focus of this review—extraction tools for quantitative data—should be more explicitly stated. This emphasis needs to be clearer in the introduction and reflected in the title, as mentioned earlier. Specifically, the first paragraph of the Introduction should be revised to concentrate on the review topic—quantitative data extraction and existing tools—rather than a general introduction to meta-science or related areas. Additional details are needed on how this review contributes to and complements existing reviews on the topic. This information should be included in the \"Related Research\" section.\n\nObjectives:\nIt would be helpful to define what is included under “social science research domains”.\n\nMethods:\nAuthors should be transparent and explicit about the guidelines and standards for both conduct and reporting that were used. Please clarify this at the beginig of the Methods section. The methods section should begin by addressing any deviations from the protocol. If there were no deviations, this should be clearly stated as well. Did you use any automation technologies to screen or select studies for this review? If yes, please clarify.\n\nMethods/Eligibility criteria:\nThe eligibility criteria should be explicit about the field within which methods for (semi)automated data extraction are applied. A definition of “(semi)automated” is needed. The eligibility criteria currently state that semi-automated approaches will be eligible but then refer to “any automated approach to data extraction” in the next sentence. This needs to be clarified—are the focus and criteria on semi-automated or automated approaches? Be more explicit and precise in the description of the eligibility criteria, and ensure alignment with the protocol. Instead of “We excluded studies labeled as editorials, briefs..” you may write “Editorials, briefs, …were not considered eligible” (and similar changes may be applied to the following sentence)\n\nMethods/Searches\nBe explicit about the citation indices included in your Web of Science subscription and note which library was used to access WoS. This will increase transparency and replicability of your searches. Clarify why following Schmidt et al.'s search strategy was important, given the different scope of this review. Consider including more social science databases to ensure comprehensive coverage. Did you include the Social Science Citation Index (within WoS)? Provide explanations for all abbreviations (IEEE, ACL, etc.) in the text.\n\nMethods/Study selection\nClarify if three researchers simultaneously screened titles and abstracts (TA), and whether inter-rater reliability (IRR) was calculated for TA screening. How you trained reviewers to apply eligibility criteria? The sentence, “In cases where level of abstraction and potential for transferability could not be determined from the abstract alone, full text articles were reviewed and discussed by all three researchers until consensus was reached”, should more clearly state that there was NO full-text screening of all records (if this is correct), only of a sub-sample where abstracts did not clearly describe AI technology, etc.\n\nRelatedly, Figure 1 should be adjusted to avoid giving the false impression that all records were screened in full text. This review seems to involve META-data extraction rather than DATA extraction. Please adjust the text and figures accordingly. It is not clear if IRR assessments were conducted for meta-data extraction. Please clarify/be explicit. If IRR was not done, describe how researchers were trained to use the extraction form. The sentence, “coding forms allowed for input of “other” responses (e.g., APA data elements) that were not included in extant reviews that focus on medical and clinical data extraction (e.g., PICO elements)” is unclear. Consider removing or clarifying and linking it better with the rest of the text. Describe the procedure for screening and meta-data extraction of studies authored by the review team.\n\nMethods/Critical appraisal and Synthesis\nThese sections are missing. Please state clearly if a critical appraisal of included studies was conducted and if so, how was it performed. Also, describe how synthesis was conducted.\n\nResults/Challenges\nClarify that the described challenges reflect issues within the body of evidence included in this (baseline) review (otherwise this section can be mixed up with review limitations).\n\nConclusions/Limitations\nOrganize limitations into those related to the methodology used and those related to the evidence base. Discuss limitations related to the focus on publications in English, the inexhaustive list of search sources, and the lack of grey literature.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Partly", "responses": [ { "c_id": "12505", "date": "04 Oct 2024", "name": "Amanda Legate", "role": "Author Response", "response": "Dear Dr. Macura, Thank you for your thoughtful and detailed feedback on our manuscript. We appreciate the time and effort you have invested in providing suggestions to enhance our work. We also value rigorous research methods and reporting transparency and would like to clarify several points regarding the reporting guidelines we adhered to and the journal's policies and requirements. Our manuscript follows the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. As noted in the F1000Research “Article Standards of Reporting” (https://f1000research.com/about/policies#stofrep), systematic reviews published in this journal must adhere to PRISMA guidelines. We have ensured that our reporting aligns with PRISMA's emphasis on transparency, replicability, and comprehensiveness. We would like to express our genuine appreciation for the important work you and your colleagues have done in developing the ROSES (Reporting standards for Systematic Evidence Syntheses) guidelines for systematic evidence synthesis in environmental science. Improving transparency and standardization in research reporting is a goal we fully support. While we acknowledge the value of the ROSES guidelines, they were not the reporting standard required or appropriate for our systematic review. We noticed that many of your comments seem to assess our manuscript against the ROSES guidelines (Haddaway et al., 2017a; 2017b; 2018; Haddaway & Macura, 2018). For example, the suggestion to emphasize \"meta-data extraction\" aligns more with ROSES, whereas PRISMA does not require such differentiation and focuses on clarity in describing the data collection process, whether it involves meta-data or primary data points. We believe it is essential to assess our work based on the scope and framework provided by PRISMA rather than extend it beyond its current focus to fit an alternative reporting framework. We are committed to making revisions that enhance the clarity and rigor of our research while remaining consistent with the standards required by the journal. Thank you again for your constructive feedback and for considering our clarifications. References Haddaway, N. R., & Macura, B. (2018). The role of reporting standards in producing robust literature reviews. Nature Climate Change, 8(6), 444–447. https://doi.org/10.1038/s41558-018-0180-3 Haddaway, N. R., Macura, B., Whaley, P., & Pullin, A. S. (2017a). ROSES for systematic map reports (Version 1.0) [Data file]. https://doi.org/10.6084/m9.figshare.5897299 Haddaway, N. R., Macura, B., Whaley, P., & Pullin, A. S. (2017b). ROSES for systematic review reports (Version 1.0) [Data file]. https://doi.org/10.6084/m9.figshare.5897272 Haddaway, N. R., Macura, B., Whaley, P., & Pullin, A. S. (2018). ROSES reporting standards for systematic evidence syntheses: Pro forma, flow-diagram and descriptive summary of the plan and conduct of environmental systematic reviews and systematic maps. Environmental Evidence, 7(7). https://doi.org/10.1186/s13750-018-0121-7 Comment 1 [Title] Clarify the type of data being extracted (qualitative, quantitative, or mixed). Comment 2 [Title] Since this review does not include any qualitative or quantitative synthesis per se, but rather provides an overview of the field (methods for semi-automated data extraction), I suggest removing \"living systematic review\" and adding \"living systematic map.\" Comment 1 & 2: Response Thank you for these valuable suggestions regarding the title. We have considered (1) specifying the type of data being extracted in the title and (2) changing the title from \"living systematic review\" to \"living systematic map.\" However, we have retained the original title to ensure consistency with our pre-registered protocol, adhere to PRISMA reporting standards, and comply with F1000Research guidelines. Comment 3 [Abstract] The summary of methods could include more detailed information on searches, screening, critical appraisal, and synthesis. Please specify which standards for review conduct were followed. Comment 3: Response Thank you for the suggestion to provide more detailed information on searches, screening, critical appraisal, and synthesis in the abstract to better align with ROSES reporting recommendations. To ensure compliance with the journal's requirements, we followed the PRISMA guidelines for a structured summary, which emphasize conciseness in presenting objectives, eligibility criteria, methods, results, and conclusions. While we understand the desire for additional details, we believe the current abstract aligns with these guidelines but will review it again to ensure optimal clarity. Comment 4 [Abstract] The summary of results could provide more information (briefly) about the included studies. Comment 4: Response Thank you for the recommendation to provide more information about the included studies within the abstract. We will incorporate a brief summary of the included studies' key characteristics and findings in future updates to this review to enhance clarity and completeness. Comment 5 [Keywords] Avoid repeating terms already present in the title Comment 5: Response Thank you for highlighting ROSES guidance indicating that keywords do not repeat the title but rather provide additional context. Where appropriate, we will revise keywords to avoid redundancy and enhance discoverability. Comment 6 [Introduction] The focus of this review—extraction tools for quantitative data—should be more explicitly stated. This emphasis needs to be clearer in the introduction and reflected in the title, as mentioned earlier. Specifically, the first paragraph of the Introduction should be revised to concentrate on the review topic—quantitative data extraction and existing tools—rather than a general introduction to meta-science or related areas. Comment 6: Response Thank you for your feedback on clarifying the focus of our review. Our study does not exclusively focus on extraction tools for quantitative data; it encompasses approaches to data extraction for both quantitative and qualitative data elements relevant to evidence synthesis in systematic reviews and meta-analyses within social sciences. To better reflect this broader focus, we have revised the objective section to explicitly state that the review covers data extraction tools for a range of data types. We hope this adjustment will provide clearer insight into the comprehensive scope of our review. Comment 7 [Introduction] Additional details are needed on how this review contributes to and complements existing reviews on the topic. This information should be included in the \"Related Research\" section. Comment 7: Response Thank you for this insightful comment. We agree on the importance of clearly situating our review within the existing literature to highlight its unique contributions. Although we did not adhere to ROSES guidelines for explaining the review's relevance to existing literature, we followed PRISMA guidelines in the \"Related Literature\" section to identify relevant prior reviews and synthesize their focus, findings, and limitations. We will consider ways to enhance this section to better emphasize our review's distinct contributions moving forward. Comment 8 [Objectives] It would be helpful to define what is included under “social science research domains”. Comment 8: Response Thank you for this suggestion. Our pre-registered research protocol and the \"Baseline Review Search Strategy\" document (available in the project's OSF repository) provide a comprehensive list of over 100 subject categories included under social science research domains, ranging from sociology and political science to interdisciplinary areas such as \"Social Sciences Mathematical Methods.\" To enhance clarity, we have updated the objectives section to include more details and a reference to the extended data file. Comment 9 [Methods] Authors should be transparent and explicit about the guidelines and standards for both conduct and reporting that were used. Please clarify this at the beginning of the Methods section. Comment 9: Response We acknowledge that the ROSES guidelines recommend transparency in reporting the guidelines and standards for both conduct and reporting at the beginning of the Methods section. However, in accordance with the journal's article guidelines for living systematic reviews (available from: https://f1000research.com/for-authors/article-guidelines/living-systematic-reviews), this information is provided in the \"Reporting Guidelines\" section. Comment 10 [Methods] The methods section should begin by addressing any deviations from the protocol. If there were no deviations, this should be clearly stated as well. Comment 10: Response Thank you for highlighting this important aspect. While we did not adopt the ROSES reporting standards for this research, we recognize their guidance on stating any deviations from the protocol at the beginning of the methods section. We have addressed any deviations in the appropriate sections of the paper, and additional descriptions are provided in the extended data files to ensure transparency and replicability. Comment 11 [Methods] Did you use any automation technologies to screen or select studies for this review? If yes, please clarify. Comment 11: Response Thank you for your question. The use of automation technologies is detailed in the \"Search Sources\" and \"Study Selection\" subsections of the Methods section. Additionally, to ensure transparency and replicability, further details are provided in the \"Software Availability\" section, as per F1000Research guidelines. Comment 12 [Methods/Eligibility criteria] The eligibility criteria should be explicit about the field within which methods for (semi)automated data extraction are applied. Comment 12: Response Thank you for this comment. To ensure clarity, we have referenced the extended data files in the text, which provide comprehensive details and a full list of over 100 research fields. These details are openly available in the project repository, as specified in the protocol (please see response to Comment 8). Comment 13 [Methods/Eligibility criteria] A definition of “(semi)automated” is needed. The eligibility criteria currently state that semi-automated approaches will be eligible but then refer to “any automated approach to data extraction” in the next sentence. This needs to be clarified—are the focus and criteria on semi-automated or automated approaches? Be more explicit and precise in the description of the eligibility criteria and ensure alignment with the protocol. Comment 13: Response Thank you for your suggestion to clarify the phrasing regarding the eligibility criteria. We have revised the description to specify that the focus is on any \"technique\" applied for extracting data from literature in a semi-automated manner. This adjustment aligns with the study protocol. Comment 14 [Methods/Eligibility criteria] Instead of “We excluded studies labeled as editorials, briefs..” you may write “Editorials, briefs, …were not considered eligible” (and similar changes may be applied to the following sentence). Comment 14: Response Thank you for the suggestion. We have revised the text to use passive construction, as recommended. We have also applied similar changes to the following sentence for consistency. Comment 15 [Methods/ Searches] Be explicit about the citation indices included in your Web of Science subscription and note which library was used to access WoS. This will increase transparency and replicability of your searches. Comment 15: Response Thank you for this suggestion. To avoid redundancy in the manuscript, we have added a statement directing readers to the extended data files, which provide additional detail related to WoS indices and search settings. Comment 16 [Methods/ Searches] Clarify why following Schmidt et al.'s search strategy was important, given the different scope of this review. Comment 16: Response Thank you for this comment. To clarify, we followed Schmidt et al.'s search strategy to ensure comprehensive coverage of relevant databases and consistency in methodological rigor, which is important even with a different scope. To avoid redundancy, we have added a reference in the manuscript directing readers to the extended data file and research protocol in our open-access repository, where this rationale is explained in detail. Comment 17 [Methods/ Searches] Consider including more social science databases to ensure comprehensive coverage. Comment 17: Response Thank you for this valuable suggestion. We appreciate the importance of comprehensive coverage and will consider including additional social science databases in future updates to further enhance the scope of our review. Comment 18 [Methods/ Searches] Did you include the Social Science Citation Index (within WoS)? Comment 18: Response Yes, the Social Science Citation Index within Web of Science was included. We have updated the text to clarify that all editions, settings, and search syntax used are detailed in the extended data files available in the open-access repository. Comment 19 [Methods/ Searches] Provide explanations for all abbreviations (IEEE, ACL, etc.) in the text. Comment 19: Response Thank you for the suggestion. We have added explanations for all source abbreviations (e.g., IEEE, ACL) in the text to improve clarity for readers. Comment 20 [Methods/ Study selection] Clarify if three researchers simultaneously screened titles and abstracts (TA), and whether inter-rater reliability (IRR) was calculated for TA screening. How you trained reviewers to apply eligibility criteria? Comment 20: Response Thank you for your question. The \"Study Selection\" section of the paper details independent screening procedures, training process for reviewers on applying eligibility criteria, and inter-rater reliability (IRR) considerations. Comment 21 [Methods/ Study selection] The sentence, “In cases where level of abstraction and potential for transferability could not be determined from the abstract alone, full text articles were reviewed and discussed by all three researchers until consensus was reached”, should more clearly state that there was NO full-text screening of all records (if this is correct), only of a sub-sample where abstracts did not clearly describe AI technology, etc. Comment 21: Response Thank you for this observation. While ROSES guidelines provide alternative flowchart formatting and descriptions, we adhered to PRISMA guidelines. According to the PRISMA flowchart (Figure 1), a total of 11,336 records were identified, and after deduplication, 10,644 articles underwent title and abstract screening. As indicated in the flowchart, only 46 articles proceeded to the full-text screening stage, which occurred separately. Comment 22 [Methods/ Study selection] Relatedly, Figure 1 should be adjusted to avoid giving the false impression that all records were screened in full text. Comment 22: Response Thank you for highlighting this concern. The current figure indicates that 46 articles were included in the full-text screening stage, making it clear that not all records were screened in full text. However, we will consider expanding the flowchart in future updates to provide additional details that could further enhance transparency and clarity. Comment 23 [Methods/ Study selection] This review seems to involve META-data extraction rather than DATA extraction. Please adjust the text and figures accordingly. Comment 23: Response Thank you for your observation. While ROSES emphasizes distinguishing between meta-data extraction and data extraction, PRISMA does not make this distinction as explicitly. Our paper follows PRISMA guidelines, focusing on transparency and completeness in documenting the tools, databases, and criteria used for extraction. Comment 24 [Methods/ Study selection] It is not clear if IRR assessments were conducted for meta-data extraction. Please clarify/be explicit. If IRR was not done, describe how researchers were trained to use the extraction form. Comment 24: Response Thank you for raising this point. The \"Study Selection\" section of the paper details this information and discusses inter-rater reliability (IRR) assessments. Comment 25 [Methods/ Study selection] The sentence, “coding forms allowed for input of “other” responses (e.g., APA data elements) that were not included in extant reviews that focus on medical and clinical data extraction (e.g., PICO elements)” is unclear. Consider removing or clarifying and linking it better with the rest of the text. Comment 25: Response Thank you for this suggestion. We have refined the statement to improve clarity and ensure it is better linked with the surrounding text. Comment 26 [Methods/ Study selection] Describe the procedure for screening and meta-data extraction of studies authored by the review team. Comment 26: Response Thank you for highlighting ROSES guidance surrounding procedures for handling studies authored by the review team. However, no alternative procedures were implemented; therefore, there are no additional procedures to report. Comment 27 [Methods/ Critical appraisal and Synthesis] These sections are missing. Please state clearly if a critical appraisal of included studies was conducted and if so, how was it performed. Also, describe how synthesis was conducted. Comment 27: Response Thank you for your comment. These sections are specific to ROSES guidelines. These sections are not required by PRISMA or the journal's reporting standards. Comment 28 [Results/Challenges] Clarify that the described challenges reflect issues within the body of evidence included in this (baseline) review (otherwise this section can be mixed up with review limitations). Comment 28: Response To avoid confusion with review limitations, we have revised the first sentence of this section to clarify that the challenges discussed specifically reflect issues within the body of evidence included in this baseline review. Comment 29 [Conclusions/Limitations] Organize limitations into those related to the methodology used and those related to the evidence base. Comment 29: Response While our research and protocol were developed following PRISMA guidelines rather than ROSES, which requires a structured discussion of limitations, we appreciate the value of differentiating between methodological constraints and evidence base gaps. We will consider this distinction in future updates to enhance clarity. Comment 30 [Conclusions/Limitations] Discuss limitations related to the focus on publications in English, the inexhaustive list of search sources, and the lack of grey literature. Comment 30: Response Thank you for the suggestion. We have updated the limitations section to address the focus on publications in English, the inexhaustive list of search sources, and the lack of grey literature." } ] }, { "id": "298395", "date": "30 Aug 2024", "name": "Lena Schmidt", "expertise": [ "Reviewer Expertise Systematic review automation", "automated data extraction (clinical trials)", "natural language processing", "living reviews" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for providing this interesting review about automated data extraction from social science studies and model architectures, evaluation, data processing and more. Especially the information in tables, such as tables 3, 4, and 5 are adding a lot of value. I am not an expert in social science studies but am familiar with the general field of automated data extraction. Therefore I have just some very minor comments and questions for clarification below:\nThe reference from Yu et al. below is mostly concerning screening automation and not data extraction if I am not missing a major point in the paper. If that is correct then there may exist better works to reference in this context? “the process of extracting data from primary research is a labor-intensive effort, fraught with the potential for human error (see Pigott & Polanin, 2020; Yu et al., 2018).” I am not an expert in social science research, but a few included references in Table 2 caught my eye. For example Iwatsuki et al. (2017) about detecting in-line mathematical expressions or Torres et al. (2012) about software engineering or later Nayak et al. (2021) about cotton industry? Regarding this sentence in the conclusions, it might be more up-to-date to reference the review update from 2023 with 76 included papers: “For example, while an LSR focusing on clinical research that is based on the PICO framework yielded 53 studies that included original data extraction (Schmidt et al., 2021)” One of the challenges with living updates is to adapt the search whenever there are new developments in a field of research. You may have already considered adapting the search strategy to make sure that new methods relying on large language models (LLM) like GPT or T5 are picked up? There may be relevant articles coming through soon, for example https://arxiv.org/abs/2405.14445 may be of interest for a future review update as it looks at social science study data extraction and if it is, then it would be good to make sure that the search can pick up the terminology correctly. In the methodology section, could you please state the dates when the search relevant to the baseline review cutoff was conducted (for each data source if different) ?\"\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [ { "c_id": "12500", "date": "26 Sep 2024", "name": "Amanda Legate", "role": "Author Response", "response": "We are honored that you agreed to review our research and sincerely appreciate your thoughtful review and feedback. Please find responses to each comment below. Comment 1 The reference from Yu et al. below is mostly concerning screening automation and not data extraction if I am not missing a major point in the paper. If that is correct then there may exist better works to reference in this context? “the process of extracting data from primary research is a labor-intensive effort, fraught with the potential for human error (see Pigott & Polanin, 2020; Yu et al., 2018).” Comment 1: Response Thank you for catching this oversight. You are absolutely correct; Yu et al. (2018) primarily focused on screening automation for primary study selection rather than data extraction stages of SLRs. We have removed this reference from the sentence to align with the context. Comment 2 I am not an expert in social science research, but a few included references in Table 2 caught my eye. For example Iwatsuki et al. (2017) about detecting in-line mathematical expressions or Torres et al. (2012) about software engineering or later Nayak et al. (2021) about cotton industry? Comment 2: Response Thank you for your insights on the relevance of references in Table 2. Our search strategy was intentionally broad to include studies utilizing (semi)automated data extraction methods across various domains, provided they were not solely focused on clinical research. The goal was to ensure comprehensiveness; however, we understand your concern regarding the ambiguity of some references' relevance to social sciences. As our study is a \"living\" review, we see this as an excellent opportunity to consider refining our inclusion criteria in future updates. We will explore more targeted approaches that can help streamline the search strategy, potentially focusing on research that more directly applies to social sciences or explicitly demonstrates transferable methodologies that align with the needs of social science researchers. Additionally, we are discussing options for collaborating with experts who specialize in bibliometric analysis or search strategy optimization to ensure that our review remains focused, relevant, and complementary to your work. Comment 3 Regarding this sentence in the conclusions, it might be more up-to-date to reference the review update from 2023 with 76 included papers: “For example, while an LSR focusing on clinical research that is based on the PICO framework yielded 53 studies that included original data extraction (Schmidt et al., 2021)”. Comment 3: Response Thank you for pointing out this important update, we appreciate your diligence in ensuring that references are current and reflective of the most recent findings. The manuscript has been revised to reference the 2023 update of your LSR to accurately reflect the most up-to-date results. Comment 4 One of the challenges with living updates is to adapt the search whenever there are new developments in a field of research. You may have already considered adapting the search strategy to make sure that new methods relying on large language models (LLM) like GPT or T5 are picked up? There may be relevant articles coming through soon, for example https://arxiv.org/abs/2405.14445 may be of interest for a future review update as it looks at social science study data extraction and if it is, then it would be good to make sure that the search can pick up the terminology correctly. Comment 4: Response Thank you for highlighting the importance of adapting the search strategy to capture emerging developments in automation technologies, particularly those involving large language models (LLMs) like GPT or T5. We completely agree that a key aspect of maintaining the relevance and rigor of a living systematic review is to continuously update the search strategy to reflect the current state-of-the-art in the field. We will incorporate this valuable feedback into future iterations by updating our search terms and strategies to include LLM-related methodologies and terminologies, ensuring the inclusion of new and relevant articles. The paper you referenced (https://arxiv.org/abs/2405.14445) serves as an excellent example, and we will use it to refine our search criteria. This approach will help us stay current with advances in data extraction techniques. Thank you for providing specific references to guide this adaptation. Comment 5 In the methodology section, could you please state the dates when the search relevant to the baseline review cutoff was conducted (for each data source if different) ?\" Comment 5: Response Thank you for this thoughtful suggestion. While we reported the search dates in the extended data files housed in OSF, we agree with you that including them directly in the Methods section would add clarity and value for readers. We have updated the section to specify the dates when searches were conducted for each data source, ensuring this information is clear and accessible to readers." } ] } ]	1	https://f1000research.com/articles/13-664
https://f1000research.com/articles/10-363/v1	10 May 21	{ "type": "Research Article", "title": "COVID-19 lockdown and lifestyles: A narrative review", "authors": [ "Sathyanarayanan Doraiswamy", "Sohaila Cheema", "Ahmad Al Mulla", "Ravinder Mamtani", "Sohaila Cheema", "Ahmad Al Mulla", "Ravinder Mamtani" ], "abstract": "Background: The primary objective worldwide during the coronavirus disease 2019 (COVID-19) pandemic has been controlling disease transmission. However, lockdown measures used to mitigate transmission have affected human behavior and altered lifestyles, with a likely impact on chronic non-communicable diseases. More than a year into the pandemic, substantial peer-reviewed literature has emerged on altered lifestyles following the varying lockdown measures imposed globally to control the virus spread. We explored the impact of lockdown measures on six lifestyle factors, namely diet, physical activity, sleep, stress, social connectedness, and the use of tobacco, alcohol, or other harmful substances.\nMethods: We comprehensively searched PubMed and the World Health Organization’s global literature database on COVID-19 and retrieved 649 relevant articles for the narrative review. A critical interpretative synthesis of the articles was performed.\nResults: Most of the articles included in the review identified the negative effect of lockdown measures on each of the lifestyle factors in many parts of the world. Encouraging lifestyle trends were also highlighted in a few articles. Such trends can positively influence the outcome of lifestyle-related chronic diseases, such as obesity and diabetes.\nConclusions: The COVID-19 pandemic provides an opportunity to better understand the negative impact of strict lockdown measures on lifestyles. At the same time, it helps us identify and initiate positive behavioral changes, which, if consolidated, could improve chronic disease outcomes. It is up to governments, communities, and healthcare/academic entities to derive benefit from lessons learned from the pandemic, with the ultimate objective of better educating and promoting healthy lifestyles among communities.", "keywords": [ "COVID-19", "Lifestyle", "Diet", "Physical activity", "Stress", "Smoking", "Substance", "Alcohol", "Emotional well-being", "Social connectedness" ], "content": "Introduction\n\nThe ongoing coronavirus disease 2019 (COVID-19) pandemic has caused thousands of deaths, overloaded health systems, and disrupted social and economic infrastructure worldwide. While the world remains focused on controlling the pandemic, we cannot ignore its impact on lifestyles and, in turn, on chronic non-communicable diseases (NCDs), which account for over 70% of global mortality. COVID-19 transmission-mitigating measures—requiring people to stay at home and practice physical distancing—afford us the opportunity to examine lifestyle factors and understand their effect on NCDs.\n\nVarious degrees of COVID-19 lockdown measures, including travel and movement restrictions, have helped reduce the spread of the virus. However, these measures also diminish access to healthy food; widen inequities between communities; result in suboptimal physical activity levels; exacerbate anxiety and stress; impair the quality of optimum sleep; and encourage substance abuse to allay anxiety and fear of the disease1. Substantial published literature has emerged on altered lifestyles during the pandemic; however, to our knowledge, there has not been any synthesis of this literature.\n\nWe conducted an extensive narrative review to help understand lifestyle factors, particularly those related to NCDs, in the COVID-19 context. The review aims to synthesize alterations (positive or negative) in lifestyle factors among individuals and communities, that arose because of varying countries’ lockdown measures. The review can be an instructive and valuable source for healthcare institutions and stakeholders interested in improving healthy lifestyles and healthcare during future lockdown measures. Additionally, it can inspire further research in the emerging field of lifestyle medicine and its role before, during, and after crisis situations, such as pandemics. For the review, we recognize the American College of Lifestyle Medicine (ACLM) definition of a healthy lifestyle as one that includes eating a predominantly plant-based diet, being physically active, sleeping well, managing stress, remaining socially connected, and refraining from the use of tobacco, alcohol, and other harmful substances. With optimum practice, these six healthy lifestyle factors can prevent, treat, and, in some cases, even reverse NCDs. This narrative review will focus on these lifestyle factors and how they may have been altered during the COVID-19 pandemic.\n\n\nMethods\n\nThe narrative review was conducted using a best-evidence synthesis approach put forth by Green et al.2 Following this approach, the expectation from a successful narrative review is to: “present information that is written using the required elements for a narrative review, be well structured, synthesize the available evidence about the topic, and convey a clear message.”2 Following the Scale for the Assessment of Narrative Review Articles (SANRA)3, the methodology with the checklist is reported as Supplementary Material 1 in the Extended Data4.\n\nThe search strategy included a combination of keywords and controlled vocabulary (such as MeSH terms). The keywords included the following: COVID-19 AND (lifestyle OR dietary habits OR physical activity OR sleep OR tobacco OR alcohol OR substance OR stress OR relationships) AND (lockdown OR quarantine OR isolation). We searched using these terms in PubMed and the World Health Organization (WHO) global literature database on coronavirus disease initially in September 2020 and updated the search in PubMed on 31 January 2021. We placed no restrictions on language, geography, or publication date. The reference lists of the retrieved articles were also scanned for additional articles with relevance to our review. The number of retrieved items from each database is provided in the Extended data, in Supplementary Material 24.\n\nWe included all articles that discussed lifestyle factors in the general population within the COVID-19 pandemic context. The review focused on the six lifestyle factors included in the definition of a healthy lifestyle by the American College of Lifestyle Medicine.\n\nArticles were excluded if they did not focus specifically on the six lifestyle factors (dietary habits, physical activity, sleep, tobacco or other substance use, stress, and emotional well-being and social connectedness) or did not discuss lifestyle within the COVID-19 context. We excluded articles that discussed lifestyle change in healthcare workers as they are a specialized group and subject to additional stressors beyond the effects of the lockdown measures. Additionally, we excluded published literature reporting modeled effects of lockdown during COVID-19.\n\nIdentified articles meeting the inclusion criteria were imported into Endnote X95. Thereafter, the authors screened the title and abstract of the identified articles. Full texts of all relevant articles were further screened for useful data to be eventually included in the critical interpretive synthesis6. From each article, qualitative and quantitative information on the COVID-19-related lockdown and its effects on any of the six lifestyle factors (diet, physical activity, stress, connectedness, sleep, and tobacco or other substance use) on healthy individuals and those with pre-existing NCDs were extracted. In articles that were primary studies with quantitative data, we specifically scrutinized the study design, results, and the conclusion. In articles other than primary studies, we focused on the discussion and conclusion sections. For qualitative studies, opinions/perspectives, and viewpoints, we took a meta ethnographic approach7 as part of our interpretative synthesis. Though the ACLM definition combines smoking, alcohol, and substance use as one lifestyle factor, we reviewed these separately to explore them in greater depth. The information extracted from the articles was classified according to the six lifestyle factors and is summarized in the Results.\n\n\nResults\n\nOur search yielded a total of 2620 articles. Following the title, abstract, and full-text screening, 649 articles relevant to the narrative review scope were qualitatively synthesized according to the six lifestyle factors – dietary habits, physical activity, sleep, tobacco or other substance use, stress, and emotional well-being and social connectedness. Though all included articles are reported in the Extended data, in Supplementary Material 34, the manuscript bibliography was restricted to an optimal number applying the principle of ‘concept saturation’8 for several analytical findings.\n\nMost of the literature included in the narrative review referring to dietary habits indicate an alteration in the eating behavior of people in many parts of the world during the COVID-19 pandemic9–11. Most survey-based studies report an increase in the intake of unhealthy foods by the majority of respondents, a small number highlight a higher intake of healthy foods, and some studies, such as one from Spain with 1036 participants, report a wide variation in the type of food (healthy vs unhealthy) consumed by the participants12. One Polish study with 2381 participants reported that 34% of respondents ate more during the lockdown13, while another study from the same country with 1097 participants reported that 30% of the participants gained weight during the lockdown14. Whereas, among 3533 respondents from Italy, 46.1% reported consuming more food and 19.5% had gained weight15. A similar proportion (46%) of the Galcian population from Spain also reported eating more than before the lockdown and 44% of the 1350 adults in the study reported weight gain16. A qualitative study from Ghana found similar eating behavior leading to weight gain during the lockdown17. This weight gain was more pronounced in people with pre-existing overweight/obesity18. In richer households, staying home encouraged excessive use of unhealthy foods, such as processed and fast foods in many parts of the world15,19–21. An Italian study reported an increased uptake of ‘comfort foods’ including chocolates and ice-creams used by participants to allay lockdown anxiety15. In a study of 938 French adults during the lockdown, an individual’s mood was a significant factor for food choice21. Similarly, a high prevalence of ‘emotional eating’ was reported in Saudi Arabian women22 and among a cohort of 675 Spanish individuals23. Additionally, some people including children inclined towards snacking to overcome boredom24, and that led to relatively quick excessive weight gain15,16,25–28. A Chinese retrospective study of 10,000 students found an increase in body mass index in most of the participants29.\n\nStaying home has also limited access to fresh vegetables and fruits, particularly in the most vulnerable and poorest sections of the society due to limited availability, accessibility, and affordability14,30. Poorer households have been overwhelmed by food insecurity, as demonstrated by a study from Iran reporting 61% of 392 families facing some level of food insecurity31.\n\nIn some situations staying at home encouraged many individuals to eat a fresh, home-made, balanced diet32, as evidenced by a reduction in the consumption of fast food33, fewer purchases of ready-made meals, and by the dominance of online/in-person grocery shopping as the major source of food and food purchases in some countries16,34. A study from China showed that families that did online shopping included a greater variety of foods in their diet than in normal circumstances35. A large study of 7514 participants from Spain—predominantly young, university-educated females—reported a higher intake of fruits, vegetables, or legumes than during the pre-pandemic times36. Gender (females faring better), family members staying at home, (less) TV watching while eating, and (higher) maternal education were determined to be factors influencing healthy food intake37.\n\nIn the review, we find that individuals who were overweight/obese pre-pandemic gained weight during the pandemic, while the undernourished lost more weight14,15. A study in Italy of 88 families found that children with obesity found it difficult to practice a healthy lifestyle during the pandemic, despite participating in a food education program in a hospital. Their unhealthy food consumption and sedentary lifestyle were attributed to a great deal of stress experienced by the children due to interruption of school and sports activities among other factors38. Studies also reported that individuals with eating disorders and other psychiatric disorders diagnosed prior to the lockdown fared worse during the lockdown period due to low self-directedness and less adaptive coping20,39–44.\n\nThe lockdown period saw a general reduction in physical activity levels as evidenced from the studies included in the review. A study from China of 339 participants revealed a significant reduction in the average exercise intensity for both males and females during the lockdown period (average steps per day, before vs during: 7038±1923 vs 3741±1042 steps, p < 0.001 for females and 8321±3000 vs 3728±1726 step, p < 0.001 for males)45. A similar observation was made in Italy where 68% of participants in a study with a sample size of 490 adults reported a decrease in exercise levels46. In a Polish study sample of 238, 43% of participants also reported a reduction in their physical activity during the lockdown period14. An international, multi-country online survey of 1047 participants found that the number of days per week of all physical activity declined by 24% during the lockdown period. The number of minutes per day spent on physical activity decreased by 33.5% while sitting time increased by 5–8 hours among the respondents47. Diminished physical activity levels were also reported in other countries, such as Australia48, United Kingdom (UK)49, and the United States (US)50,51. Longitudinal tracking of steps among participants in a physical activity program in Australia saw a decrease in the number of steps during lockdown, which returned to normal with the lifting of restrictions52. A similar improvement in physical activity levels was observed after the end of lockdown in Greece53.\n\nThe working-from-home environment has predisposed individuals to spend more time sitting, leaning, reclining, or lying down on the bed20. There is no predictable pattern as to who was less active during the lockdown period. While some studies found that previously physically active individuals became less active during the lockdown period51,54, other studies found no change50 or reported a further reduction in physical activity among previously inactive individuals54. A cross-sectional study in 64 cities in China, with 369 participants, concluded that previously physically active individuals were in greater distress as a consequence of the lockdown55. Studies among preschoolers56, children and adolescents in Spain57 and Brazil found a downward trend in physical activity levels and an increase in screen time/sedentary behavior among children during the lockdown period58. A similar reduction in physical activity levels among children and adolescents was also reported in studies from Canada, Germany, UK, Italy, and Spain59–64. A study in India found a reduction in physical activity and increased screen time among men and those belonging to the upper socio-economic strata65. Ironically, a study from Germany found that participants who regularly consumed alcohol and expressed greater satisfaction with their life were more physically active66. It was also observed that older people who were single/alone67, affected by frailty68, used to exercising in groups, or who were not accustomed to online apps (which support exercise routines) experienced a reduction in physical activity and/or increased levels of sedentary behavior69–71.\n\nLockdown provided an opportunity to be creative in finding ways to stay physically active. In South Korea, for example, it was observed that the public bicycle-sharing system recorded an increase in commuter and weekend users72. It is, however, to be noted that such initiatives required commitment from citizens and authorities to ensure adherence to physical distancing, hand hygiene, facemask use, and cleaning of public facility/site surfaces. Staying physically active in home environments is possible, and its feasibility was shown during COVID-19 lockdown periods in countries like Japan73, Scotland74, and Switzerland75, particularly among children with good parental support and encouragement. A study of 213 university students in Spain found an increase in the mean number of days they were engaged in moderate and vigorous physical activity76. The use of physical activity apps was useful in improving physical activity in the US51. A recent study of 1521 adults from the UK reported that, although most adults claimed to have maintained or increased their engagement in physical activity during the pandemic, the majority did not meet the recommended physical activity guidelines77. Studies performed in several countries, including a large study of 43,995 individuals from Brazil78, reconfirm that individuals who were physically active during the lockdown period were more resilient and had lower odds of suffering from stress, anxiety, and depression79–88.\n\nStay-at-home restrictions affected the sleep of people in many parts of the world89,90. A global study involving 6882 participants from 59 countries found a large proportion (66.2%) reported changes in their sleep patterns during the pandemic91. In a large cross-sectional study across France, two weeks after the lockdown, 74% of the 1005 nationally representative participants reported problems trying to sleep as compared to 49% in a previous survey pre-lockdown92. An Italian study including 400 university students and administrative staff reported that 40% of the respondents suffered from insomnia, while 15% specifically had issues in sleep initiation93. A similar proportion (40.7%) among a sample of 1491 adults in Australia reported a negative change in sleep levels48. Factors found to be associated with disturbed sleep were increased blue light exposure from extended screen time, browsing the internet to keep busy, and working remotely from home93,94. Older age, living with a partner, and living in a higher income country were associated with better sleep health, while loss of job, challenges experienced in transitioning to working from home, being unable to pay important bills, and an increase in arguments and conflicts at home were associated with poorer sleep health95. Poor sleep and anxiety/depression were found to be closely associated in a few studies96–98.\n\nRespondents in some studies reported sleeping more during the lockdown period. This was particularly true for preschoolers, children, and adolescents, as observed in studies from Brazil, Spain, Canada, and China20,58–60,76. Among adults who slept more, the reported sleep quality was poor91,99. Those who slept more also experienced sleepiness during the day and increased daytime sleep duration, as reported in a study of 203 corporate professionals and 325 university students in India100. In the same study, it was also observed that females, younger people, and those experiencing loneliness and COVID-19-related worries had greater difficulty with sleep100.\n\nFrequent awakening and increased sleeping difficulty were noted in 69.6% of 365 patients in Portugal who had pre-existing sleep-disordered breathing101. One study reported an increased frequency in the uptake of sleeping pills among study participants92. Increased stress due to COVID-19, information overload, inconsistent bedtime, and low mood are all contributors to insomnia and its harmful effects on overall health102.\n\nA few studies reported that individuals with previously erratic sleep patterns and social jetlag, were provided with an opportunity to normalize their sleep patterns and improve sleep hygiene for optimum functioning99,103–106. One study from the US found that reduced rigid workload and school schedules led to an improvement in the overall sleep quality for some individuals107, and a study in Canada found students were better able to sleep and reported reduced daytime sleepiness during the lockdown108. A beneficial impact of quarantine on sleep was documented by a large global study of 14,000 individuals from 11 countries. A very small proportion of people were found to suffer from anxiety-induced insomnia in this study109. At least one study showed that sleep problems encountered post-lockdown declined over time95.\n\nTobacco. Few studies are available on smoking behavior during COVID-19 lockdowns. Among those available, we found variations (increases, decreases, and remaining at pre-lockdown levels) in the smoking patterns among the respondents110. A cross-sectional study involving 345 participants in the US found that half of respondents retained their pre-lockdown level of smoking, one quarter of them reduced smoking, and the remainder increased smoking111. The same study also found that while 20% of respondents showed an increased motivation to quit, 15% showed a reduction in motivation111. In a study of 957 participants from the Netherlands, 14.1% reported smoking less during the pandemic, while 18.9% reported smoking more112. In Australia, 6.9% of 1491 adults reported a negative change in their smoking habits after the introduction of lockdown measures48. In a multi-country study involving 6800 combustible and e-cigarette users from Italy, India, South Africa, UK, and the US, indoor smoking had increased in India and Italy, thus increasing the risk of secondhand smoke exposure among family members113. Anxiety, boredom, and stress experienced by many people during COVID-19 contributed to increased smoking in some individuals16,110,114,115. Stress and inactivity were cited as the main reasons for increased smoking during lockdown by a cohort of patients with cardiovascular disease in France116.\n\nDespite many deterrents, motivated individuals saw the lockdown period as an opportunity to become healthy and quit smoking111. The motivation to quit was more discernible among those who smoked tobacco cigarettes than electronic cigarettes111. Smokers who had a family member or someone close to them suffer from COVID-19 displayed a greater motivation to quit111. One study reported that many parents wanted to appear on their best behavior in front of their children during lockdown and postulated that this was one of the reasons for them cutting down on their cigarette intake when spending more time at home117. In a qualitative study in the US, several participants mentioned that their cessation efforts improved due to a decrease in opportunities for social smoking and because they were spending more time at home. However, other individuals in the same study claimed an increase in smoking due to lack of the same restrictions at home compared to those imposed at their workplaces110.\n\nOther harmful substances. Among other substances that cause dependence, alcohol stands out as one of the most commonly used psychoactive substances during the lockdown period114,118–120, despite alcohol supply not being assured in many countries. A study from India documented that alcohol shop closures led to alcohol-dependent individuals experiencing withdrawal symptoms and suicides121. Where alcohol was available, some people resorted to increased alcohol intake to overcome adverse psychological outcomes of the lockdown, including stress and insomnia122,123. Data from the Office for National Statistics in the UK demonstrates that alcohol sales rose by over 30% in month-on-month volume when compared to the previous year. In a survey of 6416 people from China, 32% of regular alcohol drinkers reported increased consumption during the lockdown period124. In Australia, 26.6% of 1491 participants reported an increase in alcohol consumption during the lockdown48. A higher frequency of drinking was selectively observed in men, young adults aged 18-24 years, and those living in big cities125. A study in Italy observed that emergency admission of adolescents and young people in one hospital due to alcohol-related emergencies increased manifold during the lockdown61. In a survey of 1555 people in the UK, one third reported that they had stopped or reduced drinking during the lockdown, while one fifth drank more frequently during the same period126. A survey of 4072 participants in Poland found a reduced frequency of drinking in most participants125.\n\nIt was identified that those who consume alcohol found it more difficult to cope with the mental health impact of the pandemic and associated lockdowns118. A large study from Australia found that people who were heavy drinkers, middle-aged, and had higher incomes before the pandemic, increased drinking during the pandemic127. This study also found that individuals who had experienced recent job loss, were stressed/depressed, or had altered eating and sleep habits consumed larger amounts of alcohol than those who weren’t128. A study from the US found an increase in harmful alcohol use and related behaviors over the six months of lockdown-related measures129.\n\nA survey of 1555 patients with pre-existing alcoholic disorders in the UK concluded that ‘lockdown represents a risk factor for increased alcohol consumption in people with alcohol use disorders and relapse for those who were previously abstinent’130. Those who do relapse are at a high risk of harmful drinking and require a custom-tailored approach for follow-up and intervention.\n\nA study of university students before and after university closures in the US revealed that those students who moved from on campus accommodation with peers to their homes with parents demonstrated a significant reduction in their drinking than those who remained in their pre-pandemic locations131. A study of 1951 students from Belgium found that pre-lockdown drinking motives reliably predicted alcohol consumption during the lockdown132.\n\nWith regard to addictive drugs, the European Monitoring Centre for Drugs and Drug Addiction determined that people using addictive drugs may be at higher risk during the crisis, particularly because of the aging cohort of opioid users and any associated comorbidities. Though the data is sparse at the present time, experts agree that movement restrictions reduced the availability of illicit drugs133, thereby increasing the demand for addiction treatment. The limited availability of these services added to the suffering of this population. There was one study from France, however, which found an increase in cannabis use among 31.2% (195 of 620) of regular cannabis users making up 5.44% (620 of 11,391) of total participants134. Another study from the Netherlands found increased use of cannabis among daily cannabis users135. In addition, studies have demonstrated high anxiety levels among pre-COVID-19 substance users and COVID-19 substance initiators136.\n\nWatching, reading, or listening to the constant stream of COVID-19-related news, perceived health risks137, and a perceived lack of autonomy138 led to increased anxiety among individuals and families in many countries139–144. The 2020 National Health Interview survey found that US adults were eight times more likely to fit the criteria for serious mental distress during the lockdown as compared to before145. A study from China reported the psychological impacts of COVID-19, expressed as mild-to-severe anxiety, among 25% of 7143 college students146. In total, 65% of 432 respondents in another study from Hong Kong reported clinical levels of depression, anxiety, and/or stress. Older adults, especially those in isolation and with cognitive decline147,148, and their caregivers149 were identified to be more prone to anxiety, stress, and depression9,139. A high prevalence of stress and post-traumatic stress disorders was documented among Nepalese150, Lebanese151, Saudi Arabian152, Vietnamese153, and Philippine nationals154 at the height of lockdown. High levels of anxiety and depression were also documented in studies from India155–157, Ecuador158, Albania159, Ireland160, Hungary88,161, Spain162, Palestine163, the UK164, Kuwait165, Brazil, and Portugal166. The prevalence of people reporting clinical depression and anxiety in a sample of 1215 respondents in Italy was recorded to be 32.3% and 35.7%, respectively (compared to 15.39% and 21.40%, respectively, during pre-COVID-19 times)142. A similar finding was made by another study from the country167. One study from Jordan of 5274 participants found that four out of every ten participants in home quarantine suffered from some degree of anxiety168.\n\nArticles also suggest that quarantined children169, adolescents170, university students171–174 and adults175, mothers of young children176, and other healthy adults suffered from symptoms of poor mental health, such as post-traumatic stress, anger, and confusion177,178. One study in Turkey found a difference in the self-reported quality of life (better) of children as opposed to the perception of their parents179. Only a few studies made a clear distinction between the stress levels experienced by the general population as part of the community quarantine versus those who were quarantined as part of contact tracing or after testing COVID-19 positive. A few studies seem to suggest greater stress experienced by both those under isolation180,181 and others under home quarantine as part of contact tracing182. One study from China, however, found that home self-quarantine was associated with increased happiness as compared to those who were in community quarantine183. A study from the UK found that a majority of the older people interviewed identified positive aspects of lockdown and felt better prepared to deal with the lockdown184.\n\nHigher stress levels associated with lockdown measures were observed in some groups, such as women185–187 (particularly pregnant women188,189), single/divorced adults81, older people (particularly with pre-existing mental health conditions175,190), parents with young children191, university students and young adults192–194, workers195, those self-medicating196, the economically deprived143, those with pre-existing depression197, bipolar disorders198, and other chronic medical conditions139,189,199–201. A large study of 56,679 participants in China found that quarantine had a profound effect on the mental health of specific vulnerable groups, including those with pre-existing mental disorders, chronic physical diseases, frontline workers, and those living in the most affected areas202. A similar large study of 53,524 participants from 26 countries during the pandemic found higher levels of stress associated with being young, female gender, lower level of education, being single, number of children in the family, and living in a country experiencing severe community spread203.\n\nExtreme stress driven by fear of COVID-19 infection, financial crisis, loneliness, the pressure to quarantine and isolate when tested positive, stigma, and the unavailability of alcohol have been identified as drivers of suicidal ideation and suicide during the pandemic and the associated lockdowns181,204–206. A healthy diet and refraining from reading updates about COVID-19 were very often shown to be the best predictors of lower levels of anxiety and depressive symptoms207. A longitudinal study reported that fear of COVID-19 decreased over time since the introduction of lockdown, but depression levels increased in a cohort of Chinese individuals208. There were mixed results from New Zealand, one of the countries known to have best managed the pandemic, where 62% of those surveyed in a study reported ‘silver linings’ during the lockdown, such as enjoying working from home and a less polluted environment, while the same study found 16% of participants suffering from anxiety and 39% reporting low well-being209. A qualitative study from Italy found that, beyond the difficulties associated with lockdown, parents of children with neurodevelopmental disorders appreciated spending more quality time with their children, thus contributing to enhanced parent-child relationships210. Some longitudinal studies have found the mental health of individuals to improve over time as extreme fear and the sense of emergency has subsided211.\n\nThe restriction of movement during the pandemic has led to a significant reduction in social activity among family, friends/neighbors, and for entertainment212,213. This contributed to diminished life satisfaction in >30% of participants in a large, multi-continent study involving 1047 participants213. A study of 571 healthy adults in Israel found greater psychological distress, poor connectedness, and lowered resilience among women, young adults, and the unemployed214. An online survey of 309 residents in Europe and the US revealed that 100% of participants faced some degree of social isolation during the lockdown period. This study found that younger adults (aged 18–29 years) reported higher self-isolation than older groups. Those feeling socially isolated were also less satisfied with their food habits, work, and housing215. Prolonged social media use has had a deleterious effect on the overall social well being of individuals as reported by studies in Saudi Arabia212 and Italy216.\n\nStudies have found that a lack of social interaction has a more profound effect on people with higher income and education214. Lack of social interaction also has a negative impact as more time passes for older people, as evidenced by large cross-sectional studies in the UK217,218 and Switzerland219. Children and adolescents have reported being more restless, irritable, and inattentive during the lockdown220 with increased screen time being the likely contributor221,222 along with worsening of relationships223 and dysfunctional parenting224. Girls and women confined to homes and quarantine facilities faced increased family tensions, an overload of domestic work, and remain vulnerable to physical and emotional abuse225. Intimate partner violence—characterized by physical, sexual, or emotional violence between partners—is also of concern during challenging times of staying home and physical distancing226. A study in Switzerland found that older adults who managed to maintain social communication at a satisfactory level were able to manage their stress level, thus underscoring the importance of social connectedness219.\n\nStudies show that patients with pre-existing NCDs have found it difficult to maintain a healthy lifestyle during the COVID-19 pandemic and associated lockdown measures introduced by countries227. Patients with coronary heart disease228–232, neurological disorders233,234, diabetes235,236 and cancer237,238 have had to compromise on their physical activity routine, dietary patterns, and social connectedness in particular227,236,239,240 as did families with children who had chronic respiratory diseases193,241. Poor glycemic control in diabetics due to altered lifestyle was reported in many studies242–248, while one study in India reported an improvement in the glycemic status of patients with type II diabetes mellitus249. In a study from France, 45% of 195 patients with chronic heart disease had a >25% reduction in physical activity and 24% of patients had gained >2kg weight229. A study of parents of 125 children with disabilities in the UK found that 61% of them reporting a reduction in physical activity levels and over 90% reported a negative impact on their children’s mental health250. A qualitative study in Ireland came to a similar conclusion regarding increased mental health difficulties among children with Autistic Spectrum Disorder251,252. Patients fearful of acquiring COVID-19 infection have also been found to postpone medical care for their chronic problems253, leading to greater physical and psychological distress, while adding to the suffering of chronically ill patients227,254,255. Some studies found an improvement in patients with conditions such as migraine256,257, whereas other studies found limited or no change in the lifestyle of those with other chronic diseases258.\n\n\nDiscussion\n\nOur narrative review highlights the altered lifestyles of people worldwide during the lockdown period of the pandemic. Both positive and negative changes in the six lifestyle factors have occurred and their impact has varied in different instances. These findings could be instructive to health practitioners and health departments in their strategies to manage chronic disease.\n\nWith regard to dietary habits, at the start of the pandemic the United Nations Systems Standing Committee on Nutrition warned that the COVID-19 pandemic would disrupt food systems globally. The committee predicted a deterioration in the nutritional status of individuals due to altered dietary practices259. Particular concern was expressed over ‘food environments’, with regard to both external (availability and quality) and internal (accessibility, affordability, acceptability, and desirability) dimensions of the food systems259. Observations, more than a year after the onset of the pandemic, now appear to confirm earlier fears of malnutrition and disrupted food environments, particularly in disadvantaged communities260. In general, the availability of healthy, plant-based food is ample in well-to-do communities. However, access to such food during the pandemic could be limited, at least in some settings and for specific populations. This lack of access may present health risks, such as lower immunity and adverse chronic disease outcomes, to individuals in those settings. Alternatively, staying at home has encouraged individuals in some populations to eat fresh, homemade food261, likely due to additional time available to cook. Home-cooking not only helps cut down the intake of unhealthy processed and fast foods but also has proven emotional and health benefits. Further research is needed to understand the motivational factors behind healthy dietary practices during the pandemic and whether pre-pandemic awareness and practices likely had a positive influence.\n\nIt is well known that any amount of physical activity, no matter how little, is beneficial. Sedentary behavior associated with excessive television watching, increased internet browsing, playing screen games, and using mobile devices are shown to negatively impact chronic disease outcomes262. With parks and gymnasiums closed and public movement in the open discouraged, people’s ability to remain physically active has been challenged during the lockdown period. Though the majority of studies have shown a reduction in physical activity levels and increased sedentariness during the lockdown, it is heartening to note that some individuals in select settings have seen an opportunity to be creative in finding ways of staying even minimally active (e.g., gardening, exploring online free exercise routines, and walking up and down the stairs/steps) in a home environment69,263.\n\nAdequate sleep improves concentration and diligent decision-making. Disrupted and suboptimal sleep on the other hand has been correlated with an elevated body mass index, obesity, metabolic syndrome, and type 2 diabetes264. Exposure to blue light also increases night-time heart rate, blood pressure, and core body temperature, and suppresses melatonin and sleepiness. The high prevalence of insomnia and an increase in screen time during the lockdown periods are concerning and a reversal of some of these newfound habits will be important in order to promote sleep hygiene in communities and reap the benefits of sleep in improving mood, immunity, and overall health and well-being of individuals and communities.\n\nReports of people hoarding cigarettes and alcohol along with food and toilet paper during the early phases of the pandemic are suggestive of the fact that smoking cessation and quitting alcohol may not have been a priority during the lockdown period; our review confirms this. Some smokers wanting to quit may have found accessing smoking cessation clinics a challenge due to the suspension of non-essential health services, and this lack of access to addiction clinicals will have also affected those dependent on alcohol and other psychoactive substances. Getting substance cessation and control programs back on track at local, national, and international levels will require a redoubling of efforts as countries start relaxing lockdown measures.\n\nMost of the studies in our review have unequivocally pointed towards high stress levels among populations worldwide during COVID-19 lockdowns. Stress is causally associated with risky behaviors, such as smoking, physical inactivity, and heavy alcohol use, lending to additional concern since these are independent risk factors for chronic diseases. However, on the positive side, staying at home provides an opportunity for families to bond and engage in activities at their convenience, which can elicit relaxation and calming responses. Examples of such activities include prayers, meditation, and breathing exercises, all having positive health benefits265. Nevertheless, we did not find any studies where communities claimed to be using such positive coping measures to alleviate stress. This may indicate a lack of awareness in communities regarding the importance of healthy lifestyle measures for stress management, as well as public health professionals/healthcare practitioners not emphasizing the importance of addressing lifestyle-related factors adequately.\n\nMore importantly, one cannot deny that of all the lifestyle factors altered during COVID-19 lockdowns, the crucial one has been the loss of connectedness and social networking. This is unfortunate since positive resonance and micro-moments of connectivity encountered in situations of togetherness are associated with health and longevity. Virtual connectivity, though inadequately studied, and small acts of kindness where possible during this period, remain the best measures of improving relationships and connectedness. The lockdown has no doubt led to an increase in family time, at least for nuclear families in most instances. This may have been an opportune time for families to bond and strengthen relationships. One concern of staying home, however, has been reports of increased domestic violence266. Future research is likely to provide more answers to the questions surrounding the nature of relationships and domestic activities, and their overall impact—positive or negative—on mental and physical health.\n\nDuring this period, patients with pre-existing NCDs have suffered both from their inability to maintain a healthy lifestyle and neglect from national health authorities and hospitals with guidance issued to delay routine care and non-urgent procedures. Since the advisory by the US Medicare and Medicaid Centers in mid-March 2020 to delay non-urgent procedures, adult patient visits for primary care and gastroenterology services declined by 49% and 61%, respectively267. This could, inevitably, compromise patients receiving timely care. Tapper and Asrani268 discuss care in the context of managing patients with liver cirrhosis (a common complication of obesity and diabetes) during COVID-19 and suggest three challenging phases in treating patients with chronic disease: 1) the current ‘intense period’ with a delay in routine care, 2) a ‘return to the norm’ when physical distancing ends and health systems respond to a backlog of cases, and 3) a ‘protracted period’ of poor outcomes due to unabated disease progression. The world is headed towards a catch-up period concerning NCDs due to altered lifestyles and concomitant treatment backlog.\n\nThe American College of Lifestyle Medicine proposes healthy lifestyle measures to reduce chronic disease risk and improve immunity during this period1 (Table 1). Though the measures may appear relatively easy and simple enough to implement, many people may not adhere to these recommendations for a variety of reasons, including poverty, lack of education, unaffordability of technological resources, cramped living spaces, and poor city planning. Governments, health care practitioners, and communities should do everything possible to break those barriers and ensure access to healthy lifestyle measures for all.\n\nThis narrative review is a comprehensive analysis of the existing literature on the impact of COVID-19-related lockdown on the lifestyles of people globally. As the review is narrative, we included all the relevant and available published literature on the subject to ensure comprehensiveness. We have not done a quality assessment of each of the publications and instead used data as reported in the articles. Most of the studies included in our review are observational, which is an inherent limitation of the review study design. Despite this general limitation—as is the case with all narrative reviews—we do not consider this a major impediment to our research pursuit, as our analysis relies largely on trends and qualitative aspects of data. We only searched two databases for the study and with the huge volume of studies in this broad subject, it is possible we might have inadvertently missed a very small number of studies in our synthesis. The point of concept saturation was based on judgement of the authors though acceptable in an interpretivist paradigm, this can be seen as a limitation in a positivist paradigm. We also acknowledge that home quarantine, institutional quarantine, community quarantine, and isolation can each have different levels of impact on lifestyles, but did not find an adequate number of studies in each category to analyze them separately.\n\n\nConclusions\n\nCOVID-19 has disrupted our lifestyle balance. Based on its rapid assessment of service delivery for NCDs in 163 countries, the World Health Organization has identified that the COVID-19 pandemic could throw the global health progress on NCDs off track269. This requires that we act as one world and make every effort to promote healthy lifestyles in communities worldwide. COVID-19 will likely redefine conventional public health by placing additional emphasis on healthy lifestyles, disease prevention, and self-care. Given the strong evidence in favor of lifestyle medicine, the incorporation of lifestyle medicine in day-to-day medical practice and public health approaches is likely to receive worldwide attention. Serious consideration should be given to augmenting professional health curricula by including topics such as evidence-based public health practices, lifestyle medicine, and building health systems that can address the holistic needs of local populations before, during, and after crises. Also, integrating basic health, infectious disease, and lifestyle education in school and undergraduate college education would be a step in the right direction. It would be up to the governments, communities, and healthcare delivery systems to learn and benefit from the lifestyle medicine lessons learnt—during and consequent to the COVID-19 pandemic—with the ultimate objective of promoting healthy lifestyles in communities.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nHarvard Dataverse: COVID-19 and lifestyle - a narrative review - supplementary material. https://doi.org/10.7910/DVN/ZIA8LI4\n\nThis project contains the following extended data:\n\nSupplementary Materials.docx (Supplementary material 1: SANRA—a scale for the quality assessment of narrative review articles; Supplementary material 2: Search results and Supplementary Material 3: Included Studies (2021-04-24))\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).", "appendix": "Author contributions\n\n\n\nSathyanarayanan Doraiswamy (SD), Sohaila Cheema (SC), Ahmad Al Mulla (AM), and Ravinder Mamtani (RM) collectively contributed to the conception of the study. SD carried out the literature search, screening, and data extraction. Analysis and manuscript drafting were carried out by SD with support from SC, AM and RM. All authors read, edited, and approved the final manuscript.\n\n\nAcknowledgments\n\nWe would like to thank Silva Kouyoumjian, Clinical Research Coordinator, Tobacco Control Center, Hamad Medical Corporation, Qatar for a friendly peer review of the manuscript, Cathleen de Groot, Manager, User Service, Distributed eLibrary Weill Cornell Medicine-Qatar for her editing and formatting services and Anupama Jithesh, Projects Coordinator, Institute for Population Health, Weill Cornell Medicine-Qatar for assisting in data tabulation.\n\n\nReferences\n\nLeanne M: Lifestyle Medicine: More Relevant Than Ever in the Face of COVID-19. 2020. Reference Source\n\nGreen BN, Johnson CD, Adams A: Writing narrative literature reviews for peer-reviewed journals: secrets of the trade. J Chiropr Med. 2006; 5(3): 101–117. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaethge C, Goldbeck-Wood S, Mertens S: SANRA-a scale for the quality assessment of narrative review articles. Res Integr Peer Rev. 2019; 4: 5. Publisher Full Text\n\nDoraiswamy S: COVID-19 and lifestyle - a narrative review - supplementary material. Harvard Dataverse, V1. 2021. http://www.doi.org/10.7910/DVN/ZIA8LI\n\nHupe M: EndNote X9. Journal of Electronic Resources in Medical Libraries. 2019; 16(3–4): 117–119. Publisher Full Text\n\nDixon-Woods M: Critical interpretive synthesis: what it is and why it is needed. In: 14th Cochrane Colloquium. Dublin, UK Cochrane.org. 2006. Reference Source\n\nAtkins S, Lewin S, Smith H, et al.: Conducting a meta-ethnography of qualitative literature: Lessons learnt. BMC Med Res Methodol. 2008; 8: 21. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPacheco-Vega R: How to do a literature review: Citation tracing, concept saturation and results mind-mapping. 2016. Reference Source\n\nDi Santo SG, Franchini F, Filiputti B, et al.: The Effects of COVID-19 and Quarantine Measures on the Lifestyles and Mental Health of People Over 60 at Increased Risk of Dementia. Front Psychiatry. 2020; 11: 578628. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCheikh Ismail L, Osaili TM, Mohamad MN, et al.: Assessment of eating habits and lifestyle during the coronavirus 2019 pandemic in the Middle East and North Africa region: a cross-sectional study. Br J Nutr. 2020: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuber BC, Steffen J, Schlichtiger J, et al.: Alteration of physical activity during COVID-19 pandemic lockdown in young adults. J Transl Med. 2020; 18(1): 410. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPerez-Rodrigo C, Gianzo Citores M, Hervas Barbara G, et al.: Patterns of Change in Dietary Habits and Physical Activity during Lockdown in Spain Due to the COVID-19 Pandemic. Nutrients. 2021; 13(2): 300. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGórnicka M, Drywień ME, Zielinska MA, et al.: Dietary and Lifestyle Changes During COVID-19 and the Subsequent Lockdowns among Polish Adults: A Cross-Sectional Online Survey PLifeCOVID-19 Study. Nutrients. 2020; 12(8): 2324. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSidor A, Rzymski P: Dietary Choices and Habits during COVID-19 Lockdown: Experience from Poland. Nutrients. 2020; 12(6): 1657. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nScarmozzino F, Visioli F: Covid-19 and the Subsequent Lockdown Modified Dietary Habits of Almost Half the Population in an Italian Sample. Foods. 2020; 9(5): 675. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSinisterra Loaiza LI, Vázquez Belda B, Miranda López JM, et al.: [Food habits in the Galician population during confinement byCOVID-19]. Nutr Hosp. 2020; 37(6): 1190–1196. PubMed Abstract \| Publisher Full Text\n\nAnsah EW, Sarfo JO, Apaak D: Physical activity and dietary behaviors: a phenomenological analysis of experiences of Ghanaians during the COVID-19 lockdown. Pan Afr Med J. 2020; 37(2): 199. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobinson E, Boyland E, Chisholm A, et al.: Obesity, eating behavior and physical activity during COVID-19 lockdown: A study of UK adults. Appetite. 2021; 156: 104853. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCicero AFG, Fogacci F, Giovannini M, et al.: COVID-19-Related Quarantine Effect on Dietary Habits in a Northern Italian Rural Population: Data from the Brisighella Heart Study. Nutrients. 2021; 13(2): 309. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPietrobelli A, Pecoraro L, Ferruzzi A, et al.: Effects of COVID-19 Lockdown on Lifestyle Behaviors in Children with Obesity Living in Verona, Italy: A Longitudinal Study. Obesity (Silver Spring). 2020; 28(8): 1382–1385. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarty L, de Lauzon-Guillain B, Labesse M, et al.: Food choice motives and the nutritional quality of diet during the COVID-19 lockdown in France. Appetite. 2021; 157: 105005. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Musharaf S: Prevalence and Predictors of Emotional Eating among Healthy Young Saudi Women during the COVID-19 Pandemic. Nutrients. 2020; 12(10): 2923. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLópez-Moreno M, López MTI, Miguel M, et al.: Physical and Psychological Effects Related to Food Habits and Lifestyle Changes Derived from Covid-19 Home Confinement in the Spanish Population. Nutrients. 2020; 12(11): 3445. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBin Zarah A, Enriquez-Marulanda J, Andrade JM: Relationship between Dietary Habits, Food Attitudes and Food Security Status among Adults Living within the United States Three Months Post-Mandated Quarantine: A Cross-Sectional Study. Nutrients. 2020; 12(11): 3468. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPellegrini M, Ponzo V, Rosato R, et al.: Changes in Weight and Nutritional Habits in Adults with Obesity during the \"Lockdown\" Period Caused by the COVID-19 Virus Emergency. Nutrients. 2020; 12(7): 2016. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPhilippe K, Chabanet C, Issanchou S, et al.: Child eating behaviors, parental feeding practices and food shopping motivations during the COVID-19 lockdown in France: (How) did they change? Appetite. 2021; 161: 105132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKriaucioniene V, Bagdonaviciene L, Rodríguez-Pérez C, et al.: Associations between Changes in Health Behaviours and Body Weight during the COVID-19 Quarantine in Lithuania: The Lithuanian COVIDiet Study. Nutrients. 2020; 12(10): 3119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGiacalone D, Frøst MB, Rodríguez-Pérez C: Reported Changes in Dietary Habits During the COVID-19 Lockdown in the Danish Population: The Danish COVIDiet Study. Front Nutr. 2020; 7: 592112. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang S, Guo B, Ao L, et al.: Obesity and activity patterns before and during COVID-19 lockdown among youths in China. Clin Obes. 2020; 10(6): e12416. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShammi M, Bodrud-Doza M, Towfiqul Islam ARM, et al.: COVID-19 pandemic, socioeconomic crisis and human stress in resource-limited settings: A case from Bangladesh. Heliyon. 2020; 6(5): e04063. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPakravan-Charvadeh MR, Savari M, Khan HA, et al.: Determinants of household vulnerability to food insecurity during COVID-19 lockdown in a mid-term period in Iran. Public Health Nutr. 2021: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRossinot H, Fantin R, Venne J: Behavioral Changes During COVID-19 Confinement in France: A Web-Based Study. Int J Environ Res Public Health. 2020; 17(22): 8444. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHusain W, Ashkanani F: Does COVID-19 change dietary habits and lifestyle behaviours in Kuwait: a community-based cross-sectional study. Environ Health Prev Med. 2020; 25(1): 61. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao A, Li Z, Ke Y, et al.: Dietary Diversity among Chinese Residents during the COVID-19 Outbreak and Its Associated Factors. Nutrients. 2020; 12(6): 1699. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang J, Zhao A, Ke Y, et al.: Dietary Behaviors in the Post-Lockdown Period and Its Effects on Dietary Diversity: The Second Stage of a Nutrition Survey in a Longitudinal Chinese Study in the COVID-19 Era. Nutrients. 2020; 12(11): 3269. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodríguez-Pérez C, Molina-Montes E, Verardo V, et al.: Changes in Dietary Behaviours during the COVID-19 Outbreak Confinement in the Spanish COVIDiet Study. Nutrients. 2020; 12(6): 1730. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRuiz-Roso MB, de Carvalho Padilha P, Mantilla-Escalante DC, et al.: Covid-19 Confinement and Changes of Adolescent's Dietary Trends in Italy, Spain, Chile, Colombia and Brazil. Nutrients. 2020; 12(6): 1807. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNicodemo M, Spreghini MR, Manco M, et al.: Childhood Obesity and COVID-19 Lockdown: Remarks on Eating Habits of Patients Enrolled in a Food-Education Program. Nutrients. 2021; 13(2): 383. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCooper M, Reilly EE, Siegel JA, et al.: Eating disorders during the COVID-19 pandemic and quarantine: an overview of risks and recommendations for treatment and early intervention. Eat Disord. 2020: 1–23. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarchitelli S, Mazza C, Lenzi A, et al.: Weight Gain in a Sample of Patients Affected by Overweight/Obesity with and without a Psychiatric Diagnosis during the Covid-19 Lockdown. Nutrients. 2020; 12(11): 3525. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobertson M, Duffy F, Newman E, et al.: Exploring changes in body image, eating and exercise during the COVID-19 lockdown: A UK survey. Appetite. 2021; 159: 105062. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCastellini G, Cassioli E, Rossi E, et al.: The impact of COVID-19 epidemic on eating disorders: A longitudinal observation of pre versus post psychopathological features in a sample of patients with eating disorders and a group of healthy controls. Int J Eat Disord. 2020; 53(11): 1855–1862. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaenas I, Caravaca-Sanz E, Granero R, et al.: COVID-19 and eating disorders during confinement: Analysis of factors associated with resilience and aggravation of symptoms. Eur Eat Disord Rev. 2020; 28(6): 855–863. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMachado PPP, Pinto-Bastos A, Ramos R, et al.: Impact of COVID-19 lockdown measures on a cohort of eating disorders patients. J Eat Disord. 2020; 8(1): 57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHe M, Xian Y, Lv X, et al.: Changes in Body Weight, Physical Activity, and Lifestyle During the Semi-lockdown Period After the Outbreak of COVID-19 in China: An Online Survey. Disaster Med Public Health Prep. 2020; 1–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCancello R, Soranna D, Zambra G, et al.: Determinants of the Lifestyle Changes during COVID-19 Pandemic in the Residents of Northern Italy. Int J Environ Res Public Health. 2020; 17(17): 6287. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmmar A, Brach M, Trabelsi K, et al.: Effects of COVID-19 Home Confinement on Eating Behaviour and Physical Activity: Results of the ECLB-COVID19 International Online Survey. Nutrients. 2020; 12(6): 1583. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStanton R, To QG, Khalesi S, et al.: Depression, Anxiety and Stress during COVID-19: Associations with Changes in Physical Activity, Sleep, Tobacco and Alcohol Use in Australian Adults. Int J Environ Res Public Health. 2020; 17(11): 4065. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcCarthy H, Potts HWW, Fisher A: Physical Activity Behavior Before, During, and After COVID-19 Restrictions: Longitudinal Smartphone-Tracking Study of Adults in the United Kingdom. J Med Internet Res. 2021; 23(2): e23701. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeyer J, McDowell C, Lansing J, et al.: Changes in Physical Activity and Sedentary Behavior in Response to COVID-19 and Their Associations with Mental Health in 3052 US Adults. Int J Environ Res Public Health. 2020; 17(18): 6469. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang Y, Koenigstorfer J: Determinants of physical activity maintenance during the Covid-19 pandemic: a focus on fitness apps. Transl Behav Med. 2020; 10(4): 835–842. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTo QG, Duncan MJ, Van Itallie A, et al.: Impact of COVID-19 on Physical Activity Among 10,000 Steps Members and Engagement With the Program in Australia: Prospective Study. J Med Internet Res. 2021; 23(1): e23946. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBourdas DI, Zacharakis ED: Evolution of changes in physical activity over lockdown time: Physical activity datasets of four independent adult sample groups corresponding to each of the last four of the six COVID-19 lockdown weeks in Greece. Data Brief. 2020; 32: 106301. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOng JL, Lau T, Massar SAA, et al.: COVID-19-related mobility reduction: heterogenous effects on sleep and physical activity rhythms. Sleep. 2021; 44(2): zsaa179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang SX, Wang Y, Rauch A, et al.: Unprecedented disruption of lives and work: Health, distress and life satisfaction of working adults in China one month into the COVID-19 outbreak. Psychiatry Res. 2020; 288: 112958. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlonso-Martínez AM, Ramírez-Vélez R, García-Alonso Y, et al.: Physical Activity, Sedentary Behavior, Sleep and Self-Regulation in Spanish Preschoolers during the COVID-19 Lockdown. Int J Environ Res Public Health. 2021; 18(2): 693. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMon-López D, Bernardez-Vilaboa R, Fernandez-Balbuena AA, et al.: The Influence of COVID-19 Isolation on Physical Activity Habits and Its Relationship with Convergence Insufficiency. Int J Environ Res Public Health. 2020; 17(20): 7406. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLopez-Gil JF, Tremblay MS, Brazo-Sayavera J: Changes in Healthy Behaviors and Meeting 24-h Movement Guidelines in Spanish and Brazilian Preschoolers, Children and Adolescents during the COVID-19 Lockdown. Children (Basel). 2021; 8(2): 83. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLópez-Bueno R, López-Sánchez GF, Casajús JA, et al.: Health-Related Behaviors Among School-Aged Children and Adolescents During the Spanish Covid-19 Confinement. Front Pediatr. 2020; 8: 573. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoore SA, Faulkner G, Rhodes RE, et al.: Impact of the COVID-19 virus outbreak on movement and play behaviours of Canadian children and youth: a national survey. Int J Behav Nutr Phys Act. 2020; 17(1): 85. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuerrero MD, Vanderloo LM, Rhodes RE, et al.: Canadian children's and youth's adherence to the 24-h movement guidelines during the COVID-19 pandemic: A decision tree analysis. J Sport Health Sci. 2020; 9(4): 313–321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmidt SCE, Anedda B, Burchartz A, et al.: Physical activity and screen time of children and adolescents before and during the COVID-19 lockdown in Germany: a natural experiment. Sci Rep. 2020; 10(1): 21780. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRogers NT, Waterlow NR, Brindle H, et al.: Behavioral Change Towards Reduced Intensity Physical Activity Is Disproportionately Prevalent Among Adults With Serious Health Issues or Self-Perception of High Risk During the UK COVID-19 Lockdown. Front Public Health. 2020; 8: 575091. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTornaghi M, Lovecchio N, Vandoni M, et al.: Physical activity levels across COVID-19 outbreak in youngsters of Northwestern Lombardy. J Sports Med Phys Fitness. 2020. PubMed Abstract \| Publisher Full Text\n\nChopra S, Ranjan P, Singh V, et al.: Impact of COVID-19 on lifestyle-related behaviours- a cross-sectional audit of responses from nine hundred and ninety-five participants from India. Diabetes Metab Syndr. 2020; 14(6): 2021–2030. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaertl T, De Bock F, Huebl L, et al.: Physical Activity during COVID-19 in German Adults: Analyses in the COVID-19 Snapshot Monitoring Study (COSMO). Int J Environ Res Public Health. 2021; 18(2): 507. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSalman D, Beaney T, Robb CE, et al.: Impact of social restrictions during the COVID-19 pandemic on the physical activity levels of older adults: an analysis of the CHARIOT COVID-19 Rapid Response Study. medRxiv. 2021; 2021.2001.2026.21250520. Publisher Full Text\n\nShinohara T, Saida K, Tanaka S, et al.: Association between frailty and changes in lifestyle and physical or psychological conditions among older adults affected by the coronavirus disease 2019 countermeasures in Japan. Geriatr Gerontol Int. 2021; 21(1): 39–42. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConstandt B, Thibaut E, De Bosscher V, et al.: Exercising in Times of Lockdown: An Analysis of the Impact of COVID-19 on Levels and Patterns of Exercise among Adults in Belgium. Int J Environ Res Public Health. 2020; 17(11): 4144. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartinez-de-Quel O, Suarez-Iglesias D, Lopez-Flores M, et al.: Physical activity, dietary habits and sleep quality before and during COVID-19 lockdown: A longitudinal study. Appetite. 2021; 158: 105019. PubMed Abstract \| Publisher Full Text\n\nRichardson DL, Duncan MJ, Clarke ND, et al.: The influence of COVID-19 measures in the United Kingdom on physical activity levels, perceived physical function and mood in older adults: A survey-based observational study. J Sports Sci. 2021; 39(8): 887–899. PubMed Abstract \| Publisher Full Text\n\nPark S, Kim B, Lee J: Social Distancing and Outdoor Physical Activity During the COVID-19 Outbreak in South Korea: Implications for Physical Distancing Strategies. Asia Pac J Public Health. 2020; 32(6–7): 360–362. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAung MN, Yuasa M, Koyanagi Y, et al.: Sustainable health promotion for the seniors during COVID-19 outbreak: a lesson from Tokyo. J Infect Dev Ctries. 2020; 14(4): 328–331. PubMed Abstract \| Publisher Full Text\n\nJanssen X, Fleming L, Kirk A, et al.: Changes in Physical Activity, Sitting and Sleep across the COVID-19 National Lockdown Period in Scotland. Int J Environ Res Public Health. 2020; 17(24): 9362. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGilic B, Ostojic L, Corluka M, et al.: Contextualizing Parental/Familial Influence on Physical Activity in Adolescents before and during COVID-19 Pandemic: A Prospective Analysis. Children (Basel). 2020; 7(9): 125. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRomero-Blanco C, Rodríguez-Almagro J, Onieva-Zafra MD, et al.: Physical Activity and Sedentary Lifestyle in University Students: Changes during Confinement Due to the COVID-19 Pandemic. Int J Environ Res Public Health. 2020; 17(18): 6567. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpence JC, Rhodes RE, McCurdy A, et al.: Determinants of physical activity among adults in the United Kingdom during the COVID-19 pandemic: The DUK-COVID study. Br J Health Psychol. 2020; 26(2): 588–605. PubMed Abstract \| Publisher Full Text\n\nWerneck AO, Silva DR, Malta DC, et al.: Physical inactivity and elevated TV-viewing reported changes during the COVID-19 pandemic are associated with mental health: A survey with 43,995 Brazilian adults. J Psychosom Res. 2021; 140: 110292. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchuch FB, Bulzing RA, Meyer J, et al.: Associations of moderate to vigorous physical activity and sedentary behavior with depressive and anxiety symptoms in self-isolating people during the COVID-19 pandemic: A cross-sectional survey in Brazil. Psychiatry Res. 2020; 292: 113339. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmatori S, Donati Zeppa S, Preti A, et al.: Dietary Habits and Psychological States during COVID-19 Home Isolation in Italian College Students: The Role of Physical Exercise. Nutrients. 2020; 12: 3660. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShah SMA, Mohammad D, Qureshi MFH, et al.: Prevalence, Psychological Responses and Associated Correlates of Depression, Anxiety and Stress in a Global Population, During the Coronavirus Disease (COVID-19) Pandemic. Community Ment Health J. 2021; 57(1): 101–110. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSfendla A, Hadrya F: Factors Associated with Psychological Distress and Physical Activity During the COVID-19 Pandemic. Health Secur. 2020; 18(6): 444–453. PubMed Abstract \| Publisher Full Text\n\nDobler CL, Krüger B, Strahler J, et al.: Physical Activity and Mental Health of Patients with Pulmonary Hypertension during the COVID-19 Pandemic. J Clin Med. 2020; 9(12): 4023. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nErnstsen L, Havnen A: Mental health and sleep disturbances in physically active adults during the COVID-19 lockdown in Norway: does change in physical activity level matter? Sleep Med. 2021; 77: 309–312. PubMed Abstract \| Publisher Full Text\n\nCarriedo A, Cecchini JA, Fernández-Río J, et al.: Resilience and physical activity in people under home isolation due to COVID-19: A preliminary evaluation. Ment Health Phys Act. 2020; 19: 100361. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCostabile T, Carotenuto A, Lavorgna L, et al.: COVID-19 pandemic and mental distress in multiple sclerosis: implications for clinical management. Eur J Neurol. 2020; 10.1111/ene.14580. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVancini RL, Camargo-Neto L, de Lira CAB, et al.: Physical Activity and Sociodemographic Profile of Brazilian People during COVID-19 Outbreak: An Online and Cross-Sectional Survey. Int J Environ Res Public Health. 2020; 17(21): 7964. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSzabó C, Pukánszky J, Kemény L: Psychological Effects of the COVID-19 Pandemic on Hungarian Adults. Int J Environ Res Public Health. 2020; 17(24): 9565. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee PH, Marek J, Nálevka P: Sleep pattern in the US and 16 European countries during the COVID-19 outbreak using crowdsourced smartphone data. Eur J Public Health. 2021; 31(1): 23–30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCellini N, Canale N, Mioni G, et al.: Changes in sleep pattern, sense of time and digital media use during COVID-19 lockdown in Italy. J Sleep Res. 2020; 29(4): e13074. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYuksel D, McKee GB, Perrin PB, et al.: Sleeping when the world locks down: Correlates of sleep health during the COVID-19 pandemic across 59 countries. Sleep Health. 2021; 7(2): 134–142. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeck F, Léger D, Fressard L, et al.: Covid-19 health crisis and lockdown associated with high level of sleep complaints and hypnotic uptake at the population level. J Sleep Res. 2021; 30(1): e13119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarelli S, Castelnuovo A, Somma A, et al.: Impact of COVID-19 lockdown on sleep quality in university students and administration staff. J Neurol. 2021; 268(1): 8–15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLahiri A, Jha SS, Acharya R, et al.: Correlates of insomnia among the adults during COVID19 pandemic: evidence from an online survey in India. Sleep Med. 2021; 77: 66–73. PubMed Abstract \| Publisher Full Text\n\nBeck F, Leger D, Cortaredona S, et al.: Would we recover better sleep at the end of Covid-19? A relative improvement observed at the population level with the end of the lockdown in France. Sleep Med. 2021; 78: 115–119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Ajlouni YA, Park SH, Alawa J, et al.: Anxiety and depressive symptoms are associated with poor sleep health during a period of COVID-19-induced nationwide lockdown: a cross-sectional analysis of adults in Jordan. BMJ Open. 2020; 10(12): e041995. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBartoszek A, Walkowiak D, Bartoszek A, et al.: Mental Well-Being (Depression, Loneliness, Insomnia, Daily Life Fatigue) during COVID-19 Related Home-Confinement-A Study from Poland. Int J Environ Res Public Health. 2020; 17(20): 7417. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPérez-Carbonell L, Meurling IJ, Wassermann D, et al.: Impact of the novel coronavirus (COVID-19) pandemic on sleep. J Thorac Dis. 2020; 12(Suppl 2): S163–S175. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSinha M, Pande B, Sinha R: Impact of COVID-19 lockdown on sleep-wake schedule and associated lifestyle related behavior: A national survey. J Public Health Res. 2020; 9(3): 1826. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMajumdar P, Biswas A, Sahu S: COVID-19 pandemic and lockdown: cause of sleep disruption, depression, somatic pain, and increased screen exposure of office workers and students of India. Chronobiol Int. 2020; 37(8): 1191–1200. PubMed Abstract \| Publisher Full Text\n\nPinto J, van Zeller M, Amorim P, et al.: Sleep quality in times of Covid-19 pandemic. Sleep Med. 2020; 74: 81–85. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCajochen C, Münch M, Kobialka S, et al.: High sensitivity of human melatonin, alertness, thermoregulation, and heart rate to short wavelength light. J Clin Endocrinol Metab. 2005; 90(3): 1311–1316. PubMed Abstract \| Publisher Full Text\n\nAltena E, Baglioni C, Espie CA, et al.: Dealing with sleep problems during home confinement due to the COVID-19 outbreak: Practical recommendations from a task force of the European CBT-I Academy. J Sleep Res. 2020; 29(4): e13052. PubMed Abstract \| Publisher Full Text\n\nBlume C, Schmidt MH, Cajochen C: Effects of the COVID-19 lockdown on human sleep and rest-activity rhythms. Curr Biol. 2020; 30(14): R795–R797. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWright KP Jr, Linton SK, Withrow D, et al.: Sleep in university students prior to and during COVID-19 Stay-at-Home orders. Curr Biol. 2020; 30(14): R797–R798. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKocevska D, Blanken TF, Van Someren EJW, et al.: Sleep quality during the COVID-19 pandemic: not one size fits all. Sleep Med. 2020; 76: 86–88. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGao C, Scullin MK: Sleep health early in the coronavirus disease 2019 (COVID-19) outbreak in the United States: integrating longitudinal, cross-sectional, and retrospective recall data. Sleep Med. 2020; 73: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGruber R, Saha S, Somerville G, et al.: The impact of COVID-19 related school shutdown on sleep in adolescents: a natural experiment. Sleep Med. 2020; 76: 33–35. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoitblat Y, Burger J, Leit A, et al.: Stay-at-home circumstances do not produce sleep disorders: An international survey during the COVID-19 pandemic. J Psychosom Res. 2020; 139: 110282. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJoyce AA, Styklunas GM, Rigotti NA, et al.: Quit Experiences among Primary Care Patients Enrolled in a Smoking Cessation Pilot RCT Early in the COVID-19 Pandemic. Int J Environ Res Public Health. 2021; 18(3): 1011. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKlemperer EM, West JC, Peasley-Miklus C, et al.: Change in Tobacco and Electronic Cigarette Use and Motivation to Quit in Response to COVID-19. Nicotine Tob Res. 2020; 22(9): 1662–1663. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBommele J, Hopman P, Walters BH, et al.: The double-edged relationship between COVID-19 stress and smoking: Implications for smoking cessation. Tob Induc Dis. 2020; 18: 63. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYach D: Tobacco Use Patterns in Five Countries During the COVID-19 Lockdown. Nicotine Tob Res. 2020; 22(9): 1671–1672. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFerrante G, Camussi E, Piccinelli C, et al.: Did social isolation during the SARS-CoV-2 epidemic have an impact on the lifestyles of citizens? Epidemiol Prev. 2020; 44(5–6 Suppl 2): 353–362. PubMed Abstract \| Publisher Full Text\n\nMartínez-Lezaun I, Santamaría-Vázquez M, Del Líbano M: Influence of Confinement by COVID-19 on the Quality of Sleep and the Interests of University Students. Nat Sci Sleep. 2020; 12: 1075–1081. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChagué F, Boulin M, Eicher J, et al.: Alarming increased rate of smoking and associated lifestyle behaviours in patients with chronic cardiac diseases during COVID-19 pandemic related lockdown. Archives of Cardiovascular Diseases Supplements. 2021; 13(1): 127. Publisher Full Text\n\nCaponnetto P, Inguscio L, Saitta C, et al.: Smoking behavior and psychological dynamics during COVID-19 social distancing and stay-at-home policies: A survey. Health Psychol Res. 2020; 8(1): 9124. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChodkiewicz J, Talarowska M, Miniszewska J, et al.: Alcohol Consumption Reported during the COVID-19 Pandemic: The Initial Stage. Int J Environ Res Public Health. 2020; 17(13): 4677. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoschuetz N, Cheng S, Mei L, et al.: Changes in Alcohol Use Patterns in the United States During COVID-19 Pandemic. WMJ. 2020; 119(3): 171–176. PubMed Abstract\n\nGarnett C, Jackson S, Oldham M, et al.: Factors associated with drinking behaviour during COVID-19 social distancing and lockdown among adults in the UK. Drug Alcohol Depend. 2021; 219: 108461. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBalhara YPS, Singh S, Narang P: Effect of lockdown following COVID-19 pandemic on alcohol use and help-seeking behavior: Observations and insights from a sample of alcohol use disorder patients under treatment from a tertiary care center. Psychiatry Clin Neurosci. 2020; 74(8): 440–441. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHobin E, Smith B: Is another public health crisis brewing beneath the COVID-19 pandemic? Can J Public Health. 2020; 111(3): 392–396. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJacob L, Smith L, Armstrong NC, et al.: Alcohol use and mental health during COVID-19 lockdown: A cross-sectional study in a sample of UK adults. Drug Alcohol Depend. 2020; 219: 108488. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSun Y, Li Y, Bao Y, et al.: Brief Report: Increased Addictive Internet and Substance Use Behavior During the COVID-19 Pandemic in China. Am J Addict. 2020; 29(4): 268–270. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSzajnoga D, Klimek-Tulwin M, Piekut A: COVID-19 lockdown leads to changes in alcohol consumption patterns. Results from the Polish national survey. J Addict Dis. 2020;39(2): 215–225. PubMed Abstract \| Publisher Full Text\n\nThe Lancet Gastroenterology HDrinking alone: COVID-19, lockdown, and alcohol-related harm. Lancet Gastroenterol Hepatol. 2020; 5(7): 625. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNeill E, Meyer D, Toh WL, et al.: Alcohol use in Australia during the early days of the COVID-19 pandemic: Initial results from the COLLATE project. Psychiatry Clin Neurosci. 2020; 74(10): 542–549. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmits E, Glowacz F: Changes in Alcohol Use During the COVID-19 Pandemic: Impact of the Lockdown Conditions and Mental Health Factors. Int J Ment Health Addict. 2021; 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKillgore WDS, Cloonan SA, Taylor EC, et al.: Alcohol dependence during COVID-19 lockdowns. Psychiatry Res. 2020; 296: 113676. PubMed Abstract \| Publisher Full Text\n\nKim JU, Majid A, Judge R, et al.: Effect of COVID-19 lockdown on alcohol consumption in patients with pre-existing alcohol use disorder. Lancet Gastroenterol Hepatol. 2020; 5(10): 886–887. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWhite HR, Stevens AK, Hayes K, et al.: Changes in Alcohol Consumption Among College Students Due to COVID-19: Effects of Campus Closure and Residential Change. J Stud Alcohol Drugs. 2020; 81(6): 725–730. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBollen Z, Pabst A, Creupelandt C, et al.: Prior drinking motives predict alcohol consumption during the COVID-19 lockdown: A cross-sectional online survey among Belgian college students. Addict Behav. 2021; 115: 106772. PubMed Abstract \| Publisher Full Text\n\nDietze PM, Peacock A: Illicit drug use and harms in Australia in the context of COVID-19 and associated restrictions: Anticipated consequences and initial responses. Drug Alcohol Rev. 2020; 39(4): 297–300. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRolland B, Haesebaert F, Zante E, et al.: Global changes and factors of increase in caloric/salty food, screen, and substance use during the early COVID-19 containment phase in France: a general population online survey. JMIR Public Health Surveill. 2020; 6(3): e19630. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCousijn J, Kuhns L, Larsen H, et al.: For better or for worse? A pre-post exploration of the impact of the COVID-19 lockdown on cannabis users. Addiction. 2021. PubMed Abstract \| Publisher Full Text\n\nRogers AH, Shepherd JM, Garey L, et al.: Psychological factors associated with substance use initiation during the COVID-19 pandemic. Psychiatry Res. 2020; 293: 113407. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobinson E, Daly M: Explaining the rise and fall of psychological distress during the COVID-19 crisis in the United States: Longitudinal evidence from the Understanding America Study. Br J Health Psychol. 2020; 26(2): 570–587. PubMed Abstract \| Publisher Full Text\n\nSchwinger M, Trautner M, Kärchner H, et al.: Psychological Impact of Corona Lockdown in Germany: Changes in Need Satisfaction, Well-Being, Anxiety, and Depression. Int J Environ Res Public Health. 2020; 17(23): 9083. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLima CKT, Carvalho PMM, Lima I, et al.: The emotional impact of Coronavirus 2019-nCoV (new Coronavirus disease). Psychiatry Res. 2020; 287: 112915. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBenke C, Autenrieth LK, Asselmann E, et al.: Lockdown, quarantine measures, and social distancing: Associations with depression, anxiety and distress at the beginning of the COVID-19 pandemic among adults from Germany. Psychiatry Res. 2020; 293: 113462. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlanchuelo-Gómez A, Odriozola-González P, Irurtia MJ, et al.: Longitudinal evaluation of the psychological impact of the COVID-19 crisis in Spain. J Affect Disord. 2020; 277: 842–849. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFiorenzato E, Zabberoni S, Costa A, et al.: Cognitive and mental health changes and their vulnerability factors related to COVID-19 lockdown in Italy. PLoS One. 2021; 16(1): e0246204. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGloster AT, Lamnisos D, Lubenko J, et al.: Impact of COVID-19 pandemic on mental health: An international study. PLoS One. 2020; 15(12): e0244809. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarre-Olmo J, Turró-Garriga O, Martí-Lluch R, et al.: Changes in lifestyle resulting from confinement due to COVID-19 and depressive symptomatology: A cross-sectional a population-based study. Compr Psychiatry. 2021; 104: 152214. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTwenge JM, Joiner TE: Mental distress among U.S. adults during the COVID-19 pandemic. J Clin Psychol. 2020; 76(12): 2170–2182. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCao W, Fang Z, Hou G, et al.: The psychological impact of the COVID-19 epidemic on college students in China. Psychiatry Res. 2020; 287: 112934. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarguilla A, Fernández-Lebrero A, Estragués-Gázquez I, et al.: Effects of COVID-19 Pandemic Confinement in Patients With Cognitive Impairment. Front Neurol. 2020; 11: 589901. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCagnin A, Di Lorenzo R, Marra C, et al.: Behavioral and Psychological Effects of Coronavirus Disease-19 Quarantine in Patients With Dementia. Front Psychiatry. 2020; 11: 578015. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGallagher S, Wetherell MA: Risk of depression in family caregivers: unintended consequence of COVID-19. BJPsych Open. 2020; 6(6): e119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKandel S, Lamsal M, Yadav SA, et al.: Lifestyle, behavior, perception and practices of Nepalese during lockdown due to COVID-19 pandemic. JNMA J Nepal Med Assoc. 2020; 58(229): 690–695. PubMed Abstract \| Free Full Text\n\nFawaz M, Samaha A: COVID-19 quarantine: Post-traumatic stress symptomatology among Lebanese citizens. Int J Soc Psychiatry. 2020; 66(7): 666–674. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlshehri FS, Alatawi Y, Alghamdi BS, et al.: Prevalence of post-traumatic stress disorder during the COVID-19 pandemic in Saudi Arabia. Saudi Pharm J. 2020; 28(12): 1666–1673. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDuong KNC, Le Bao TN, Nguyen PTL, et al.: Psychological Impacts of COVID-19 During the First Nationwide Lockdown in Vietnam: Web-Based, Cross-Sectional Survey Study. JMIR Form Res. 2020; 4(12): e24776. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTee ML, Tee CA, Anlacan JP, et al.: Psychological impact of COVID-19 pandemic in the Philippines. J Affect Disord. 2020; 277: 379–391. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVerma S, Mishra A: Depression, anxiety, and stress and socio-demographic correlates among general Indian public during COVID-19. Int J Soc Psychiatry. 2020; 66(8): 756–762. PubMed Abstract \| Publisher Full Text\n\nPandey D, Bansal S, Goyal S, et al.: Psychological impact of mass quarantine on population during pandemics-The COVID-19 Lock-Down (COLD) study. PLoS One. 2020; 15(10): e0240501. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHazarika M, Das S, Bhandari SS, et al.: The psychological impact of the COVID-19 pandemic and associated risk factors during the initial stage among the general population in India. Open J Psychiatry Allied Sci. 2021; 12(1): 31–35. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaz C, Mascialino G, Adana-Díaz L, et al.: Behavioral and sociodemographic predictors of anxiety and depression in patients under epidemiological surveillance for COVID-19 in Ecuador. PLoS One. 2020; 15(9): e0240008. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKamberi F, Jaho J, Mechili EA, et al.: Effect of Covid-19 pandemic on mental health among Albanian people residing in the country and abroad - Implications for mental care. Arch Psychiatr Nurs. 2020; 34(6): 507–512. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHyland P, Shevlin M, McBride O, et al.: Anxiety and depression in the Republic of Ireland during the COVID-19 pandemic. Acta Psychiatr Scand . 2020; 142(3): 249–256. PubMed Abstract \| Publisher Full Text\n\nSzabó C, Pukánszky J, Kemény L: Psychological Effects of the COVID-19 Pandemic on Hungarian Adults. Int J Environ Res Public Health. 2020; 17(24): 9565. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOdriozola-González P, Planchuelo-Gómez Á, Irurtia MJ, et al.: Psychological symptoms of the outbreak of the COVID-19 confinement in Spain. J Health Psychol. 2020; 1359105320967086. PubMed Abstract \| Publisher Full Text\n\nAl Zabadi H, Alhroub T, Yaseen N, et al.: Assessment of Depression Severity During Coronavirus Disease 2019 Pandemic Among the Palestinian Population: A Growing Concern and an Immediate Consideration. Front Psychiatry. 2020; 11: 570065. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPieh C, Budimir S, Delgadillo J, et al.: Mental health during COVID-19 lockdown in the United Kingdom. Psychosom Med. 2020. PubMed Abstract \| Publisher Full Text\n\nBurhamah W, AlKhayyat A, Oroszlányová M, et al.: The psychological burden of the COVID-19 pandemic and associated lockdown measures: Experience from 4000 participants. J Affect Disord. 2020; 277: 977–985. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPassos L, Prazeres F, Teixeira A, et al.: Impact on Mental Health Due to COVID-19 Pandemic: Cross-Sectional Study in Portugal and Brazil. Int J Environ Res Public Health. 2020; 17(18): 6794. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFiorillo A, Sampogna G, Giallonardo V, et al.: Effects of the lockdown on the mental health of the general population during the COVID-19 pandemic in Italy: Results from the COMET collaborative network. Eur Psychiatry. 2020; 63(1): e87. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMassad I, Al-Taher R, Massad F, et al.: The impact of the COVID-19 pandemic on mental health: early quarantine-related anxiety and its correlates among Jordanians. East Mediterr Health J. 2020; 26(10): 1165–1172. PubMed Abstract \| Publisher Full Text\n\nOrgilés M, Morales A, Delvecchio E, et al.: Immediate Psychological Effects of the COVID-19 Quarantine in Youth From Italy and Spain. Front Psychol. 2020; 11: 579038. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPigaiani Y, Zoccante L, Zocca A, et al.: Adolescent Lifestyle Behaviors, Coping Strategies and Subjective Wellbeing during the COVID-19 Pandemic: An Online Student Survey. Healthcare (Basel). 2020; 8(4): 472. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan AH, Sultana MS, Hossain S, et al.: The impact of COVID-19 pandemic on mental health & wellbeing among home-quarantined Bangladeshi students: A cross-sectional pilot study. J Affect Disord. 2020; 277: 121–128. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSzczepańska A, Pietrzyka K: The COVID-19 epidemic in Poland and its influence on the quality of life of university students (young adults) in the context of restricted access to public spaces. Z Gesundh Wiss. 2021; 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlfawaz HA, Wani K, Aljumah AA, et al.: Psychological well-being during COVID-19 lockdown: Insights from a Saudi State University's Academic Community. J King Saud Univ Sci. 2021; 33(1): 101262. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSzkody E, Stearns M, Stanhope L, et al.: Stress-Buffering Role of Social Support during COVID-19. Fam Process. 2020. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlkhamees AA, Aljohani MS, Alghesen MA, et al.: Psychological Distress in Quarantine Designated Facility During COVID-19 Pandemic in Saudi Arabia. Risk Manag Healthc Policy. 2020; 13: 3103–3120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMalkawi SH, Almhdawi K, Jaber AF, et al.: COVID-19 Quarantine-Related Mental Health Symptoms and their Correlates among Mothers: A Cross Sectional Study. Matern Child Health J. 2020; 25(5): 695–705. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHolt-Lunstad J: The Potential Public Health Relevance of Social Isolation and Loneliness: Prevalence, Epidemiology, and Risk Factors. Public Policy Aging Rep. 2018; 27(4): 127–130. Publisher Full Text\n\nHan TMW, Gong H: Investigation and analysis of negative emotion among university students during home quarantine of COVID-19. Journal of Xi'an Jiaotong University (Medical Sciences). 2021; 42: 132–136. Reference Source\n\nAdıbelli D, Sümen A: The effect of the coronavirus (COVID-19) pandemic on health-related quality of life in children. Child Youth Serv Rev. 2020; 119: 105595. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHerat M: “I feel like death on legs”: COVID-19 isolation and mental health. Soc Sci Humanit Open. 2020; 2: 100042. Publisher Full Text\n\nKang E, Lee SY, Kim MS, et al.: The Psychological Burden of COVID-19 Stigma: Evaluation of the Mental Health of Isolated Mild Condition COVID-19 Patients. J Korean Med Sci. 2021; 36(3): e33. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRossi R, Socci V, Talevi D, et al.: COVID-19 Pandemic and Lockdown Measures Impact on Mental Health Among the General Population in Italy. Front Psychiatry. 2020; 11: 790. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLu H, Nie P, Qian L: Do Quarantine Experiences and Attitudes Towards COVID-19 Affect the Distribution of Mental Health in China? A Quantile Regression Analysis. Appl Res Qual Life. 2020; 1–18. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrown L, Mossabir R, Harrison N, et al.: Life in lockdown: A telephone survey to investigate the impact of COVID-19 lockdown measures on the lives of older people (≥ 75 years). Age Ageing. 2020; 50(2): 341–346. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBigalke JA, Greenlund IM, Carter JR: Sex differences in self-report anxiety and sleep quality during COVID-19 stay-at-home orders. Biol Sex Differ. 2020; 11(1): 56. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBonati M, Campi R, Zanetti M, et al.: Psychological distress among Italians during the 2019 coronavirus disease (COVID-19) quarantine. BMC Psychiatry. 2021; 21(1): 20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrati G: Mental health and its psychosocial predictors during national quarantine in Italy against the coronavirus disease 2019 (COVID-19). Anxiety Stress Coping. 2021; 34(2): 1–12. PubMed Abstract \| Publisher Full Text\n\nAtesyakar N, Ecevitoglu A, Duman EA: Preliminary findings on the impact of COVID-19 pandemic on mood and daily routines of women from the BABIP birth cohort. Psychoneuroendocrinology. 2020; 119: 104965. Publisher Full Text\n\nLebel C, MacKinnon A, Bagshawe M, et al.: Elevated depression and anxiety symptoms among pregnant individuals during the COVID-19 pandemic. J Affect Disord. 2020; 277: 5–13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHyland P, Shevlin M, McBride O, et al.: Anxiety and depression in the Republic of Ireland during the COVID-19 pandemic. Acta Psychiatr Scand. 2020; 142(3): 249–256. PubMed Abstract \| Publisher Full Text\n\nGadermann AC, Thomson KC, Richardson CG, et al.: Examining the impacts of the COVID-19 pandemic on family mental health in Canada: findings from a national cross-sectional study. BMJ Open. 2021; 11(1): e042871. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTang W, Hu T, Hu B, et al.: Prevalence and correlates of PTSD and depressive symptoms one month after the outbreak of the COVID-19 epidemic in a sample of home-quarantined Chinese university students. J Affect Disord. 2020; 274: 1–7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGlowacz F, Schmits E: Psychological distress during the COVID-19 lockdown: The young adults most at risk. Psychiatry Res. 2020; 293: 113486. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFu W, Yan S, Zong Q, et al.: Mental health of college students during the COVID-19 epidemic in China. J Affect Disord. 2021; 280(Pt A): 7–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSerralta FB, Zibetti MR, Evans C: Psychological Distress of University Workers during COVID-19 Pandemic in Brazil. Int J Environ Res Public Health. 2020; 17(22): 8520. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoodwin R, Hou WK, Sun S, et al.: Psychological and behavioural responses to COVID-19: a China-Britain comparison. J Epidemiol Community Health. 2021; 75(2): 189–192. PubMed Abstract\n\nWerneck AO, Silva DRD, Malta DC, et al.: Lifestyle behaviors changes during the COVID-19 pandemic quarantine among 6,881 Brazilian adults with depression and 35,143 without depression. Cien Saude Colet. 2020; 25(suppl 2): 4151–4156. PubMed Abstract \| Publisher Full Text\n\nYocum AK, Zhai Y, McInnis MG, et al.: Covid-19 pandemic and lockdown impacts: A description in a longitudinal study of bipolar disorder. J Affect Disord. 2021; 282: 1226–1233. PubMed Abstract \| Publisher Full Text\n\nBallivian J, Alcaide ML, Cecchini D, et al.: Impact of COVID-19-Related Stress and Lockdown on Mental Health Among People Living With HIV in Argentina. J Acquir Immune Defic Syndr. 2020; 85(4): 475–482. PubMed Abstract \| Publisher Full Text\n\nHavermans T, Houben J, Vermeulen F, et al.: The impact of the COVID-19 pandemic on the emotional well-being and home treatment of Belgian patients with cystic fibrosis, including transplanted patients and paediatric patients. J Cyst Fibros. 2020; 19(6): 880–887. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarris RJ, Downey L, Smith TR, et al.: Life in lockdown: experiences of patients with IBD during COVID-19. BMJ Open Gastroenterol. 2020; 7(1): e000541. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang Y, Shi L, Que J, et al.: The impact of quarantine on mental health status among general population in China during the COVID-19 pandemic. Mol Psychiatry. 2021; 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKowal M, Coll-Martín T, Ikizer G, et al.: Who is the Most Stressed During the COVID-19 Pandemic? Data From 26 Countries and Areas. Appl Psychol Health Well Being. 2020; 12(4): 946–966. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCaballero-Domínguez CC, Jiménez-Villamizar MP, Campo-Arias A: Suicide risk during the lockdown due to coronavirus disease (COVID-19) in Colombia. Death Stud. 2020; 1–6. PubMed Abstract \| Publisher Full Text\n\nDsouza DD, Quadros S, Hyderabadwala ZJ, et al.: Aggregated COVID-19 suicide incidences in India: Fear of COVID-19 infection is the prominent causative factor. Psychiatry Res. 2020; 290: 113145. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPatsali ME, Mousa DV, Papadopoulou EVK, et al.: University students' changes in mental health status and determinants of behavior during the COVID-19 lockdown in Greece. Psychiatry Res. 2020; 292: 113298. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFullana MA, Hidalgo-Mazzei D, Vieta E, et al.: Coping behaviors associated with decreased anxiety and depressive symptoms during the COVID-19 pandemic and lockdown. J Affect Disord. 2020; 275: 80–81. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDuan H, Yan L, Ding X, et al.: Impact of the COVID-19 pandemic on mental health in the general Chinese population: Changes, predictors and psychosocial correlates. Psychiatry Res. 2020; 293: 113396. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEvery-Palmer S, Jenkins M, Gendall P, et al.: Psychological distress, anxiety, family violence, suicidality, and wellbeing in New Zealand during the COVID-19 lockdown: A cross-sectional study. PLoS One. 2020; 15(11): e0241658. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBentenuto A, Mazzoni N, Giannotti M, et al.: Psychological impact of Covid-19 pandemic in Italian families of children with neurodevelopmental disorders. Res Dev Disabil. 2021; 109: 103840. PubMed Abstract \| Publisher Full Text\n\nGonzález-Sanguino C, Ausín B, Castellanos MA, et al.: Mental health consequences of the Covid-19 outbreak in Spain. A longitudinal study of the alarm situation and return to the new normality. Prog Neuropsychopharmacol Biol Psychiatry. 2021; 107: 110219. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Qahtani AM, Elgzar WT, Ibrahim HA: COVID-19 Pandemic: Psycho-social Consequences During the Social Distancing Period Among Najran City Population. Psychiatr Danub. 2020; 32(2): 280–286. PubMed Abstract \| Publisher Full Text\n\nAmmar A, Chtourou H, Boukhris O, et al.: COVID-19 Home Confinement Negatively Impacts Social Participation and Life Satisfaction: A Worldwide Multicenter Study. Int J Environ Res Public Health. 2020; 17(17): 6237. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLipskaya-Velikovsky L: COVID-19 Isolation in Healthy Population in Israel: Challenges in Daily Life, Mental Health, Resilience, and Quality of Life. Int J Environ Res Public Health. 2021; 18(3): 999. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nClair R, Gordon M, Kroon M, et al.: The effects of social isolation on well-being and life satisfaction during pandemic. Humanit Soc Sci Commun. 2021; 8: 28. Publisher Full Text\n\nBoursier V, Gioia F, Musetti A, et al.: Facing Loneliness and Anxiety During the COVID-19 Isolation: The Role of Excessive Social Media Use in a Sample of Italian Adults. Front Psychiatry. 2020; 11: 586222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOgden RS: The passage of time during the UK Covid-19 lockdown. PLoS One. 2020; 15(7): e0235871. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGroarke JM, Berry E, Graham-Wisener L, et al.: Loneliness in the UK during the COVID-19 pandemic: Cross-sectional results from the COVID-19 Psychological Wellbeing Study. PLoS One. 2020; 15(9): e0239698. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMacdonald B, Hülür G: Well-Being and Loneliness in Swiss Older Adults during the COVID-19 Pandemic: The Role of Social Relationships. Gerontologist. 2020; 61(2): 240–250. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSama BK, Kaur P, Thind PS, et al.: Implications of COVID-19-induced nationwide lockdown on children's behaviour in Punjab, India. Child Care Health Dev. 2021; 47(1): 128–135. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nImran N, Aamer I, Sharif MI, et al.: Psychological burden of quarantine in children and adolescents: A rapid systematic review and proposed solutions. Pak J Med Sci. 2020; 36(5): 1106–1116. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXiao S, Yan Z, Zhao L: Physical Activity, Screen Time, and Mood Disturbance Among Chinese Adolescents During COVID-19. J Psychosoc Nurs Ment Health Serv. 2020; 1–7. PubMed Abstract \| Publisher Full Text\n\nGambin M, Sękowski M, Woźniak-Prus M, et al.: Generalized anxiety and depressive symptoms in various age groups during the COVID-19 lockdown in Poland. Specific predictors and differences in symptoms severity. Compr Psychiatry. 2021; 105: 152222. PubMed Abstract \| Publisher Full Text\n\nEzpeleta L, Navarro JB, de la Osa N, et al.: Life Conditions during COVID-19 Lockdown and Mental Health in Spanish Adolescents. Int J Environ Res Public Health. 2020; 17(19): 7327. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKroshus E: Gender, marital status, and commercially prepared food expenditure. J Nutr Educ Behav. 2008; 40(6): 355–360. PubMed Abstract \| Publisher Full Text\n\nEvans ML, Lindauer M, Farrell ME: A Pandemic within a Pandemic - Intimate Partner Violence during Covid-19. N Engl J Med. 2020; 383(24): 2302–2304. PubMed Abstract \| Publisher Full Text\n\nSaqib MAN, Siddiqui S, Qasim M, et al.: Effect of COVID-19 lockdown on patients with chronic diseases. Diabetes Metab Syndr. 2020; 14(6): 1621–1623. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSassone B, Mandini S, Grazzi G, et al.: Impact of COVID-19 Pandemic on Physical Activity in Patients With Implantable Cardioverter-Defibrillators. J Cardiopulm Rehabil Prev. 2020; 40(5): 285–286. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCransac-Miet A, Zeller M, Chagué F, et al.: Impact of COVID-19 lockdown on lifestyle adherence in stay-at-home patients with chronic coronary syndromes: Towards a time bomb. Int J Cardiol. 2021; 323: 285–287. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl Fagih A, Al Onazi M, Al Basiri S, et al.: Remotely monitored inactivity due to COVID-19 lockdowns. Potential hazard for heart failure patients. Saudi Med J. 2020; 41(11): 1211–1216. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOkely JA, Corley J, Welstead M, et al.: Change in Physical Activity, Sleep Quality, and Psychosocial Variables during COVID-19 Lockdown: Evidence from the Lothian Birth Cohort 1936. Int J Environ Res Public Health. 2020; 18(1): 210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChagué F, Boulin M, Eicher JC, et al.: Impact of lockdown on patients with congestive heart failure during the coronavirus disease 2019 pandemic. ESC Heart Fail. 2020; 7(6): 4420–4423. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaschi R, Luca A, Nicoletti A, et al.: Changes in Motor, Cognitive, and Behavioral Symptoms in Parkinson's Disease and Mild Cognitive Impairment During the COVID-19 Lockdown. Front Psychiatry. 2020; 11: 590134. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKalron A, Dolev M, Greenberg-Abrahami M, et al.: Physical activity behavior in people with multiple sclerosis during the COVID-19 pandemic in Israel: Results of an online survey. Mult Scler Relat Disord. 2021; 47: 102603. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPal R, Yadav U, Verma A, et al.: Awareness regarding COVID-19 and problems being faced by young adults with type 1 diabetes mellitus amid nationwide lockdown in India: A qualitative interview study. Prim Care Diabetes. 2021; 15(1): 10–15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGhosh A, Arora B, Gupta R, et al.: Effects of nationwide lockdown during COVID-19 epidemic on lifestyle and other medical issues of patients with type 2 diabetes in north India. Diabetes Metab Syndr. 2020; 14(5): 917–920. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBiagioli V, Albanesi B, Belloni S, et al.: Living with cancer in the COVID-19 pandemic: An Italian survey on self-isolation at home. Eur J Cancer Care (Engl). 2021; 30(2): e13385. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGallagher S, Bennett KM, Roper L: Loneliness and depression in patients with cancer during COVID-19. J Psychosoc Oncol. 2020; 1–7. PubMed Abstract \| Publisher Full Text\n\nRuiz-Roso MB, Knott-Torcal C, Matilla-Escalante DC, et al.: COVID-19 Lockdown and Changes of the Dietary Pattern and Physical Activity Habits in a Cohort of Patients with Type 2 Diabetes Mellitus. Nutrients. 2020; 12(8): 2327. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarçal IR, Fernandes B, Viana AA, et al.: The Urgent Need for Recommending Physical Activity for the Management of Diabetes During and Beyond COVID-19 Outbreak. Front Endocrinol (Lausanne). 2020; 11: 584642. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZorcec T, Jakovska T, Micevska V, et al.: Pandemic with COVID-19 and Families with Children with Chronic Respiratory Diseases. Pril (Makedon Akad Nauk Umet Odd Med Nauki). 2020; 41(2): 95–101. PubMed Abstract \| Publisher Full Text\n\nAl Agha AE, Alharbi RS, Almohammadi OA, et al.: Impact of COVID-19 lockdown on glycemic control in children and adolescents. Saudi Med J. 2021; 42(1): 44–48. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTao J, Gao L, Liu Q, et al.: Factors contributing to glycemic control in diabetes mellitus patients complying with home quarantine during the coronavirus disease 2019 (COVID-19) epidemic. Diabetes Res Clin Pract. 2020; 170: 108514. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOlickal JJ, Chinnakali P, Suryanarayana BS, et al.: Effect of COVID19 pandemic and national lockdown on persons with diabetes from rural areas availing care in a tertiary care center, southern India. Diabetes Metab Syndr. 2020; 14(6): 1967–1972. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhader MA, Jabeen T, Namoju R: A cross sectional study reveals severe disruption in glycemic control in people with diabetes during and after lockdown in India. Diabetes Metab Syndr. 2020; 14(6): 1579–1584. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nÖnmez A, Gamsızkan Z, Özdemir Ş, et al.: The effect of COVID-19 lockdown on glycemic control in patients with type 2 diabetes mellitus in Turkey. Diabetes Metab Syndr. 2020; 14(6): 1963–1966. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFisher L, Polonsky W, Asuni A, et al.: The early impact of the COVID-19 pandemic on adults with type 1 or type 2 diabetes: A national cohort study. J Diabetes Complications. 2020; 34(12): 107748. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGhesquière L, Garabedian C, Drumez E, et al.: Effects of COVID-19 pandemic lockdown on gestational diabetes mellitus: A retrospective study. Diabetes Metab. 2021; 47(2): 101201. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRastogi A, Hiteshi P, Bhansali A: Improved glycemic control amongst people with long-standing diabetes during COVID-19 lockdown: a prospective, observational, nested cohort study. Int J Diabetes Dev Ctries. 2020; 1–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTheis N, Campbell N, De Leeuw J, et al.: The effects of COVID-19 restrictions on physical activity and mental health of children and young adults with physical and/or intellectual disabilities. Disabil Health J. 2021; 101064. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nO'Sullivan K, Clark S, McGrane A, et al.: A Qualitative Study of Child and Adolescent Mental Health during the COVID-19 Pandemic in Ireland. Int J Environ Res Public Health. 2021; 18(3): 1062. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDi Stefano V, Battaglia G, Giustino V, et al.: Significant reduction of physical activity in patients with neuromuscular disease during COVID-19 pandemic: the long-term consequences of quarantine. J Neurol. 2021; 268(1): 20–26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIrmak AY, Çelikkalp U, Ekuklu G: Evaluation of the chronic disease management and depression levels of people over 65 years of age during the COVID-19 pandemic period. Perspect Psychiatr Care. 2020. PubMed Abstract \| Publisher Full Text\n\nKang C, Yang S, Yuan J, et al.: Patients with chronic illness urgently need integrated physical and psychological care during the COVID-19 outbreak. Asian J Psychiatr. 2020; 51: 102081. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCroizier C, Bouillon-Minois JB, Bay JO, et al.: COVID-19 lockdown and mental health: why we must look into oncology units. Psychol Med. 2020; 1–2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDelussi M, Gentile E, Coppola G, et al.: Investigating the Effects of COVID-19 Quarantine in Migraine: An Observational Cross-Sectional Study From the Italian National Headache Registry (RICe). Front Neurol. 2020; 11: 597881. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVerhagen IE, van Casteren DS, Lentsch SV, et al.: Effect of lockdown during COVID-19 on migraine: A longitudinal cohort study. Cephalalgia. 2021; 333102420981739. PubMed Abstract \| Publisher Full Text\n\nSankar P, Ahmed WN, Mariam Koshy V, et al.: Effects of COVID-19 lockdown on type 2 diabetes, lifestyle and psychosocial health: A hospital-based cross-sectional survey from South India. Diabetes Metab Syndr. 2020; 14(6): 1815–1819. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUNSSCN: The COVID-19 pandemic is disrupting people’s food environments: a resource list on Food Systems and Nutrition responses. 2020. Reference Source\n\nFood and Agriculture Organization of the United Nations: The State of Food Security and Nutrition in the World 2020. Rome. 2020. Reference Source\n\nDi Renzo L, Gualtieri P, Pivari F, et al.: Eating habits and lifestyle changes during COVID-19 lockdown: an Italian survey. J Transl Med. 2020; 18(1): 229. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatthews CE, George SM, Moore SC, et al.: Amount of time spent in sedentary behaviors and cause-specific mortality in US adults. Am J Clin Nutr. 2012; 95(2): 437–445. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDing D, Del Pozo Cruz B, Green MA, et al.: Is the COVID-19 lockdown nudging people to be more active: a big data analysis. Br J Sports Med. 2020; 54(20): 1183–1184. PubMed Abstract \| Publisher Full Text\n\nFerrie JE, Kivimäki M, Akbaraly TN, et al.: Change in Sleep Duration and Type 2 Diabetes: The Whitehall II Study. Diabetes Care. 2015; 38(8): 1467–1472. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarmon RL, Myers MA: Prayer and meditation as medical therapies. Phys Med Rehabil Clin N Am. 1999; 10(3): 651–662. PubMed Abstract \| Publisher Full Text\n\nSediri S, Zgueb Y, Ouanes S, et al.: Women's mental health: acute impact of COVID-19 pandemic on domestic violence. Arch Womens Ment Health. 2020; 23(6): 749–756. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIssaka RB, Somsouk M: Colorectal Cancer Screening and Prevention in the COVID-19 Era. JAMA Health Forum. 2020; 1: e200588. Publisher Full Text\n\nTapper EB, Asrani SK: The COVID-19 pandemic will have a long-lasting impact on the quality of cirrhosis care. J Hepatol. 2020; 73(2): 441–445. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Rapid assessment of service delivery for NCDs during the COVID-19 pandemic. Geneva. 2020. Reference Source" }	[ { "id": "115298", "date": "06 Jan 2022", "name": "Ahmed Shihab Albahri", "expertise": [ "Reviewer Expertise medical informatics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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\nMy comments can be explained below:\n\nRemove references from the conclusion section.\n\nThere is no clear conclusion that has been raised in this manuscript. Provide more criticism in the abstract, introduction, and conclusion.\n\nWhy do authors depend their search based on two databases only? What about other reliable databases such as Web of Science, Science Direct, and Scopus? I think there is no justification for this concern.\n\nHow can narrative review include a method like a systematic review? What is the difference? The authors should report that to the readers.\n\nI can see the introduction is not suitable when it is presented. The introduction should clarify many subjects within. Thus, the introduction needs to clarify the motivation, challenges, contribution, objective, significance, and others. All the information should be presented in sequence idea.\n\nWrite the conclusion and consider the following comments: Highlight your analysis and reflect only the important points for the whole paper. Mention the benefits. Mention the implication in the last of this section.\n\nThe authors mentioned, \"Articles were excluded if they did not focus specifically on the six lifestyle factors (dietary habits, physical activity, sleep, tobacco or other substance use, stress, and emotional well-being and social connectedness) or did not discuss lifestyle within the COVID-19 context.\" Why? what about others factors. Normally, this type of review is a comprehensive, critical, and objective analysis of the current knowledge on a topic. While we see here, the authors specified these factors from the beginning. I need the authors to defend this comment in the revised manuscript within the \"method\" section.\n\nI am surprised the introduction contains only one reference. Also, there is no comparison with any published review articles. Therefore, the authors should provide a clear comparison with academic literature based on specific points. At least four published articles should be included in the benchmark comparison. I added some citations that the authors could use in this comparison.\n\nIn conclusion, I see this manuscript is sound and a high-quality study.\n\nBest Wishes\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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? No", "responses": [ { "c_id": "12501", "date": "26 Sep 2024", "name": "Sathyanarayanan Doraiswamy", "role": "Author Response", "response": "The authors would like to thank the reviewer for the comments. Our point-by-point response is as below: 1. Remove references from the conclusion section. This has now been done. 2. There is no clear conclusion that has been raised in this manuscript. Provide more criticism in the abstract, introduction, and conclusion. The conclusion has been revised based on the valuable suggestions provided by the reviewer. 3. Why do authors depend their search based on two databases only? What about other reliable databases such as Web of Science, Science Direct, and Scopus? I think there is no justification for this concern. Justification now provided in the methods section. 4. How can narrative review include a method like a systematic review? What is the difference? The authors should report that to the readers. Key difference highlighted and a reference for further reading included in the introduction section. 5. I can see the introduction is not suitable when it is presented. The introduction should clarify many subjects within. Thus, the introduction needs to clarify the motivation, challenges, contribution, objective, significance, and others. All the information should be presented in sequence idea. The introduction is presented in sequence in tandem with comments from all reviewers. 6. Write the conclusion and consider the following comments: Highlight your analysis and reflect only the important points for the whole paper. Mention the benefits. Mention the implication in the last of this section. The first part of the conclusion has been rewritten in accordance with the reviewer’s kind suggestion. 7. The authors mentioned, \"Articles were excluded if they did not focus specifically on the six lifestyle factors (dietary habits, physical activity, sleep, tobacco or other substance use, stress, and emotional well-being and social connectedness) or did not discuss lifestyle within the COVID-19 context.\" Why? what about others factors. Normally, this type of review is a comprehensive, critical, and objective analysis of the current knowledge on a topic. While we see here, the authors specified these factors from the beginning. I need the authors to defend this comment in the revised manuscript within the \"method\" section. The review looks at six evidence-based lifestyle factors identified by the American College of Lifestyle Medicine. This is mentioned in the introduction and re-emphasized in the methods section. 8. I am surprised the introduction contains only one reference. Also, there is no comparison with any published review articles. Therefore, the authors should provide a clear comparison with academic literature based on specific points. At least four published articles should be included in the benchmark comparison. I added some citations that the authors could use in this comparison. Four articles are now included in the introduction section. The specific articles kindly identified by the reviewer have also been included in the introduction and discussion sections." } ] }, { "id": "127652", "date": "26 Jun 2024", "name": "Magdalena Górnicka", "expertise": [ "Reviewer Expertise nutrition", "nutritional assessment", "dietary habits" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 narrative review focuses on the impact of COVID-19 lockdown on six lifestyle factors: diet, physical activity, sleep, stress, social connectedness, and the use of tobacco, alcohol, or other harmful substances. The authors collected a significant number of articles, closely related to the title and the aim.\nI consider the description of the methodology for including articles in the review to be sufficiently described.\nI have one major comment:\nIn the subsection Dietary habits, the authors also took into account the results concerning changes in body weight, which are a result / consequence of nutrition but not a lifestyle factor. In my opinion, this subsection requires modification and showing changes in dietary habits. Conclusions should take into account changes in body weight, which were also mainly conditioned by decreased activity.\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": "12502", "date": "26 Sep 2024", "name": "Sathyanarayanan Doraiswamy", "role": "Author Response", "response": "The authors would like to thank the reviewer for the comments. Our point-by-point response is as below: In the subsection Dietary habits, the authors also took into account the results concerning changes in body weight, which are a result / consequence of nutrition but not a lifestyle factor. In my opinion, this subsection requires modification and showing changes in dietary habits. Conclusions should take into account changes in body weight, which were also mainly conditioned by decreased activity. Response: The subsection on dietary habits has now been reorganized to distinguish between habits and consequences." } ] }, { "id": "291274", "date": "29 Jun 2024", "name": "Anna Williams", "expertise": [ "Reviewer Expertise Medical and health publications", "plain language writing", "public health", "maternal and newborn health", "midwifery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 describes the global literature on how people's patterns of behavior changed during COVID-19 lockdowns in regard to diet, physical activity, sleep, and substance use, and the effects on stress, emotional wellbeing and non-communicable diseases. It provides a narrative review with a critical interpretive synthesis and recommends increased public health investment and efforts around lifestyle medicine, or disease prevention through healthy lifestyle habits.\nThe article is well-written and presents a comprehensive analysis.\nMy largest comments are:\n1) The timeframe of the 'lockdown period' is not explicitly defined. Across countries, lockdowns were shaped by national and sub-national policies, and likely varied substantially in their implementation. It would be helpful if, at minimum, a defined lockdown period of time that the search focused on were stated. Some reflection on how lockdown timeframes and policies differed across and within countries would contribute helpful nuance to the overall analysis.\n2) The use of the present perfect tense (e.g., has had...has encouraged etc.) instead of the past tense makes it feel as if lockdowns are still happening, when at this point, they are now in the past. Suggest revising to consistently use the past tense.\nMore minor comments:\n3) In Dietary Habits, Galican should be Galician.\n4) Recommend that consideration be given, in the mention of families not engaging in meditation and yoga at home, to that families often destress through joint leisure activities, such as playing games and doing projects together.\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? Yes", "responses": [ { "c_id": "12503", "date": "26 Sep 2024", "name": "Sathyanarayanan Doraiswamy", "role": "Author Response", "response": "The authors would like to thank the reviewer for the comments. Our point-by-point response is as below: 1) The timeframe of the 'lockdown period' is not explicitly defined. Across countries, lockdowns were shaped by national and sub-national policies, and likely varied substantially in their implementation. It would be helpful if, at minimum, a defined lockdown period of time that the search focused on were stated. Some reflection on how lockdown timeframes and policies differed across and within countries would contribute helpful nuance to the overall analysis. Lockdown timeframes are now included in the introduction section. 2) The use of the present perfect tense (e.g., has had...has encouraged etc.) instead of the past tense makes it feel as if lockdowns are still happening, when at this point, they are now in the past. Suggest revising to consistently use the past tense. Tense has been corrected to past tense in all applicable places. More minor comments: 3) In Dietary Habits, Galican should be Galician. This is now corrected. 4) Recommend that consideration be given, in the mention of families not engaging in meditation and yoga at home, to that families often destress through joint leisure activities, such as playing games and doing projects together. This is now included in the sub-section on emotional well-being and social connectedness." } ] }, { "id": "291270", "date": "25 Jul 2024", "name": "Cavid Baba", "expertise": [ "Reviewer Expertise neurology", "multiple sclerosis", "cognition", "rehabilitation" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a narrative review looking at the lifestyle changes during the COVID-19 lockdown. The researchers used the American College of Lifestyle Medicine (ACLM) definition of a healthy lifestyle with six parameters. I appreciate the researchers' effort to increase the value of the narrative review by using a best-evidence synthesis approach referenced in the paper. However, my main concern is the timing of the publication, as the search was done more than three years ago.\nThe following are the questions that drew my attention:\n\nThe manuscript's title suggests a focus on the COVID-19 pandemic. However, in several sections of the text, the researchers focused on modifications and preventive measures during times of crisis, such as lockdown. I would advise that researchers be more detailed in their interpretations of the outcomes. Because the reasons of a crisis or lockdown can vary, so can the effects. Either modify the manuscript's name or make your interpretations totally relevant to COVID-19, or at least to the lockdown during highly transmissive and fatal respiratory diseases. In the introduction section, researchers use the statement \"The review can be instructive…\" - a narrative review can assist grasp the topic and provide hints, but it is still not regarded a method of high evidence, therefore the term is not acceptable. In the introduction, the purpose of the review was presented as understanding of lifestyle factors and how they may have altered during COVID-19. However, the discussion and conclusion focused on ways to improve healthy lifestyle and preventive measures to protect that habit. I recommend that researchers focus on the purpose of the review and let the community decide the actions. The search dates cover articles published from September 2020 to January 31, 2021, which is too short to include all relevant and important research, especially since articles related to COVID-19 are still being published. This is a significant drawback for review articles, which should be published in a timely manner to maintain their value. Another option is to extend the search and re-write the article. The researchers removed papers unrelated to COVID-19. As previously noted, if the issue is lockdown during a transmissible disease, the other papers should have been added. Otherwise, terminology and expressions throughout the document should be specific to COVID-19. Why were articles that examined the same factors among healthcare workers excluded? What do researchers mean when they state \"additional stressors beyond the effects of the lockdown measures\"? If they are more susceptible to contracting the virus, delivery and transportation workers are also at risk. If it is anything else, please provide a reasonable explanation as to why the pressures of other professions, in addition to the consequences of the lockdown, are not regarded significant enough to eliminate from the search. The review's goal is to examine how people's lifestyles changed during the pandemic. I don't see why the researchers made such a difference. The researchers created statements by merging articles from various geographical and cultural backgrounds. Dietary choices and physical exercise, for example, can vary. What is normal in one culture may be unhealthy in another, therefore the changes observed during the lockdown are not proportional. I'm not sure if such a global mix of specific lifestyle behaviors is fair for comparison.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "12504", "date": "26 Sep 2024", "name": "Sathyanarayanan Doraiswamy", "role": "Author Response", "response": "The authors would like to thank the reviewer for the comments. Our point-by-point response is as below: The manuscript's title suggests a focus on the COVID-19 pandemic. However, in several sections of the text, the researchers focused on modifications and preventive measures during times of crisis, such as lockdown. I would advise that researchers be more detailed in their interpretations of the outcomes. Because the reasons of a crisis or lockdown can vary, so can the effects. Either modify the manuscript's name or make your interpretations totally relevant to COVID-19, or at least to the lockdown during highly transmissive and fatal respiratory diseases. Author Response: The review’s objective is to explore the impact of COVID-19-related lockdown measures on six lifestyle factors: diet, physical activity, sleep, stress, social connectedness, and the use of tobacco, alcohol, or other harmful substances. This has now been made explicit in the introduction in line with the reviewer’s kind suggestion. In the introduction section, researchers use the statement \"The review can be instructive…\" - a narrative review can assist grasp the topic and provide hints, but it is still not regarded a method of high evidence, therefore the term is not acceptable. Author Response: This has now been altered to reflect the guiding nature of a narrative review. In the introduction, the purpose of the review was presented as understanding of lifestyle factors and how they may have altered during COVID-19. However, the discussion and conclusion focused on ways to improve healthy lifestyle and preventive measures to protect that habit. I recommend that researchers focus on the purpose of the review and let the community decide the actions. Author Response: The conclusion has now been altered. The section on conclusion also includes recommendations from the findings of the review for a variety of stakeholders including communities to consider. Authors have ensured that all recommendations are evidence based and have also called for further research when available evidence is inadequate. The search dates cover articles published from September 2020 to January 31, 2021, which is too short to include all relevant and important research, especially since articles related to COVID-19 are still being published. This is a significant drawback for review articles, which should be published in a timely manner to maintain their value. Another option is to extend the search and re-write the article. Author Response: As mentioned in the methods section, the review included a search of the global literature database on COVID-19 and lifestyles, initially in September 2020, and updated the search in PubMed on 31 January 2021. Hence, the review included all studies from the onset of the pandemic until 31 January 2021. To ensure timely publication, the review was immediately published in F1000 in the same year. Identifying peer reviewers took time, and with the peer review complete now, addressing the reviewers' comments in a satisfactory manner will help index the article. This will help greater reach and can inspire further research. Given the narrative nature of the article, the evidence generated should be sufficient in the humble view of the authors for other researchers to carry out more robust reviews such as systematic reviews and metanalysis on the impact of COVID-19 related lockdown on each of the six lifestyle factors. The researchers removed papers unrelated to COVID-19. As previously noted, if the issue is lockdown during a transmissible disease, the other papers should have been added. Otherwise, terminology and expressions throughout the document should be specific to COVID-19. Author Response: The authors confirm that they have maintained language specific to COVID-19 throughout the manuscript. Why were articles that examined the same factors among healthcare workers excluded? What do researchers mean when they state \"additional stressors beyond the effects of the lockdown measures\"? If they are more susceptible to contracting the virus, delivery and transportation workers are also at risk. If it is anything else, please provide a reasonable explanation as to why the pressures of other professions, in addition to the consequences of the lockdown, are not regarded significant enough to eliminate from the search. The review's goal is to examine how people's lifestyles changed during the pandemic. I don't see why the researchers made such a difference. Author Response: The reasons for exclusion have now been elaborated in the manuscript by highlighting the additional stressors faced by health workers in the methods section. These additional stressors make them a very specific group affected by COVID-19. The review focusses only on general population and restricts itself to age, income and gender differentials where applicable. The researchers created statements by merging articles from various geographical and cultural backgrounds. Dietary choices and physical exercise, for example, can vary. What is normal in one culture may be unhealthy in another, therefore the changes observed during the lockdown are not proportional. I'm not sure if such a global mix of specific lifestyle behaviors is fair for comparison. Author Response: This limitation of the study is now made explicit under the limitations section." } ] } ]	1	https://f1000research.com/articles/10-363
https://f1000research.com/articles/11-1083/v1	22 Sep 22	{ "type": "Case Report", "title": "Case Report: Angio Behçet in a child", "authors": [ "Ikram Chamtouri", "Habib Besbes", "Mabrouk Abdelali", "Slaheddine Chouchene", "Habib Besbes", "Mabrouk Abdelali", "Slaheddine Chouchene" ], "abstract": "Behçet’s disease (BD) is rare in children. Herein, we report a case of 12-year-old male child with a history of left superficial femoral vein thrombosis and bilateral pulmonary embolism, admitted for multiple thrombosis located in the inferior vena cava, right atrium and ventricle associated with multiple pulmonary artery aneurisms and fissurations concomitant to oral aphthosis, which was suggestive of BD. Despite corticoids and immunosuppressive therapy, the child had a massive hemoptysis resulting in his death. The association between intracardiac thrombosis, pulmonary aneurism and venous thrombosis should raise suspicion of angio-Behçet, which could be lethal.", "keywords": [ "behcet", "pulmonary artery aneurism", "thrombosis" ], "content": "Introduction\n\nBehçet’s disease (BD) is the only primary vasculitis that affects both arteries and veins of any size.1 Cardiac complications are rare but they represented one of the prognostically devastating manifestations of BD.2 They predominate in the right heart and are often associated with pulmonary artery aneurysm.3 Physicians are frequently faced with a therapeutic dilemma due to the absence of consensus for treatment of such complications. To the best of our knowledge, there is no evidence about the prevalence and the prognosis of pulmonary artery involvement in children with BD. Herein, we reported a case of a child presenting with Angio-Behçet, revealed by intra right ventricle thrombus and pulmonary artery aneurysm. It should be kept in mind that some life-threatening features in the pediatric population may occur earlier than mucocutaneous findings.\n\n\nCase report\n\nAn African 12-year-old male child was admitted for cough, hemoptysis and progressive dyspnea. He had a history of left superficial femoral vein thrombosis and a massive bilateral pulmonary embolism three months before, which had been treated with low molecular weight heparin (15 UI/kg/h intravenously) and oral vitamin K antagonists (VKAs) (1 mg per day). He mentioned an episode of oral ulcers with no genital lesions. He denied any history of joint pains, skin rash or visual complaints but he has suffered from recurrent headaches and anxiety. Family history was non-contributory.\n\nPhysical examination revealed thoracic collateral venous circulation and hepatomegaly with jugular veins distension. Initial laboratory results showed hemoglobin=11.2 gm/dL, platelets=232,000/mm3, and white blood cells=10×103/mm3, International Normalized Ratio (INR)=2.3 and D-Dimer=1,500 ng/L. Chest X-ray showed images of bilateral perihilar condensations and electrocardiogram showed a right bundle branch block. Pulmonary computed tomography angiography showed inferior vena cava, right atrial and right ventricular thromboses (Figure 1) associated with multiple pulmonary artery aneurisms (PAAs) with fissurations (Figure 2). There were also bilateral infiltrates and peripheral sub-pleural opacities suggestive of pulmonary infarcts (Figure 1). Thrombophilia and connective tissue screening were negative.\n\nCT, computed tomography.\n\nCT, computed tomography.\n\nDuring hospitalization, the child developed oral aphthosis suggestive of the diagnosis of angio-Behçet. VKAs were maintained with IV methylprednisolone at a dose of 15 mg/kg/day over three days. After that, a cyclophosphamide bolus at 700 mg/m2 was introduced. Despite these treatments, the child died from a massive hemoptysis leading to respiratory compromise.\n\n\nDiscussion\n\nBD is characterized by multisystemic involvement of unknown etiology, for which viral, bacterial, genetic, environmental and immunological factors have been implicated.4 The prevalence of BD in children is unknown but is probably very low, as a range of 3.3–26% of cases have been reported.5\n\nIn 2015, a recent publication established a classification criteria from the largest prospective cohort ever reported for BD in children. Three of six items are required to classify a patient as having pediatric BD.6 In fact, our patient showed three criteria for BD, oral aphthosis, neuropsychiatric signs as headaches, anxiety and cardiovascular signs that confirmed the diagnosis.\n\nCardiovascular involvement has been reported in 7–29% of patients with BD. Intracardiac thrombosis is extremely rare with an obvious predilection to the right heart location.7 Arterial damage occurs in 1–7% of patients with BD but it may be at the forefront of the clinical manifestation, as shown by our case, leading to a worse prognosis.8 PAAs occur more in men and appear in younger patients. The inflammatory process in PAAs affects the vasa vasorum of the artery, causing weakness in the vessel wall.9 These lesions frequently erode bronchi and cause massive hemoptysis.10 The treatment of BD is not well established, but colchicine, thalidomide, corticosteroids and immunosuppressants, can be used depending on the severity of systemic manifestations.4\n\nDue to rarity of intracardiac thrombosis as a complication of BD, there is no evidence-based consensus regarding best treatment. Mogulkoc et al., suggested that medical management with anticoagulants and immunosuppressant may be associated with better outcomes than surgical intervention.7 The use of anticoagulation could be dangerous in patients who presented both thrombosis and hemoptysis. The EULAR recommendations for treatment of BD concluded that there is no evidence of the benefits for the use of anticoagulants for arterial lesions of BD.11 Huong et al., reported the case of a patient with intracardiac thrombosis and bilateral pulmonary aneurysms who had complete resolution of thrombus by immunosuppressant therapy without anticoagulants.12 The use of immunosuppressants has been shown to significantly improve survival and prognosis in patients with thrombotic and arterial lesions.13 Regarding the choice of immunosuppressant, there are no strong recommendations to support superiority of one regimen over another. Cyclophosphamide has been used to induce remission. Anti-TNF agents are more frequently used in patients with multi-systemic involvement and show promising results but they are more expensive and not frequently available in some underdeveloped countries.14\n\nDespite treatment of our patient with an immunosuppressant, the prognosis was poor.\n\n\nConclusions\n\nThe association between intracardiac thrombosis, pulmonary aneurism and venous thrombosis are very characteristic of angio-Behçet in children. The prognosis is poor despite treatment. Anticoagulation therapy may be more beneficial in patients that only show intracardiac thrombosis but it should be avoided when the patient is experiencing pulmonary arteries aneurysms.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the parent of the patient.", "appendix": "References\n\nOzen S, Bilginer Y, Besbas N, et al.: Behçet disease: treatment of vascular involvement in children. Eur. J. Pediatr. 2010; 169(4): 427–430. Publisher Full Text\n\nDarie C, Knezinsky M, Demolombe-Rague S, et al.: Pseudotumeur cardiaque révélant une maladie de Behçet. Rev. Med. Interne. 2005; 26: 420–424. PubMed Abstract \| Publisher Full Text\n\nGeri G, Wechsler B, Thi Huong DL, et al.: Spectrum of cardiac lesions in Behçet disease: a series of 52 patients and review of the literature. Medicine. 2012; 91(1): 25–34. Publisher Full Text\n\nOnder M, Gurer MA: The multiple faces of Behçet's disease and its aetiological factors. Thorax. 2001; 56(7): 572–578.\n\nAtmaca L, Boyvat A, Yalcyndað FN, et al.: Behcet disease in children. Ocul. Immunol. Inflamm. 2011; 19: 103–107.\n\nKoné-Paut I, Shahram F, Darce-Bello M, et al.: Consensus classification criteria for paediatric Behçet’s disease from a prospective observational cohort: PEDBD. Ann. Rheum. Dis. 2016; 75(6): 958–964. PubMed Abstract \| Publisher Full Text\n\nMogulkoc N, Burgess MI, Bishop PW: Intracardiac thrombus in Behçet’s disease: a systematic review. Chest. 2000; 118: 479–487. Publisher Full Text\n\nKoc Y, Gullu I, Akpek G, et al.: Vascular involvement in Behçet's disease. J. Rheumatol. 1992; 19(3): 402–410. PubMed Abstract\n\nAkar S, Ozcan MA, Ateş H, et al.: Circulated activated platelets and increased platelet reactivity in patients with Behçet’s disease. Clin. Appl. Thromb. Hemost. 2006; 12(4): 451–457. PubMed Abstract \| Publisher Full Text\n\nHamuryudan V, Oz B, Tüzün H, et al.: The menacing pulmonary artery aneurysms of Behçet’s syndrome. Clin. Exp. Rheumatol. 2004 Jul-Aug; 22(4 Suppl 34): S1–S3. PubMed Abstract\n\nHatemi G, Silman A, Bang D, et al.: EULAR recommendations for the management of Behçet disease. Ann. Rheum. Dis. 2008; 67: 1656–1662. PubMed Abstract \| Publisher Full Text\n\nHuong DL, Dolmazon C, De Zuttere D, et al.: Complete recovery of right intraventricular thrombus and pulmonary arteritis in Behçet’s disease. Br. J. Rheumatol. 1997; 36: 130–132. PubMed Abstract \| Publisher Full Text\n\nSaadoun D, Asli B, Wechsler B, et al.: Long term outcome of arterial lesions in Behçet disease: a series of 101 patients. Medicine. 2012; 91: 18–24. PubMed Abstract \| Publisher Full Text\n\nAdler S, Baumgartner I, Villiger PM: Behçet’s disease: successful treatment with infliximab in 7 patients with severe vascular manifestations. A retrospective analysis. Arthritis Care Res. 2012; 64: 607–611. PubMed Abstract \| Publisher Full Text" }	[ { "id": "259708", "date": "10 May 2024", "name": "Jun Zou", "expertise": [ "Reviewer Expertise Rheumatology and immunology", "single cell technology." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 presents a rare and complex instance of Angio Behçet's disease (BD) in a pediatric patient, which is commendable for its contribution to the limited literature on this subject. The authors have described the patient's clinical presentation, treatment, and unfortunate demise which could be reorganized to improve the clarity and thoroughness. The association of intracardiac thrombosis, pulmonary artery aneurysm, and venous thrombosis as characteristic of angio-Behçet in children, which should be further emphasize the severity and potential lethality of the condition.\nRecommendations for the Author: 1. Epidemiological Data: The report would benefit from a more detailed discussion on the prevalence of BD in children, particularly in the African demographic, as the patient was of African descent. 2. Diagnostic Criteria: A clearer exposition of the diagnostic criteria for pediatric BD, as per the 2015 publication, could enhance the report's educational value. 3. Treatment Protocols: Given the therapeutic dilemma in treating BD, especially with concurrent thrombosis and hemoptysis, a comparative analysis of different treatment approaches and their outcomes in similar cases would be valuable. 4. Limitations: The study's limitations, including the inability to perform a more comprehensive genetic and immunological workup due to the patient's rapid deterioration, should be acknowledged.\nMandatory Reviewer Questions: 1.Ethical Considerations: The case report by Chamtouri et al. adheres to ethical guidelines in the treatment and reporting of the case. The clinical management of the patient has been presented with sensitivity and professionalism, reflecting the maintenance of ethical standards throughout the patient's care and manuscript preparation. 2.Consent for Publication: I note that the published case report includes a statement confirming that informed consent for publication was obtained from the patient's family. This addresses the standard practice in case reports involving minors and ensures transparency and adherence to ethical publication standards. 3.Data Availability: The report does not specify the availability of data supporting the conclusions. I recommend that the authors clarify this point by either making the data available to other researchers or providing a valid reason for its unavailability, to foster data sharing and further medical research. Please let me know if there are any additional aspects of the report that require attention or if further clarification is needed. Thank you once again for the opportunity to contribute to the peer review process. I look forward to the continued advancement of research and scholarship in our field. Approval Status: Approved with Reservations: The case report is insightful and contributes valuable information to the medical community. However, the reservations pertain to the need for additional context regarding epidemiology, a more detailed discussion on diagnostic criteria, and a comparative analysis of treatment protocols. Addressing these points could strengthen the report's impact and utility.\nReviewer's Comments Not Addressed in the Review: • The reviewer has not been able to assess the long-term management strategies for pediatric BD due to the acute nature of the case and the patient's outcome. • The potential genetic predisposition and environmental factors contributing to BD in children, which could be areas for future research, were not discussed in depth in the report.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [ { "c_id": "12490", "date": "26 Sep 2024", "name": "IKRAM CHAMTOURI", "role": "Author Response", "response": "Dear reviewer, Thank you for your remarks. All the points are changed in the manuscript. Best regards." } ] } ]	1	https://f1000research.com/articles/11-1083
https://f1000research.com/articles/13-1094/v1	26 Sep 24	{ "type": "Research Article", "title": "Enhancing climate forecasting with AI: Current state and future prospect", "authors": [ "Rakesh Kumar", "Richa Goel", "Neeru Sidana", "Aatam Prakash Sharma", "Surbhi ghai", "Tilottama Singh", "Rajesh singh", "Neeraj Priyadarshi", "Bhekisipho Twala", "Vasim Ahmad", "Rakesh Kumar", "Richa Goel", "Neeru Sidana", "Aatam Prakash Sharma", "Surbhi ghai", "Tilottama Singh", "Rajesh singh", "Neeraj Priyadarshi", "Bhekisipho Twala" ], "abstract": "Background The escalating impact of climate change underscores the critical need for advanced and sustainable climate forecasting techniques. This review examines the current state and future prospects of leveraging Artificial Intelligence (AI) for climate forecasting, focusing on enhancing accuracy and identifying complex patterns in large datasets.\n\nMethods A systematic bibliometric methodology was employed, analyzing peer-reviewed literature from the past two decades. The study screened 455 articles from Scopus and Web of Science databases using specific keywords related to AI and weather forecasting. After removing duplicates and irrelevant studies, 218 articles were selected for detailed analysis. Bibliometric analysis was conducted using RStudio software to examine publication trends, co-word co-occurrence, and thematic evolution.\n\nResults The findings indicate significant growth in AI applications for climate forecasting, particularly from 2014 to 2023. AI techniques such as machine learning, artificial neural networks, and deep learning have shown promise in improving the accuracy of weather forecasts and early warning systems. The thematic analysis identified key themes like numerical weather prediction, feature selection, and neural networks as fundamental areas of research. Additionally, AI-based early warning systems for extreme weather events were highlighted as a crucial application. Below Figure 1. shows the graphical abstract of research\n\nConclusions AI has the potential to significantly enhance climate forecasting by analyzing vast amounts of data and identifying complex patterns. Future research should focus on developing universal AI models, increasing model accuracy with explainable AI techniques, and integrating region-specific forecasts to aid decision-making in various sectors. Addressing ethical concerns and ensuring sustainable AI applications are essential for the responsible deployment of AI in climate forecasting.", "keywords": [ "Artificial Intelligence", "Climate forecasting", "Weather", "technology", "Environment" ], "content": "Introduction\n\nThe atmosphere around us is reflected in the weather. One aspect of a natural occurrence that keeps the atmosphere in balance is the weather (Subhajini, 2018). The elements of the weather include temperature, humidity, wind speed, precipitation, evaporation, air pressure, vapour pressure, length of sunshine, sea level, visibility, etc. In addition, weather forecasting affects our daily lives highlighting it as a significant scientific problem to be explored. It is one of the crucial strategy to prevent adverse weather conditions. Forecasting the weather is important for making decisions in a variety of areas, including business, energy management, tourism, agriculture, and the health of people and animals (Gautam & Bedi, 2015). Weather forecasting has been one of the world’s most difficult challenges in experimentation and technology throughout the past century (Salman, Kanigoro, & Heryadi, 2015). For a long time, environmental change has drawn a lot of interest because of the sudden shifts that occur. This study utilized a systematic bibliometric methodology to analyze peer-reviewed literature from the past two decades on the application of Artificial Intelligence (AI) in climate forecasting. The literature search was carried out on December 22, 2023, using the Scopus and Web of Science databases. The search strategy included the keywords (“Artificial Intelligence” OR “AI”) AND (“Weather forecasting” OR “Climate forecasting”), restricted to articles published in English between 1999 and 2023.\n\nInclusion criteria involved peer-reviewed articles focusing on AI applications in climate or weather forecasting. Exclusion criteria included duplicate articles, non-English publications, and non-peer-reviewed articles.\n\nHowever, due to certain limitations in improving weather forecasting implementation, it is challenging to predict the weather here and now with precision (Hussain et al., 2018). A major part of meteorology is weather forecasting (Fradkov, 2020). Accurate prediction-making is one of the main problems that meteorologists face globally. Weather alerts are crucial because they are used to safeguard lives and property. Forecasts based on temperature, wind, humidity, and outlook are crucial for farmers and, consequently, for traders in product markets. Temperature forecasts are used by utility providers to assess demand for the upcoming few days (Singhroul & Agrawal, 2021). Estimates can be used to schedule activities around periods of wind chill, heavy rain, or snowfall, as these weather conditions severely limit outside activity. They may also be utilized to weather and be ready for these circumstances. Without reliable weather forecasts, individuals may find themselves unprepared for hazardous conditions and endanger themselves or worse (Abuella & Chowdhury, 2018).\n\nThe process of creating weather forecasts involves obtaining information about the current state of the atmosphere in a certain area and using the weather to anticipate future changes to the atmosphere (Awasthi et al., 2023). Individual input is still required to select the best prediction model and create the forecast (Adam, 1991). Meteorologists predict the weather using a variety of techniques. In the early 20th century, Lewis Fry Richardson suggested numerical weather prediction. The first practical application of numerical weather prediction came in 1955 with the introduction of programmable electronic computers. Near the Earth’s surface, air pressure, temperatures, wind speeds, wind directions, humidity, and rainfall are all monitored by trained meteorologists and automated weather stations and then used in different climate models (Khan et al., 2022). Determining how to represent the weather by utilising a vast quantity of meteorological data is one of the issues in weather forecasting. For this purpose, an analysis of different data mining approaches is conducted. Users may classify, evaluate, and combine the relationships revealed in data from several dimensions or points of view with the use of data mining tools (Akhter et al., 2019). In data mining, terms like classification, learning, and prediction are frequently employed. Classification is one method used in data mining (machine learning) to predict aggregate participation for information circumstances. To predict whether the weather will be “sunny,” “rainy,” or “cloudy” on a certain day, for instance, classification (Awasthi et al., 2023). Analytical approaches and artificial intelligence methods are the two basic categories in which the methods created for load forecasting are analyzed. Time series analysis, regression techniques, the similar day method, least square estimation (LES), and wavelet transform (WT) are often employed as analytical techniques in the literature. These AI techniques include ant colony optimization (ACO), fuzzy logic (FL), support vector machines (SVM) (Aylak, 2021), genetic algorithms (GA), particle swarm optimization (PSO), and artificial neural networks (ANN) (Bochenek & Ustrnul, 2022). To achieve good forecasting, load demand-affecting factors need to be carefully identified and taken into account in forecasting studies. Consumption region and independent variables such as day of the week, and sociological, climatic, demographic, and economic conditions can be used to characterize these parameters. Statistical and economic circumstances are typically taken into account in long-term load forecasting studies (Bauer, Thorpe, & Brunet, 2015). Studies also make use of climatic variables including wind, precipitation, and humidity in addition to temperature data. Studies that exclusively use historical load data also exist (Bonavita & Laloyaux, 2020).\n\nClimate change poses a global threat with impacts that are especially severe in developing and underdeveloped countries (Chapman et al., 2022). These regions are often more vulnerable to climate-related disasters, making accurate and timely climate forecasting crucial for preparedness and resilience. The use of advanced tools, such as Artificial Intelligence (AI), has the potential to significantly enhance the accuracy and reliability of climate forecasts (Brunet et al., 2023).\n\nAI technologies, through their ability to process vast amounts of data and identify complex patterns, offer a transformative approach to climate forecasting (Chen et al., 2023a,b,c). AI can improve the accuracy of weather predictions, provide early warnings for extreme weather events, and help in understanding the intricate dynamics of climate systems. This enables policymakers to make informed decisions and take proactive measures to mitigate the adverse effects of climate change (Chapman et al., 2022).\n\nDespite the recognized potential of AI, there is a scarcity of comprehensive bibliometric studies that explore the current state and trends of AI applications in climate forecasting. This study fills that gap by providing a systematic analysis of existing literature, highlighting the contributions of AI, and identifying future research directions. By understanding the growth rate, research production patterns, and thematic developments, this study offers valuable insights for researchers, practitioners, and policymakers.\n\nThe study aims to answer the following research questions:\n\n1. What is the current growth rate and research production pattern in the field of Artificial Intelligence and Climate forecasting?\n\n2. What is the contribution of Artificial Intelligence in Climate forecasting?\n\n3. What are the future prospects of artificial intelligence in Climate forecasting?\n\nBased on these questions, the study employs a bibliometric analysis of articles retrieved from Scopus and Web of Science databases, spanning the period from 1999 to 2023. This approach ensures a comprehensive evaluation of the field, providing a foundation for future research and practical applications.\n\nThe study follows a rigorous methodological framework, adhering to the PRISMA guidelines for systematic reviews. This ensures the reproducibility and reliability of the findings. The bibliometric analysis conducted using RStudio software involves performance analysis and scientific mapping, enabling a detailed examination of publication trends, influential articles, and thematic clusters in the domain of AI and climate forecasting.\n\nThe findings of this study have significant implications for future research and practice. By identifying the most influential articles, authors, and research themes, the study provides a roadmap for future investigations. It highlights the need for developing universal AI models, enhancing model accuracy with explainable AI techniques, and integrating region-specific forecasts. This will aid in better planning and decision-making across various sectors, contributing to the broader goal of climate resilience and sustainability.\n\nThis research is justified by its potential to advance the field of climate forecasting through the application of AI, addressing critical gaps in the literature, and providing actionable insights for future research and practical applications. The enhanced accuracy and early warning capabilities offered by AI can significantly contribute to mitigating the impacts of climate change, particularly in vulnerable regions. Below Figure 2 shows the structure of study.\n\nSource: Prepared by the researcher(s).\n\nA systematic bibliometric methodology was employed, analyzing peer-reviewed literature from the past two decades (Figure 2).\n\n\nMethods\n\nThe aim of this study is to understand the scope of conducting research in the field of artificial intelligence and weather forecasting. The science mapping analysis and performance analysis were carried out using Bibliometrix R. Artificial intelligence predicts climate condition (Chen et al., 2023a,b,c). A variety of indices were used for the investigation via Performance Analysis, including citations, annual scientific productivity, highly productive nations, and highly cited publications and authors. Secondly, scientific mapping is used where different clusters that were thematically related were examined using the co-word co-occurrence analysis. A cluster is characterized as a collection of nodes or keywords that share many connections and are more closely grouped together than the other groups (Chung, Gray, & Mannino, 1998). Whereas the betweenness of centrality gauges a node’s significance by counting the shortest pathways through it and indicating its influence over the network (Cifuentes et al., 2020). Strongly correlated keywords were identified by the clustering network (Cobo et al., 2011). Figure 3 indicates PRISMA study for review of research. Lastly, to discover the research themes the overall data has been plotted on a strategic diagram. where a set of contemporary trends and related themes were extracted through analysis of the strategic diagrams. The most reliable scientific data regarding the impact of health interventions are obtained through systematic reviews that integrate meta-analyses of randomized clinical trials. Nevertheless, certain meta-analyses and systematic reviews are unclear and omit crucial details, especially when it comes to the methodology and findings (Cowls et al., 2021). The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) declaration aims to increase transparency. Authors and researchers across the world have been using the PRISMA statement to organize, draft, and publish systematic reviews and meta-analyses. To assess the level of development and relevance of the terms, respectively, the density and centrality parameters were examined with the help of artificial intelligence (Fente & Singh, 2018).\n\nThe study screened 455 articles from Scopus and Web of Science databases, following the PRISMA flow diagram (Figure 3).\n\nThe literature search was carried out by determining the theme, keywords, key strings, and database selection. On December 22, 2023, the pertinent papers were collected from the “Scopus” and “Web of Science” databases. A combination of the following string searches, restricted to the phrases that appeared in the title or abstract: (“Artificial Intelligence” OR “AI”) AND (“Weather forecasting” OR “Weather forecasting”), has been used to extract publications from the database restricted to English language. The “Scopus” database yielded 316 papers, while the “Web of Science” database produced 139 papers as a result of the advanced search. The PRISMA (Preferred Reporting Items for Systematic Reviews) screening process has been used to filter out the data set for the relevant paper to be analyzed in the study (Davenport & Diffenbaugh, 2021). The data was filtered on the basis of duplication removal, where 67 duplicates were removed. The resultant 388 papers were further screened on the basis of type of research study restricted to type: Article, resulting in removal of 65 studies. Further, the final screening based on the title and abstract relevance 105 papers were removed resulting in a finalized list of 218 papers, on which the bibliometric analysis was conducted. The study divided into two segments. In the first part technical analysis is conducted based on previous literature. In this part outcome of previous literature analysis from 1999-2023. The study was selected based on AI used in climate forecasting. In the second part bibliometric analysis conducted with the help of R studio software. This study utilized a systematic bibliometric methodology to analyze peer-reviewed literature from the past two decades on the application of Artificial Intelligence (AI) in climate forecasting. Data were extracted and analyzed using RStudio, a proprietary software for statistical computing and graphics. We have obtained the necessary copyright licenses to use RStudio for this research. The Bibliometrix package within RStudio was utilized to conduct performance analysis, scientific mapping, and thematic analysis.\n\n\nExisting relation between artificial intelligence and climate forecasting\n\nArtificial intelligence (AI) offers the potential to be significant in tackling difficulties associated with weather change. The application of AI to lower Greenhouse Gas (GHG) emissions, especially in the electric power industry, is the focus. By addressing low-hanging fruit in industries like electricity, transportation, agriculture, and buildings, AI can help tackle weather change (Davenport & Diffenbaugh, 2021). Weather change addresses data and technical difficulties and highlights the potential uses of AI in lowering emissions GHG (Devaraj et al., 2021). Meteorology relies heavily on weather predictions. Making a precise forecast is one of the most difficult things to stand up to meteorologists in any part of the globe. Given that weather warnings are used to protect people and property, they are essential. To increase the models’ accuracy, researchers have put out a variety of weather forecasting models. Precise prediction may not maybe because of noise and inaccurate or missing data. Real-world data tends to be noisy and unpredictable (Dong et al., 2023). Weather prediction systems have used a variety of techniques, such as neural network-based algorithms that use backpropagation. A neural network technique used in machine learning for feature extraction is called a stacked auto-encoder (Dupuy et al., 2021). To accomplish dynamic data interaction, or the link between expected outcomes and actual data in a dynamic context, a stacked auto-encoder neural network might be useful. There have been several noteworthy attempts in the last ten years to use statistical modeling, including machine learning systems, to address the problem of weather forecasting. favorable outcomes (Elwell & Polikar, 2011). In the last ten years, artificial intelligence has emerged, and to research coastal dynamics, machine learning models have been used. Traditional methods of predicting the weather include constraints, but a novel AI-driven strategy utilising deep learning and machine learning techniques exhibits the potential to deliver more fast and more accurate weather predictions (Era, Rahman, & Alvi, 2023). For weather forecasting, several artificial intelligence algorithms are frequently utilised. Examining historical meteorological data, predicting future weather conditions using trends and supervised machine learning methods like Random Forest and Support Vector Machines may be used to identify trends as well as neural systems. Weather forecasting has made use of Random Forests as it can handle high-dimensional data and non-linear correlations (Ling et al., 2022). Large data sets and intricate patterns may be analysed by AI systems to generate extremely precise weather forecasts. This precision is essential for proactive network management and planning (Leal Filho et al., 2022). Real-time weather updates may be obtained via AI-enhanced systems, enabling network managers to take prompt action to reduce disturbances in the network (Kumar & Palanisamy, 2020).\n\nArtificial intelligence-driven weather forecasting can help communication networks become more equipped to handle extreme weather occurrences making sure they continue to function in urgent circumstances (Gowthamy et al., 2019). By forecasting localised meteorological conditions, AI can help with resource allocation, ensuring that resources are allocated to locations where they are most required (Abdel-Kader and Salam, 2021). Artificial Intelligence can analyse unstructured data sources, like social media, and offer a more detailed picture of the present weather (Hedar et al., 2021).\n\nMedium-range weather forecasting is another important factor that is influenced and predicted using AI (Hensengerth, 2024). The AI-based weather forecasting models nevertheless rely on analytical products produced by the classic NWP system’s data assimilation process to make forecasts (Huntingford et al., 2019). Conventional weather forecasting uses millions of equations to mimic detailed atmospheric processes through complex physical models. Accurate representation of atmospheric phenomena is the goal of these models. These models consider information from weather stations, radar, satellites, and other sources, along with a variety of parameters like temperature, humidity, wind speed, and cloud cover (Pathak et al., 2022). Artificial Intelligence (AI) has multiple applications in predicting, including natural language processing, deep learning, and machine learning. AI is superior to human forecasters in several ways. It can handle big and varied datasets, spot patterns and trends, automate procedures, and adjust to shifting circumstances and uncertainties to improve forecasting models’ accuracy, dependability, simplicity, and flexibility Neema and Ohgai (2010). These forecasts use computational methods and scientific information to help us anticipate future weather phenomena, such as rain, snow, or sunshine (Grenier et al., 2023). With the advent of more affordable sensing units and improved connectivity, the Internet of Things (IoT) is becoming more accessible. As a result, the variety of gadgets and devices that can provide valuable real-time weather data is expected to expand significantly (Bi et al., 2023). Recurrent Neural Networks (RNN) and Long Short-Term Memory (LSTM) were used in 2020 to estimate the daily temperatures for the next three days, producing a model. The five temperature categories used were “Cold,” “Cool,” “Normal,” “Warm,” and “Hot.” Data The accuracy of the results was influenced by the size and distribution of the dataset used. (Chen et al., 2023a,b,c) Harnessing AI’s potential in weather forecasting is exemplified by IBM’s acquisition of The Weather Company. This acquisition empowered IBM to generate highly accurate weather forecasts using the power of AI. Such forecasts hold significant value for businesses in the communication sector as they aid in informed decision-making (Kaur et al., 2018). However, despite the groundbreaking nature of this approach, concerns arise regarding the scalability and adaptability of AI across diverse meteorological scenarios (Khotanzad et al., 1997). Weather predictions become less precise as the prediction range increases and the lack of knowledge about atmospheric dynamics. It’s easy to understand why perfect weather forecasting matters when you consider the benefits (Kim et al., 2022). These forecasts won’t stop a tornado, storm or flood from happening, but they can help us plan for them. We’ve come a long way (Laloyaux et al., 2022).\n\nArtificial intelligence (AI) is emerging as a potent tool in weather forecasting that could transform our knowledge and ability to predict weather patterns. AI has the potential to greatly increase our understanding of weather change and provide new insights into intricate weather systems. Additionally, AI is playing a crucial role in all-encompassing answers to weather catastrophes by offering more efficient, sustainable, and environmentally friendly weather forecasting technologies (Chen et al., 2023a,b,c). However, the use of AI in weather-related fields raises ethical issues like discrimination, unfair bias, and opaque decision-making, which are consistent with larger worries about AI applications. AI additionally highlights the significance of taking computation-intensive carbon footprint into account and the necessity of scientific proof to balance greenhouse gas emissions against increases in energy and resource efficiency (Kıran et al., 2012). There is an increased amount of research in the field of artificial intelligence and weather forecasting. However, there is a scarcity of bibliometric research in this area exploring the scope of conducting research in the field of artificial intelligence and weather forecasting (Singh et al., 2022). Bibliometric analysis will serve as a knowledge base for further researchers by providing all the necessary information associated with this area and what are the various domains associated with it. As above following work has already been done. Table 1 showing current state of work and future scope. Study include in Table 1 are taken from period 1999 to 2023. Reason behind to select the study to find out development of AI in climate forecasting and it future prospectus. Many researchers have developed a keen interest in the field of Artificial intelligence and weather forecasting (Martínez et al., 2022). Consequently, a bibliometric study was carried out to comprehend the present research trends in the field of Artificial intelligence and weather forecasting as well as to investigate the different other research domains connected to this field (Martín-Vázquez, Aler, & Galván, 2017).\n\n\nAnalysis publication of AI and climate forecasting\n\nFigure 4, represents the publication trends in artificial intelligence and weather forecasting. The scientific output is derived from the past four decades i.e.,1984 to 2023. The publication analysis is divided into four distinct periods, characterized by its production and significance of the articles. The study select on the based of artificial intelligence development in climate forecasting from initial period when role of AI included in climate forecasting.\n\nSource: Prepared by Author from R studio.\n\nThe first stage, the initial development stage (1984-1993), experienced a very slow and negligible growth. The total number of publications in this decade were only two. During this period researchers were trying to establish the relationship between computers and artificial intelligence. Zadeh (1984) has explained the use of artificial intelligence in computers with the example of fuzzy application. The fuzzy is nothing but an example showing how computers can think like a human along with its demerits. The second article in this also shows the usefulness of artificial intelligence in air traffic control using satellites. Artificial intelligence can be used in different aspects of day-to-day use like weather predication and information sharing (McGovern et al., 2019).\n\nThe second stage (1994-2003) has also witnessed a very a smaller number of publications where articles were published in different fields including weather forecasting, cloud classification, environmental science and climatic variation. In this decade various automated working computing programs were introduced by various authors. Authors further acknowledge the requirement of artificial intelligence in weather prediction (Medhekar, Bote, & Deshmukh, 2013).\n\nThe third phase of this topic lies between 2004 to 2013 and was characterized by the global adoption of artificial intelligence and its implications. According to scientific outcomes, a total no of 18 articles were published in these ten years. This phase can be considered as the introductory phase of the topic/relationship between artificial intelligence and weather predictions. In this phase, the relationship between artificial intelligence has been established in various aspects of research (Mehmood et al., 2021)\n\nThe last and the fourth stage (2014-2023) signifies the promotion and innovation, where the highest publication took place compared to last three decades. This stage contains 88 percentage of the articles used for the study which is 193. This stage consists of artificial intelligence and its various used in weather prediction.\n\nThe findings indicate significant growth in AI applications for climate forecasting, particularly from 2014 to 2023. The annual scientific production of AI and weather forecasting is depicted in Figure 4.\n\nThe value of articles can be seen in their citation scores. So, the analysis of the most influential article is also evaluated on the same phenomena, although the latest articles can face a disadvantage in this. Figure 5. shows the most cited and impactful articles in the area of artificial intelligence and weather prediction. With 661 citations, “Incremental Learning of Concept Drift in Nonstationary Environments” by (Muñoz-Leiva et al., 2012) is the most influential. In the article the author introduced an ensemble of classifier-based approach which can be utilized for incremental learning of concept drift, characterized by nonstationary environments. The article has also scored 42 total citations per year. With 436 citations, (Monteiro et al., 2022) conducted the second influential article “Solar photovoltaic generation forecasting methods: A review” on this theme. The study focuses on the concept of solar photovoltaic generation and its implications in power generation. The author reviewed various forecasting systems with significant information to design an optimal solar photovoltaic system (Nascimento et al., 2022).\n\nSource: Prepared by Author from R studio.\n\nThe most influential articles on this topic, based on citation scores, are illustrated in Figure 6.\n\nSource: Prepared by Author from R studio.\n\nCo-word analysis helps in identifying various factors and the global dynamics of the field under the study. Further, it uses a large knowledge base to extract various patterns of research trends. The cluster wise analysis provides the link between the topics within the cluster based on the betweenness and closeness of centrality where it will reflect the various trending topics in that field of study (Navadia et al., 2017). The Co-word co-occurrence analysis helps in exploring the various active themes of research as well as sub fields for the area under study (Nusrat & Jang, 2018). The author’s keyword in the study have been classified into four cluster based on the co-occurrence network. Figure 6 represents the interrelationship among the authors keywords and their significance as direct themes. The clusters selected on based of artificial intelligence role in climate forecasting and how many research paper published on AI on climate forecasting (Pattnayak et al., 2023).\n\nCluster 1: Artificial Intelligence and numerical weather prediction\n\nThe Figure 6 showing AI used in weather prediction. This cluster is the largest cluster related to artificial intelligence and weather forecasting where it consists of 52.9% of the key terms. The artificial intelligence algorithms are being one of the explicit approaches being utilised by researchers for weather forecasting basis where they provide best possible probabilistic forecast (Harder et al., 2022). Where the deep learning error correction methods effectively improve the prediction results of numerical weather prediction (Penny et al., 2022). The parameter of betweenness of centrality highlights that machine learning, artificial intelligence, numerical weather prediction, deep learning and forecasting are few of the central nodes among all the others keywords pertaining to this cluster. In this cluster, most closely related literatures are (Rasel, Sultana, & Meesad, 2018), (Rahayu et al., 2020), (Lam et al., 2022), (Riordan & Hansen, 2002), (Sallehuddin et al., 2007), (Sawale & Gupta, 2013), (Sedighi, 2016), (Sengoz et al., 2023), (Agrawal et al., 2023), (Sobri, Koohi-Kamali, & Abd Rahim, 2018), (Jiang et al., 2022),( Daniele & Sciacca, 2021), (Torres et al., 2021), (Yigitcanlar et al., 2021), (Trájer et al., 2022), (Yang & Wang, 2017), (Zaman et al., 2017) and (Ahmad & Kumar, 2024) where they represent the fundamental research in the field.\n\nA co-word co-occurrence analysis highlights key themes and their interrelationships (Figure 7).\n\nSource: Prepared by Author from R studio.\n\nCluster 2: Neural Networks and Numerical weather prediction\n\nThis cluster consist of 35.29% of key terms, where it explores the fundamental literature related to neural network and numerical weather prediction. The climate forecasting plays a vital role in many areas of human life. Estimating data for long-term efficient and effective results is very important, where predicting climate parameters based on AI, neural network and deep networks can optimise the data analysis and forecasting while simultaneously reducing errors (Yang et al., 2023). The artificial intelligence methods produce better results for sub seasonal to seasonal prediction (Mouatadid et al., 2023). Wherein, the scholars are suggesting the use of AI, neural networks, and numerical weather prediction to be used over conventional numerical forecast models for repeated initialisation of short-term forecast (Srivastava, Rastogi, & Kaushik, 2021). The keywords neutral network, numerical weather with prediction and statistical forecasting are central nodes among all the keywords. In this cluster, most closely related literature are (Stein, 2020), (Stuart et al., 2022), (Ravuri et al., 2021), (Ahmad, Zhang, & Yan, 2020), (UNFCCC, 2016), (Vitart et al., 2022).\n\nCluster 3: Feature selection and feature extraction\n\nThis cluster consists of 5.88% of the key terms, where it mainly explores the literature related to feature selection and feature extraction. (Vuyyuru, Rao, & Murthy, 2021) demonstrate that deep feature extraction, as opposed to feature selection, can enhance forecasting accuracy. Similarly, it is purported that automatic feature extraction methods allow deep learning (DL) algorithms to capture the inherent non-linear features, which permits them to handle big data (Wang & Huang, 2023). Wherein, the computational methods that are now in use do not investigate which climatic parameter or parameters have the greatest influence on achieving the best predicting performance. However, researchers suggest that various feature selection techniques can be utilised to identify the ideal subset of features (Wang & Mazharul Mujib, 2017). The keywords feature selection and feature extraction are the only central nodes in this cluster, where the most closely associated literature are (Wilde, 1994), (Wu, Wu, & Zhu, 2019), (Zhang & Chen, 1983), (Zhao et al., 2022).\n\nCluster 4: Learning (artificial intelligence) and power engineering computing\n\nThe literature on artificial intelligence and power engineering computers is the primary focus of this cluster, which comprises 5.88 percent of the key phrases. Numerous scholars have examined the various important advances in artificial intelligence and machine learning techniques (Gao et al., 2022). Wherein, Yang (2017) observed that the majority of these studies related to artificial intelligence and machine learning focuses on crop yield and soil properties prediction. Additionally, it is implied that the use of unmanned aerial vehicles, artificial neural networks, support vector machines, and remote sensors are rather common in weather prediction particularly in the field of agriculture (Rahim et al., 2023). In a similar vein, (Arora et al., 2023) offer a methodical and analytical analysis of the forecasting techniques, concentrating mostly on the metaheuristic and machine learning approaches. In this cluster, most closely related literature are (Xiao, Bennett, & Armstrong, 2002), (Dziejarski, Krzyżyńska, & Andersson, 2023).\n\nTo assess the current state of the themes, aggregation of the data is synthesized and represented on a strategic diagram (Figure 7). The most prominent themes for the contemporary time frame are visualized using this diagram. The strategic diagram positions these themes according to the dimensions of centrality and density. Centrality gauges the degree of interaction within the networks; while, density measures the internal strength among all the keywords in the network (Hao, Singh, & Xia, 2018).\n\nThe thematic analysis revealed several prominent themes in contemporary research, visualized in a strategic diagram (Figure 8).\n\nSource: Prepared by Author from R studio.\n\nThe strategic diagram is divided into four quadrants. In the upper right quadrant, the themes are known as motor themes exhibiting high density and centrality, where they signify well-developed, important and fundamental themes in the field of research. The themes in the upper left quadrant are highly developed but isolated themes, indicating well-developed but marginally important for the research area. The lower right quadrant represents basic and transversal themes, while they are important for the research area but still underdeveloped. Lastly, the lower left quadrant is low in density and centrality, reflecting either emerging or declining themes.\n\nThe current study presents weather forecasting, feature selection, feature extraction, machine learning, artificial intelligence, and numerical weather prediction as motor themes. Suggesting these themes as well-established, fundamental, and important for this field of research, while these themes are majorly explored by the researchers and presents a scope for future research. Secondly, satellite observations, data mining and remote sensing are niche themes. Presenting them as well-explored and well-established themes, however they do not reflect any importance for the field of research. Thirdly, random forests, solar forecasting, artificial neural network, wind power forecasting and neural network present emerging or declining themes. Lastly, weather prediction and nowcasting are basic and transversal themes representing the important yet underdeveloped themes. However, this quadrant also reflects artificial neural networks as one of the themes, suggesting it as important, underdeveloped and as emerging theme in the field of artificial intelligence and weather forecasting.\n\n\nFuture prospective of climate forecasting with AI\n\nClimate forecasting enabled by AI delivers notable improvements in timeliness, granularity, and accuracy. Large volumes of climatic data may be analyzed by it, leading to more accurate forecasts. High-resolution regional forecasts can be produced by AI algorithms, allowing for tailored predictions for regions that are vulnerable to extreme weather events. Early warning systems for extreme weather events can be made possible by AI-powered forecasting, which can identify early warning indicators of disasters and send out timely alerts. By simulating different scenarios, AI can help with planning for resilience and adaptation to climate change. By enhancing parameterizations and lowering biases, it can be used in conjunction with conventional climate models. AI systems can adjust to real-time data, guaranteeing current and accurate information in a setting that is changing quickly. Decision-makers in a variety of industries can be strengthened by AI-powered climate forecasting, which can also optimize resource allocation, risk management techniques, and climate change resilience. The following perspective of climate forecasting with AI find out in this research.\n\nResearch publication. The study provide that limited research on AI climate foresting modeling. There is challenges in accuracy, time and variable in existing model. Future research are more focus on different variables.\n\nAccuracy perspectives. The using AI model, accuracy of forecasting would be increased in term of time, quality and indexed. The real time information will be available with high accuracy. Existing AI model required more explainable like XAI model (Zhou et al., 2023).\n\nRegion-wise forecasting. Artificial intelligence can provide region wise information with high resolution equipment and software. The information may be used for planning in different sector like construction, manufacturing, transportation which can reduce overall cost of product (Fu et al., 2023).\n\nEarly warning. The AI technique used for early warning information regard to weather forecasting and climate forecasting. This information useful for various stakeholder in the region as well as save life of people.\n\nSupportive to different sector. AI techniques used for information of data for weather forecasting like water storage availability. This information is very helpful for management of resources available with department.\n\nSustainability. Sustainable environment is challenge in contemporary world. Existing AI based climate forecasting models are predicting climate variable which can be added with sustainable variables.\n\n\nDiscussion\n\nThis paper summarizes the research literature of artificial intelligence and weather forecasting from 1984 to 2023 using review of paper and Bibliometric analysis with help of software R studio. This article also highlights the quantitative and intuitive evaluation of academic progress and growth in this field. The research focuses on existing AI role in climate forecasting with help of existing research paper published and With the help of publication trends, the evolution of this field and knowledge structure is demonstrated.\n\nThis addresses a core issue in the previous studies, where articles with artificial intelligence and weather forecasting did not reveal the overall changes and bibliometric review. By studying the publication trend of this field, the development and research directions of artificial intelligence and its use in weather forecasting along with its evolution can be tracked.\n\nThis paper analyses the overall development of this research theme, providing the expansion of the theme in the upcoming future. Therefore, it also offers guidance for the upcoming researcher and provides in-depth insights into the future growth of this field. Based on bibliometric analysis the results revealed that the first article has been published in 1984 which is four decades old, with respect to that four distinct phases were developed and analyzed. Where the annual growth rate in the publication of literature has been found to be 10.32%. The current phase (2014-2023) witnessed the highest surge in publication and research diversification. One of the most notable findings has been the growth rate of the topic, approximately 88 percent of the total articles are in this phase only. The study has presented the research progress and the most prolific authors, articles and journals. The study has also tried to cover all the aspects related to artificial intelligence and weather forecasting from past research to future research directions.\n\nThe analysis was performed to find out the most relevant research and their influence on the topic. Co-word co-occurrence analysis was performed to find out the most common words associated with the theme called clusters (Kamyab et al., 2023). Furthermore, these clusters were analysed to find out the significant association with the theme. After finding the cluster and their correlation, the study took one step further and performed thematic analysis. By utilizing thematic analysis, the study tried to inform the various regions related to the theme and their importance in the upcoming time. The thematic analysis resulted in the identification of a few major themes as artificial neural networks, nowcasting, weather prediction, machine learning, weather forecasting, feature selection, feature extraction, and numerical weather prediction. Highlighting their significance to be explored as future research agenda.\n\n\nKey findings\n\nThe study conducted on the basis of previous literature about AI technology used in Enhancing Climate Forecasting and it future prospective. The study finds that different techniques of AI used in climate furcating which outcome is different based on the model. Bibliometric analysis conducted bases on AI used in climate forecasting. R studio used for analysis of research trends and important literature analysis about AI technology using in current scenario. The finding of study is as under:\n\n• The paper finds that existing researchers are in limited way. AI based models are on different variables. Universal AI technology is required for future perspective.\n\n• The study finds that publications in AI climate forecasting are in limited way which is important to focus in this area.\n\n• By examining vast amounts of data and spotting complex patterns, artificial intelligence (AI) approaches can greatly increase the accuracy of climate forecasts. More precise regional projections can be produced by them, allowing for more focused adaptation strategies.\n\n• Extreme weather occurrences can be more accurately detected and predicted by AI-based early warning systems. AI can help with resilience planning and climate change adaptation by offering useful insights.\n\n• The performance of climate models can be improved by including AI algorithms. Increased funding for research and development, stakeholder collaboration and data sharing, capacity building for climate researchers and practitioners, the ethical and responsible application of AI, community involvement, and stakeholder participation are among the recommendations.\n\n• By putting these suggestions into practice, we may fully utilize AI’s promise for climate forecasting and support more sensible decision-making and efficient climate.\n\nAs one of the world’s toughest challenges, combating climate change is another area where AI has transformational potential. With the prospective intervention of AI it can be trained to check and measure changes in iceberg melting and mapping deforestation through AI techniques.\n\nEnhancing AI models for climate forecasting\n\n1. Development of universal AI models:\n\n○ There is a need for developing universal AI models that can be applied across different climatic regions and conditions. These models should incorporate a wide range of variables to improve accuracy and reliability.\n\n2. Explainable AI (XAI) techniques:\n\n○ Implementing explainable AI techniques is crucial for enhancing the transparency and interpretability of AI models. This will help stakeholders understand the decision-making process of AI systems and build trust in their predictions.\n\n3. Real-time data integration:\n\n○ AI models should be capable of integrating real-time data to update forecasts dynamically. This will ensure that the predictions are current and can adapt to rapidly changing weather conditions.\n\nRegion-specific forecasting\n\n1. High-resolution regional forecasts:\n\n○ AI algorithms should be developed to provide high-resolution forecasts tailored to specific regions. This will enable more precise predictions and help in planning and decision-making at local levels.\n\n2. Early warning systems:\n\n○ AI-based early warning systems for extreme weather events should be enhanced to detect and predict such events with higher accuracy. These systems can save lives and reduce economic losses by providing timely alerts to communities and authorities.\n\nCollaboration and data sharing\n\n1. Increased funding and research:\n\n○ Governments and organizations should increase funding for research and development in AI-based climate forecasting. Collaborative efforts among researchers, institutions, and countries can accelerate advancements in this field.\n\n2. Data sharing and collaboration:\n\n○ Establishing platforms for data sharing and collaboration among researchers and practitioners is essential. Open access to climatic data and AI models can foster innovation and improve the overall quality of climate forecasts.\n\nEthical and responsible AI use\n\n1. Ethical considerations:\n\n○ The development and deployment of AI models should adhere to ethical guidelines to prevent bias and ensure fair use. This includes considering the social and economic impacts of AI predictions on different communities.\n\n2. Stakeholder involvement:\n\n○ Engaging stakeholders, including local communities, policymakers, and industry experts, in the development and implementation of AI models can enhance their relevance and acceptance.\n\nSustainable practices\n\n1. Integration of sustainable variables:\n\n○ AI models should incorporate sustainable variables to predict climate impacts and support environmental sustainability. This includes variables related to renewable energy sources, conservation efforts, and ecological health.\n\nApart from using AI is conserving biodiversity predicting climate change and predicting climatic disasters is strong prospects for AI for future global economies and saving humanitarian disaster by having a proactive approach in disaster management.\n\n\nImplications\n\nThe present study provides several implications for researchers, entrepreneurs, and academicians. Due to its wide range of articles from 1984 to 2023, the study can be utilized in various ways. Also, by knowing the most influential authors, articles and sources of this research domain one can easily identify and associate their work. The study would guide them in future directions by knowing the current existing gap in the literature which could help them to conduct future studies. The study provides an overall view regarding the theme so that the upcoming research can utilize the sources to receive and publish their research in relevant sources. Organizations and entrepreneurs can use the study to predict the upcoming trends in the field and experts to work with them. Technologies powered by Artificial Intelligence techniques, with extreme climate aid tech devices (Dikshit et al., 2024), have advanced dramatically, initiating breakthroughs in additional research sectors. Although a lot of individual Earth System features have been analysed with AI techniques, more general application to comprehend better the complete climate system has not occurred, and the skill to do so may be quite far from the current state of development. At this stage of development, Artificial intelligence (AI) can be used to analyse alert warning mechanism and future predictability numbers with reference to climate foreseen challenges globally. It sensory devices can turn a strong necessary requirements to make the economies prepared for such massive climatic transitions and challenges. AI can aid in understanding and improving existing data and simulations, as it has done in other systems. For instance, Airbus Defence and Space is using TensorFlow, the open-source set of AI tools from Google, to extract information from satellite images and offer valuable insights to customers. The study builds relevant implication and also provides base for future research and practical application.\n\nThe present study provides several implications for researchers, entrepreneurs, and academicians. The study spans a wide range of articles from 1984 to 2023, making it a valuable resource in multiple ways. Knowing the most influential authors, articles, and sources in this research domain allows for easy identification and association of work, guiding future research by highlighting current gaps in the literature. This can help researchers in planning and conducting future studies, offering a comprehensive view of the themes to aid in publishing relevant research.\n\nKey implications:\n\n1. Guidance for future research:\n\n○ The study highlights significant gaps and emerging themes in AI-based climate forecasting, suggesting areas where further research is needed. This includes the development of more universal and explainable AI models, integration of real-time data, and region-specific high-resolution forecasts.\n\n○ For instance, current research by Dewitte et al. (2021) demonstrates the transformative potential of AI in enhancing decadal climate prediction and weather forecasting by analyzing large volumes of unstructured data and leveraging intricate relationships.\n\n2. Practical applications for policymakers and practitioners:\n\n○ The findings can aid policymakers and practitioners in making informed decisions regarding climate resilience and adaptation strategies. The use of AI for early warning systems and high-resolution regional forecasts can significantly improve preparedness for extreme weather events.\n\n○ The deployment of AI for climate change adaptation, emphasizing the need for integrating AI with policy frameworks to address climate challenges effectively.\n\n3. Industry and entrepreneurial opportunities:\n\n○ Organizations and entrepreneurs can utilize the study to predict upcoming trends in AI applications for climate forecasting, allowing them to innovate and invest in technologies that support sustainable development and disaster management.\n\n○ The study by Kamyab et al. (2023) highlights innovative avenues for utilizing AI and big data analytics in water resource management, showcasing the potential for AI-driven solutions in various sectors.\n\n4. Enhanced understanding of AI’s role in climate science:\n\n○ The study underscores the importance of AI in advancing climate science, from improving the accuracy of weather forecasts to providing insights for long-term climate predictions.\n\n○ Research by Dikshit et al. (2024) illustrates the new era of AI in spatial modeling and climate-induced hazard assessment, emphasizing the need for more advanced AI tools to tackle climate challenges.\n\n5. Ethical and responsible use of AI:\n\n○ The study emphasizes the need for ethical considerations in the deployment of AI, including addressing biases and ensuring transparency in AI models. This aligns with the broader concerns about the responsible use of AI in various applications.\n\n\nResearch limitations\n\nNo research comes without limitations, there are some limitations in this study as well. First and foremost, due to a lack of sources the study utilized only two databases namely Scopus and Web of Science. Future researchers can use other available databases also. The analysis in the study was performed using a single software, researchers may use other or multiple software in their study. The study consists of research articles in the English language only excluding other languages. Future researchers can add different document types to their study, as this research is purely used research articles.", "appendix": "Data availability\n\nThe data that support the findings of this study were obtained from Scopus databases. Restrictions apply to the availability of these data, which were used under license for this study.\n\nFigshare: Final AI and WF. https://doi.org/10.6084/m9.figshare.26789215.v1 (Ahmad 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\nAbdel-Kader H, Salam MA-E: Hybrid Machine Learning Model for Rainfall Forecasting. J. Intelligence. 2021; 1(1): 5–12. Publisher Full Text\n\nAbuella M, Chowdhury B: Improving combined solar power forecasts using estimated ramp rates: data-driven post-processing approach. IET Renew. Power Gener. 2018; 12(10): 1127–1135. Publisher Full Text\n\nAdam JA: Satellites and artificial intelligence promise improved safety and efficiency. IEEE Spectr. 1991; 28(2): 27–32. Publisher Full Text\n\nAgrawal S, Carver R, Gazen C, et al.: A machine learning outlook: Post-processing of global medium-range forecasts. arXiv preprint arXiv:2303.16301. 2023.\n\nAhmad T, Zhang H, Yan B: A review on renewable energy and electricity requirement forecasting models for smart grid and buildings. Sustain. Cities Soc. 2020; 55: 102052. Publisher Full Text\n\nAhmad V, Kumar R: Final AI and WF.xlsx. [Dataset]. Figshare. 2024. Publisher Full Text\n\nAkhter MN, Mekhilef S, Mokhlis H, et al.: Review on forecasting of photovoltaic power generation based on machine learning and metaheuristic techniques. IET Renew. Power Gener. 2019; 13(7): 1009–1023. Publisher Full Text\n\nArora M, Kumar R, Bangwal D, et al.: An empirical study of cold chain issues and performance: Applying structural equation modeling. J. Food Process Eng. 2023; 46(12): e14439. Publisher Full Text\n\nAwasthi A, Pattnayak KC, Tandon A, et al.: Implications of climate change on surface temperature in North Indian states: evidence from CMIP6 model ensembles. Front. Environ. Sci. 2023; 11. Publisher Full Text\n\nAylak BL: Artificial intelligence and machine learning applications in agricultural supply chain: a critical commentary.2021. Reference Source\n\nBauer P, Thorpe A, Brunet G: The quiet revolution of numerical weather prediction. Nature. 2015; 525(7567): 47–55. PubMed Abstract \| Publisher Full Text\n\nBi K, Xie L, Zhang H, et al.: Accurate medium-range global weather forecasting with 3d neural networks. Nature. 2023; 1–6.\n\nBochenek B, Ustrnul Z: Machine Learning in Weather Prediction and Climate Analyses—Applications and Perspectives. Atmos. 2022; 13(2): 180. Publisher Full Text\n\nBonavita M, Laloyaux P: Machine Learning for Model Error Inference and Correction. J. Adv. Model. Earth Syst. 2020; 12(12): e2020MS002232. Publisher Full Text\n\nBrunet G, Parsons DB, Ivanov D, et al.: Advancing Weather and Climate Forecasting for Our Changing World. Bull. Am. Meteorol. Soc. 2023; 104(4): E909–E927. Publisher Full Text\n\nChapman WE, Monache LD, Alessandrini S, et al.: Probabilistic Predictions from Deterministic Atmospheric River Forecasts with Deep Learning. Mon. Weather Rev. 2022; 150(1): 215–234. Publisher Full Text\n\nChen K, Bai L, Ling F, et al.: Towards an End-to-End Artificial Intelligence Driven Global Weather Forecasting System. arXiv preprint arXiv:2312.12462. 2023a.\n\nChen K, Han T, Gong J, et al.: Fengwu: Pushing the skillful global medium-range weather forecast beyond 10 days lead. arXiv preprint arXiv:2304.02948. 2023b.\n\nChen L, Zhong X, Zhang F, et al.: Fuxi: A cascade machine learning forecasting system for 15-day global weather forecast. arXiv preprint arXiv:2306.12873. 2023c.\n\nChung HM, Gray PR, Mannino M: Introduction to Data Mining and Knowledge Discovery.1998. Publisher Full Text\n\nCifuentes J, Marulanda G, Bello A, et al.: Air Temperature Forecasting Using Machine Learning Techniques: A Review. Energies. 2020; 13(16): 4215. Publisher Full Text\n\nCobo MJ, López-Herrera AG, Herrera-Viedma E, et al.: Science Mapping Software Tools: Review, Analysis, and Cooperative Study Among Tools. J. Am. Soc. Inf. Sci. Technol. 2011; 62(7): 1382–1402. Publisher Full Text\n\nCowls J, Tsamados A, Taddeo M, et al.: The AI gambit: leveraging artificial intelligence to combat climate change—opportunities, challenges, and recommendations. Ai & Society. 2021; 1–25.\n\nDaniele P, Sciacca D: An optimisation model for the management of green areas. Int. Trans. Oper. Res. 2021; 28(6): 3094–3116. Publisher Full Text\n\nDavenport FV, Diffenbaugh NS: Using Machine Learning to Analyse Physical Causes of Climate Change: A Case Study of U.S. Midwest Extreme Precipitation. Geophys. Res. Lett. 2021; 48(15). Publisher Full Text\n\nDevaraj J, Madurai Elavarasan R, Shafiullah GM, et al.: A holistic review on energy forecasting using big data and deep learning models. Int. J. Energy Res. 2021; 45(9): 13489–13530. Publisher Full Text\n\nDewitte S, Cornelis JP, Müller R, et al.: Artificial intelligence revolutionises weather forecast, climate monitoring and decadal prediction. Remote Sens. 2021; 13(16): 3209. Publisher Full Text\n\nDikshit A, Pradhan B, Matin SS, et al.: Artificial Intelligence: A new era for spatial modelling and interpreting climate-induced hazard assessment. Geosci. Front. 2024; 15: 101815. Publisher Full Text\n\nDong J, Zeng W, Wu L, et al.: Enhancing short-term forecasting of daily precipitation using numerical weather prediction bias correcting with XGBoost in different regions of China. Eng. Appl. Artif. Intell. 2023; 117: 105579. Publisher Full Text\n\nDupuy F, Mestre O, Serrurier M, et al.: ARPEGE Cloud Cover Forecast Postprocessing with Convolutional Neural Network. Weather Forecast. 2021; 36(2): 567–586. Publisher Full Text\n\nDziejarski B, Krzyżyńska R, Andersson K: Current status of carbon capture, utilization, and storage technologies in the global economy: A survey of technical assessment. Fuel. 2023; 342: 127776. Publisher Full Text\n\nElwell R, Polikar R: Incremental Learning of Concept Drift in Nonstationary Environments. IEEE Trans. Neural Netw. 2011; 22(10): 1517–1531. PubMed Abstract \| Publisher Full Text\n\nEra CAA, Rahman M, Alvi ST: Short Term Weather Forecasting Comparison Based on Machine Learning Algorithms. 2023 Intelligent Methods, Systems, and Applications (IMSA). IEEE; 2023; pp. 369–374.\n\nFente DN, Singh DK: Weather Forecasting Using Artificial Neural Network. 2018 Second International Conference on Inventive Communication and Computational Technologies (ICI-CCT). 2018; pp. 1757–1761. Publisher Full Text\n\nFradkov AL: Early History of Machine Learning. IFAC- PapersOnLine. 2020; 53(2): 1385–1390. Publisher Full Text\n\nFu X, Zhang C, Chang F, et al.: Simulation and forecasting of fishery weather based on statistical machine learning. Information Processing in Agriculture. 2023.\n\nGao Z, Shi X, Wang H, et al.: Earthformer: Exploring space-time transformers for earth system forecasting. Adv. Neural Inf. Proces. Syst. 2022; 35: 25390–25403.\n\nGautam A, Bedi P: MR-VSM: Map Reduce based vector Space Model for user profiling-an empirical study on News data. 2015 International Conference on Advances in Computing, Communications, and Informatics (ICACCI). 2015; pp. 355–360.\n\nGowthamy J, Prakash AB, Yadav GR, et al.: Data Analysis of Weather Prediction to Solve Natural Problems by using Ai.2019.\n\nGrenier JR, Brusberg L, Wieland KA, et al.: Ultrafast laser processing of glass waveguide substrates for multi-fiber connectivity in copackaged optics. Adv. Opt. Technol. 2023; 12: 1244009. Publisher Full Text\n\nHao Z, Singh VP, Xia Y: Seasonal drought prediction: Advances, challenges, and future prospects. Rev. Geophys. 2018; 56(1): 108–141. Publisher Full Text\n\nHarder P, Yang Q, Ramesh V, et al.: Generating physically-consistent high-resolution climate data with hard-constrained neural networks. arXiv preprint arXiv:2208.05424. 2022.\n\nHedar AR, Almaraashi M, Abdel-Hakim AE, et al.: Hybrid Machine Learning for Solar Radiation Prediction in Reduced Feature Spaces. Energies. 2021; 14(23): 7970. Publisher Full Text\n\nHensengerth O: Inclusive governance of hydropower on shared rivers? Towards an international legal geography of the Lower Mekong basin. Front. Clim. 2024; 6: 1275049. Publisher Full Text\n\nHuntingford C, Jeffers ES, Bonsall MB, et al.: Machine learning and artificial intelligence to aid climate change research and preparedness. Environ. Res. Lett. 2019; 14(12): 124007. Publisher Full Text\n\nHussain J, Liatsis P, Khalaf M, et al.: A dynamic neural network architecture with immunology inspired optimization for weather data forecasting. Big Data Res. 2018; 14: 81–92. Publisher Full Text\n\nJiang Y, Li X, Huang J: Zoning Optimization Method of a Riverfront Greenspace Service Function Oriented to the Cooling Effect: A Case Study in Shanghai. Int. J. Environ. Res. Public Health. 2022; 19(23): 16191. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKıran MS, Ozceylan E, Gunduz M, et al.: A novel hybrid approach based on particle swarm optimization and ant colony algorithm to forecast energy demand of Turkey. Energy Convers. Manag. 2012; 53: 75–83. Publisher Full Text\n\nKamyab H, Khademi T, Chelliapan S, et al.: The latest innovative avenues for the utilization of artificial Intelligence and big data analytics in water resource management. Results Eng. 2023; 20: 101566. Publisher Full Text\n\nKaur P, Chaudhary P, Bijalwan A, et al.: Network traffic classification using multiclass classifier. Advances in Computing and Data Sciences: Second International Conference, ICACDS 2018, Dehradun, India, April 20-21, 2018, Revised Selected Papers, Part I 2. Singapore: Springer; 2018; pp. 208–217.\n\nKhan TA, Abbas K, Muhammad A, et al.: Artificial Intelligence Based Solar Radiation Predictive Model Using Weather Forecasts. Comput. Mater. Contin. 2022; 71(1): 109–124. Publisher Full Text\n\nKhotanzad A, Afkhami-Rohani R, Lu TL, et al.: ANNSTLF-a neural-network-based electric load forecasting system. IEEE Trans. Neural Netw. 1997; 8(4): 835–846. PubMed Abstract \| Publisher Full Text\n\nKim W, Jang D, Park SW, et al.: Construction of a Spatio-Temporal Dataset for Deep Learning-Based Precipitation Nowcasting. J. Inf. Sci. Theory Pract. 2022; 10(spc): 135–142. Publisher Full Text\n\nKumar GVB, Palanisamy K: A review of energy storage participation for ancillary services in a microgrid environment. Inventions. 2020; 5(4): 63. Publisher Full Text\n\nLaloyaux P, Kurth T, Dueben PD, et al.: Deep Learning to Estimate Model Biases in an Operational NWP Assimilation System. J. Adv. Model. Earth Syst. 2022; 14(6): e2022MS003016. Publisher Full Text\n\nLam R, Sanchez-Gonzalez A, Willson M, et al.: Graphcast: Learning skillful medium-range global weather forecasting. arXiv preprint arXiv:2212.12794. 2022.\n\nLeal Filho W, Wall T, Mucova SAR, et al.: Deploying artificial intelligence for climate change adaptation. Technol. Forecast. Soc. Chang. 2022; 180: 121662. Publisher Full Text\n\nLing F, Luo J-J, Li Y, et al.: Multi-task machine learning improves multi-seasonal prediction of the Indian ocean dipole. Nat. Commun. 2022; 13(1): 7681. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartín-Vázquez R, Aler R, Galván IM: A study on feature selection methods for wind energy prediction. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 10305 LNCS 2017; pp. 698–707. Publisher Full Text\n\nMartínez A, Juan GC, Cobo M, et al.: Impacts and Implications for Advancing in Environmental Knowledge in Hospitality Industry in COVID Society: a Bibliometric Analysis. Sustainability. 2022; 12(16): 8952. Publisher Full Text\n\nMcGovern A, Karstens CD, Smith T, et al.: Quasi-Operational Testing of Real-Time Storm-Longevity Prediction via Machine Learning. Weather Forecast. 2019; 34(5): 1437–1451. Publisher Full Text\n\nMedhekar DS, Bote M, Deshmukh SD: Heart Disease Prediction System using Naive Bayes.2013. Reference Source\n\nMehmood F, Ghani MU, Asim MN, et al.: MPF-Net: A computational multi-regional solar power forecasting framework. Renew. Sust. Energ. Rev. 2021; 151: 111559. Publisher Full Text\n\nMonteiro MJ, Couto FT, Bernardino M, et al.: A Review on the Current Status of Numerical Weather Prediction in Portugal 2021: Surface–Atmosphere Interactions. Atmos. 2022; 13(9): 1356. Publisher Full Text\n\nMouatadid S, Orenstein P, Flaspohler G, et al.: Adaptive bias correction for improved subseasonal forecasting. Nat. Commun. 2023; 14(1): 3482. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuñoz-Leiva F, Viedma-del-Jesús MI, Sánchez-Fernández J, et al.: An application of co-word analysis and bibliometric maps for detecting the most highlighting themes in the consumer behaviour research from a longitudinal perspective. Qual. Quant. 2012; 46(4): 1077–1095. Publisher Full Text\n\nNascimento L, Kuramochi T, Iacobuta G, et al.: Twenty years of climate policy: G20 coverage and gaps. Clim. Pol. 2022; 22(2): 158–174. Publisher Full Text\n\nNavadia S, Yadav P, Thomas J, et al.: Weather prediction: A novel approach for measuring and analysing weather data. IEEE Xplore; 2017, February 1. Publisher Full Text\n\nNeema MN, Ohgai A: Multi-objective location modeling of urban parks and open spaces: Continuous optimisation. Comput. Environ. Urban. Syst. 2010; 34(5): 359–376. Publisher Full Text\n\nNusrat I, Jang S-B: A Comparison of Regularization Techniques in Deep Neural Networks. Symmetry. 2018; 10(11): 648. Publisher Full Text\n\nPathak J, Subramanian S, Harrington P, et al.: Fourcastnet: A global data-driven high-resolution weather model using adaptive fourier neural operators. arXiv preprint arXiv:2202.11214. 2022.\n\nPattnayak KC, Awasthi A, Sharma K, et al.: Fate of rainfall over the North Indian states in the 1.5 and 2 C warming scenarios. Earth and Space Science. 2023; 10(2): e2022EA002671. Publisher Full Text\n\nPenny SG, Smith TA, Chen TC, et al.: Integrating Recurrent Neural Networks With Data Assimilation for Scalable Data-Driven State Estimation. J. Adv. Model. Earth Syst. 2022; 14(3): e2021MS002843. Publisher Full Text\n\nRahayu I, Djamal E, Ilyas R, et al.: Daily Temperature Prediction Using Recurrent Neural Networks and Long-Short Term Memory.2020. Reference Source\n\nRahim FA, Mohanty AK, Abdulrahman IS, et al.: Impacts of financial management practices on the economical development of small to medium size forest enterprises. Cent. Eur. J. Manag. 2023; 31(1): 22–29.\n\nRasel RI, Sultana N, Meesad P: An application of data mining and machine learning for weather forecasting. Advances in Intelligent Systems and Computing. 2018; 566: 169–178. Publisher Full Text\n\nRavuri S, Lenc K, Willson M, et al.: Skilful precipitation nowcasting using deep generative models of radar. Nature. 2021; 597(7878): 672–677. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRiordan D, Hansen BK: A fuzzy case-based system for weather prediction. International Journal of Engineering Intelligent Systems for Electrical Engineering and Communications. 2002; 10(3): 139–146. Reference Source\n\nRodionov SN, Martin JH: An expert system-based approach to prediction of year-to-year climatic variations in the North Atlantic region. Int. J. Climatol. 1999; 19(9): 951–974. Publisher Full Text\n\nSallehuddin R, Shamsuddin SMH, Hashim SZM, et al.: Forecasting time series data using hybrid grey relational artificial neural network and auto regressive integrated moving. Neural Network World. 2007; 17(6): 573.\n\nSalman G, Kanigoro B, Heryadi Y: Weather forecasting using deep learning techniques. International Conference on Advanced Computer Science and Information Systems (ICACSIS). 2015; 2015: 281–285.\n\nSawale GJ, Gupta SR: Use of Artificial Neural Network in Data Mining For Weather Forecasting.2013.\n\nSedighi M: Application of word co-occurrence analysis method in mapping of the scientific fields (case study: the field of Informetrics). Libr. Rev. 2016; 65(1–2): 52–64. Publisher Full Text\n\nSengoz C, Ramanna S, Kehler S, et al.: Machine Learning Approaches to Improve North American Precipitation Forecasts. IEEE Access. 2023; 11: 97664–97681. Publisher Full Text\n\nSingh M, Acharya N, Grover A, et al.: Short-range forecasts of global precipitation using deep learning-augmented numerical weather prediction. arXiv e-prints, arXiv–2206. 2022.\n\nSinghroul A, Agrawal S: Artificial Neural Networks in Weather Forecasting - A Review. 2021 International Conference on Advances in Technology, Management & Education (ICATME). 2021; pp. 9–14. Publisher Full Text\n\nSobri S, Koohi-Kamali S, Abd Rahim N: Solar photovoltaic generation forecasting methods: A review. Energy Convers. Manag. 2018; 156: 459–497. Publisher Full Text\n\nSrivastava MA, Rastogi A, Kaushik P: A Comprehensive Study on the Use of Various Artificial Intelligence and Machine Learning Techniques in the Field of Weather Forecasting. Weather. 2021; 76(8): 267–278.\n\nStein AL: Artificial intelligence and climate change. Yale Journal on Regulation. 2020; 37: 890.\n\nStuart NA, Hartfield G, Schultz DM, et al.: The Evolving Role of Humans in Weather Prediction and Communication. Bull. Am. Meteorol. Soc. 2022; 103(8): E1720–E1746. Publisher Full Text\n\nSubhajini C: APPLICATION OF NEURAL NETWORKS IN WEATHER FORECASTING. International Journal of Weather, Climate Change and Conservation Research. 2018; 4(1): 8–18.\n\nTorres MN, Fontecha JE, Walteros JL, et al.: City-scale optimal location planning of Green Infrastructure using piece-wise linear interpolation and exact optimisation methods. J. Hydrol. 2021; 601: 126540. Publisher Full Text\n\nTrájer AJ, Sebesty´ en V, Domokos E, et al.: Indicators for climate change-driven urban health impact assessment. J. Environ. Manag. 2022; 323: 116165. PubMed Abstract \| Publisher Full Text\n\nUNFCCC: The Paris Agreement.2016. Reference Source\n\nVitart F, Robertson AW, Spring A, et al.: Outcomes of the WMO Prize Challenge to Improve Subseasonal to Seasonal Predictions Using Artificial Intelligence. Bull. Am. Meteorol. Soc. 2022; 103(12): E2878–E2886. Publisher Full Text\n\nVuyyuru VA, Rao GA, Murthy YVS: A novel weather prediction model using a hybrid mechanism based on MLP and VAE with fire-fly optimization algorithm. Evol. Intel. 2021; 14(2): 1173–1185. Publisher Full Text\n\nWang K, Huang J: Domestic and abroad research status and prospects of solar energy resource evaluation methods. Adv. Clim. Chang. Res. 2023; 19(2): 160. Publisher Full Text\n\nWang Z, Mazharul Mujib ABM: The Weather Forecast Using Data Mining Research Based on Cloud Computing. J. Phys. Conf. Ser. 2017; 910: 012020. Publisher Full Text\n\nWilde WD: Australian Expert-Systems for Natural Systems. AI Applications. 1994; 8(3): 3–12.\n\nWu YX, Wu QB, Zhu JQ: Data-driven wind speed forecasting using deep feature extraction and LSTM. IET Renew. Power Gener. 2019; 13(12): 2062–2069. Publisher Full Text\n\nXiao N, Bennett DA, Armstrong MP: Using evolutionary algorithms to generate alternatives for multiobjective site-search problems. Environ Plan A. 2002; 34(4): 639–656. Publisher Full Text\n\nYang S, Ling F, Bai L, et al.: Improving seasonal forecast of summer precipitation in southeastern China using cyclegan deep learning bias correction. Geophys. Res. Lett. 2023; 10: 124007.\n\nYang T, Asanjan AA, Welles E, et al.: Developing reservoir monthly inflow forecasts using artificial intelligence and climate phenomenon information. Water Resour. Res. 2017; 53(4): 2786–2812. Publisher Full Text\n\nYang Z, Wang J: A new air quality monitoring and early warning system: Air quality assessment and air pollutant concentration prediction. Environ. Res. 2017; 158: 105–117. PubMed Abstract \| Publisher Full Text\n\nYigitcanlar T, Mehmood R, Corchado J: Green artificial intelligence: Towards an efficient, sustainable and equitable technology for smart cities and futures. Sustainability. 2021; 13(16): 8952. Publisher Full Text\n\nZadeh LA: Fuzzy logic, neural networks, and soft computing. Communications of the ACM. 1984; 37(3): 77–84. Publisher Full Text\n\nZaman NAFK, Kanniah KD, Kaskaoutis DG: Estimating particulate matter using satellite based aerosol optical depth and meteorological variables in Malaysia. Atmos. Res. 2017; 193: 142–162. Publisher Full Text\n\nZhang X, Chen Y: Mathematical Models of Multifactorial Decision and Weather Forecast. IFAC Proceedings Volumes. 1983; 16(13): 265–269. Publisher Full Text\n\nZhao X, Sun Q, Tang W, et al.: A comprehensive wind speed forecast correction strategy with an artificial intelligence algorithm. Front. Environ. Sci. 2022; 10(November): 1–12. Publisher Full Text\n\nZhou W, Li J, Yan Z, et al.: Progress and future prospects of decadal prediction and data assimilation: A review. Atmospheric and Oceanic Science Letters. 2023; 100441." }	[ { "id": "336400", "date": "06 Nov 2024", "name": "Bilkisu Maijamaa", "expertise": [ "Reviewer Expertise OPTIMIZATION", "OPERATIONAL RESEARCH", "STATISTICAL ANALYSIS", "PROBABILITY" ], "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 constructed, and the introductions are straight to the point and well-understood with a well-defined problem statement. aim and objective of the study are well written. Recent literature was used and the method used was just appropriate. Results well presented and conclusions drawn from the research can be used by other researchers to update adequately.\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/13-1094
https://f1000research.com/articles/12-39/v1	10 Jan 23	{ "type": "Research Article", "title": "Muhammad Shahrur's millenial interpretation of women’s issues", "authors": [ "Saifuddin Herlambang" ], "abstract": "Background: This study examines Muhammad Shahrur's theory of limits and women’s issues. This theory adjusts the muhkamat verses to remain relevant to sociocultural conditions while remining within the jurisdiction of Allah SWT. Shahrur's approach conveyed women as different from traditional ulema, and controversial. Therefore, it is necessary to describe Shahrur's theory and interpretation on women issues. Methods: This was an exploratory bibliographic study using descriptive-hermeneutic analysis. Two of Shahrur's books were selected and five chapters from Al-Kitāb wa Al-Qur’ān, Qirā’ah Mu’āshirah and five chapters from Nahw Ushūl al-Jadīdah Li al-Fiqh al-Islāmy; Fiqh al-Mar'ah . Results: Shahrur’s interpretations on women issues are: a) relationships between teenagers of the opposite sex without marriage or living together is \"halal\" if it follows their will, without a contract, being accompanied by syecih or permission, b) The maximum limit of hijab is to cover the entire body except the face and palms. In contrast, the minimum limit covers the juyūb, including cleavage under the armpits, body parts, genitals, and buttocks. Apart from these, it does not include intimate parts and adapts to the community. c) women's intimate parts are shown only to the seven groups; brothers, fathers, children of a sibling, parents of one's wives and their children, d) Polygamy has both an upper limit and lower limit. Shahrur allows polygamy under two conditions: widows with children whose husbands left them to protect them, polygamy has two limitations, limit for quantity and limit for quality, e) the law of adultery has a lower and upper limit.\n\nConclusion: According to Shahrur, women's issues are divided into four limits, sometimes they are at the upper limit and sometimes at the lower limit. Shahrur's linguistic approach finally led him to draw a conclusion that the product of Islamic law is highly dependent on the sociocultural context.", "keywords": [ "Women", "Millennial Commentary", "Muhammad Shahrur", "Theory of limits" ], "content": "Introduction\n\nIn the public domain, the condition of women and men -- when compared to the periods of colonialism and imperialism -- is now much better. Many women also get into politics, have a career, are highly educated, and so on. But this does not mean that it guarantees justice for women, especially at the religious discursive level. Today, in Indonesia as a country where the religion embraced by the majority of the population is Islam, unfair treatment of women by men, in the form of discrimination and violence, still occurs. It is true that the state must be present. However, it is too difficult for the state to deal with it alone. It needs religious support and some kind of religious commentary and or fiqh in favor of women.\n\nDevi Asmarani, a women's activist, in a Focus Group Discussion (FGD) on Women and Gender Equality, in Jakarta, on 8 October 2018, said that currently there are at least 400 Regional Regulations (Perda) that discriminate against women. “This discrimination is, for example, in the form of a Regional Regulation that limits the way women dress and limiting the time for women's activities outside the home.” According to her, the clash of views between religion and politics is one of the factors forming discriminatory attitudes towards women. Opportunities for women in Indonesia, to become regional heads or members of the Legislative, are very small, especially in areas that apply Islamic law, where discrimination still occurs.1\n\nIn addition to discrimination, the cases of violence against women in Indonesia are in fact still high in number. This is revealed from data released by the National Commission for Eradication of Violence against Women (Komnas perempuan) in 2015. In the data, it was recorded that there were at least 16,217 cases that went to Komnas Perempuan. A total of 11,207 cases of which occurred in households. A total of 6,725 out of 11,207 cases of violence against women were experienced by wives. Meanwhile, the other 2,734 cases were experienced by women whose status was girlfriend. There were 930 cases of violence against young women. The data on violence against women released by Komnas Perempuan is far less than the data presented by the Religious Courts-Religious Judiciary Agency (PA-BADILAG). According to data from PA-BADILAG, violence against women reached 321,752 cases. Thus, when combined with data from Komnas Perempuan, violence against women reached 321,752 cases.2\n\nThe leader of the Cirebon Arjawinangun Islamic Boarding School, KH Husein Muhammad, argued that the rise of cases of violence against women is partly due to the wrong interpretation of Islamic teaching text and that is a reason for people to commit violence in the name of religion.3 According to Husein, one of the texts that is often misinterpreted so that it is considered discriminatory is Surah An Nisa verse 34. The Surah is often interpreted as follows:\n\nMen are the caretakers of women, as men have been provisioned by Allah over women and tasked with supporting them financially. And righteous women are devoutly obedient and, when alone, protective of what Allah has entrusted them with. And if you sense ill-conduct from your women, advise them ˹first˺, ˹if they persist,˺ do not share their beds, ˹but if they still persist,˺ then cahtise them. But if they change their ways, do not be unjust to them. Surely Allah is Most High, All-Great.4\n\nIn the verse, according to Husein, there is the word “chastise” which is used as the basis for husbands to commit violence against their wives. In fact, Husein continued, the interpretation is not like that, it is not only women who are blamed, but men who are at fault must also be punished according to Husein.5 Such an interpretation also emphasizes the position of women as inferiors who must always obey men. Otherwise, men feel entitled to violence. Husein emphasized that Islam is not a discriminatory religion, but a wrong understanding of Islamic texts often gives rise to discriminatory views. This situation occurs partly because the interpretation of Islamic texts is not made by women due to social construction that places women's roles and functions only in the domestic area.6\n\nIf in today's millennial era, Islam gets more attention in religious studies. I think this is not only due to the development and global impact of the world's Muslim population (as mentioned by Richard C. Martin),7 or because of the emergence of religious awareness in the public domain in the modern era (as described by Jose Casanova),8 but in fact because the teachings of Islam adhered to by Muslims themselves are in fact very problematic; not yet in synergy with the needs of the times. Oftentimes, Muslims even produce views that are opposite to the normative views of Islam which highly respect human rights. Therefore, in this context, many Muslim reformers, who then called for the importance of reforming religious (Islamic) thoughts, say for example: Mohammaed Abed Aljabiri,9 Khaled M. Abou el-Fadl,10 Abdul Karim Soroush,11 Abdullah Saeed,12 and also Muhammad Shahrur.13\n\nEspecially the last one, Muhammad Shahrur is a Muslim thinker who was chosen as the focus of study in this paper. It is important to discuss Shahrur's thoughts as other contemporary Muslim thinkers, in order to reform Islamic understandings which in this century are less relevant and do not synergize with universal human rights trends. The situation of women in Muslim countries or where the majority of the population is Muslim (such as in Indonesia) who live their daily lives in a circle of discriminatory religious policies, became the focus of Muslim reformers including Shahrur, who in turn sparked many important projects for a number of Islamic harakah (Muslim movement). All harakahs agree that reform is important, especially as times continue to change, as well as the need to produce actual religious thoughts, but in the applicable domain there are sometimes differences of opinion between one another. It is reasonable because the methodologies or approaches used are not the same or vary.14 But at least, in general, there are two types of harakah Islamiyyah (Muslim movement) that emerge in this context: first, “leftists” who develop their thought based on liberal Western methodology; and “rightists” in the sense of guarding reform based on the thoughts of classical Muslim scholars.15\n\nMuhammad Shahrur, in this context as a thinker who provides many ideas about the reform of Islamic thought, especially in the field of commentary, tends to be leftist and liberal. His ideas of women in the study of commentary, for example, have sparked a lot of debates, especially when viewed from the perspective of classical fiqh (Islamic Jurisprudence). Based on the background above, this study focused on describing Muhammad Shahrur's limits theory, which defines a lower limit (al-hadd al-adna/minimum) and an upper limit (al-hadd al-a'la/maximum) and the interpretation of this limit theory on the relationship between teenagers, hijab, women aurat (vital intimate), and polygamy on women issues in the millennial era.\n\n\nMethods\n\nThis paper was deliberately written to discuss Muhammad Shahrur's commentary on women. This study used a literature review approach, which analyzed the sources in a descriptive-hermeneutic manner. Tafseer/books from millenial interpreters discussing women were considered eligible for the study. I used Pontianak State Institute for Islamic Studies library and the internet to conduct the search using the library information system with ‘women interpretation’ as keywords.\n\nI found several books of tafseer but few discuss women in the millenial era. These were: al-Kitâb wa al-Qur’ân: Qirâ’ah Mu’âshirah, al-Kitâb wa al-Qur’ân: Qirâ’ah Mu’âshirah (1990), Dirasat al-Islamiyat al-Mu'ashirah fi al-Dawlah wa al-Mujtama' (1996), al-Islâm wa al-Imân: Manzhûmah al-Qiyam (1996), and Nahwa Ushûl Jadîdah Li al-Fiqh al-Islâmy: Fiqh al-Mar’ah (2000). I then searched books eligible for millenial interpretation about women’s issues. Two Shahrur books met all the criteria above. The main sources of this study are two books written by Muhammad Shahrur, namely: Al-Kitāb wa Al-Qur’ān, Qirā’ah Mu’āshirah, and Nahw Ushūl al-Jadīdah Li al-Fiqh al-Islāmy; Fiqh al-Mar’ah. I then chose chapters that discuss women in both books. The search strategy involved looking at the table of contents in both books for women’s issues. Furthermore, a list of the most suitable items according to the aims of this study was obtained. The list of materials/items is as follows;\n\nThe data were collected through the following steps; 1) bookmarking and recording narrative texts that serve as research data, 2) Making an inventory of words or texts related to women's issues. Shahrur's book entitled Al-Kitāb wa Al-Qur’ān, Qirā’ah Mu’āshirah consists of 4 chapters with 729 pages. Chapter 1 consists of 5 sections, chapter 2 consists of 4 sections, chapter 3 consists of 3 sections, and chapter 4 consists of 2 sections with an addition of a closing chapter consisting of 5 sections. The book contains women's issues related to limits (page 453), polygamy (page 597), clothing (page 604), male and female family relationships (page 604). Meanwhile, Shahrur's book entitled Nahw Ushūl al-Jadīdah Li al-Fiqh al-Islāmy; Fiqh al-Mar’ah consists of 6 sections with 381 pages; in these sections there are texts related to women's issues, namely; polygamy (page 301), marriage (page 307), clothing (page 331-343), jewelry (362-365), and dress code for females (page 374) (see Tables 1 and 2).\n\nHermeneutics is a process of elaborating in terms of content and meaning what is hidden behind the text.16 This study aimed to interpret women’s issues in two of Shahrur's books, using hermeneutics data analysis. Paler states that hermeneutics is a process of elaborating in terms of content and meaning what is hidden behind the text.17 Michelle Byrne also states that the hermeneutics method is used to understand and interpret the text meaning,18 Based on Gadamer's elaborate understanding, interpretation and application, the analyses are inherent in the interpretation.19 After examining passages on polygamy, marriage, clothing, jewelry and dress code for females in Shahrur's books, I interpreted and analyzed these texts, and finally compared them to the verses of the Holy Qur'an and the application of Shahrur's theory of limits.\n\n\nResults and discussion\n\nMuhammad Shahrur is known as a millennial thinker, whom A. Lutfi Syaukanie classified as leftist and liberal.20 He was born in the Salihiyyah intersection, Damascus, Syria, on 11 April 1938. At the age of 19, Shahrur obtained a Tsanawiyah diploma from the Abdurrahman al-Kawakibi madrasa in 1957.21 However, these schools are not religious schools. In other words, Shahrur did not receive sufficient religious education in his childhood and youth; at least in a formal sense. Syahrûr earned his Master's degree and three years later, in 1972, he successfully completed his Doctoral program. In the same year he was officially appointed as a lecturer in the Faculty of Civil Engineering at the University of Damascus and teaches courses in Land Mechanics and Geology (Mikanika at-Turbât wa al-Mansya’ât al-Ardhiyyah).22\n\nDuring his career as a lecturer, Shahrur wrote several books which were not really his specialty. He made his best effort to combine his knowledge with Islamic teachings, especially with the Qur’an. After finding ideas, he began to combine them with verses from the Qur’an. His thoughts related to Islamic law, where he argues that there is an upper limit and a lower limit in Islamic law, finally became known as the theory of limits. While teaching, Shahrur actively wrote books. He tried to interpret the verses of the Qur’an, and in addition, he also proposed the theory of limits in law which basically states that law has an upper and lower limit. In his Al-Kitab, Shahrur derives the word Al-Quran from Al-Kitab, where the origin of the word is ka-ta-ba. It means an effort made by someone who collects various themes and composes sentences and links one event to another to form a complete piece of writing.23 Therefore, the revelation received by Prophet Muhammad (p.b.u.h) is called a kitab [book] because it contains various themes. In this book, Shahrur was heavily involved in linguistic interpretation. He divided the book into two sections: a) the first section is the kitab related to human behavior such as prayer, alms, fasting, pilgrimage. Human capacity to carry out this first section of the book is limited, and therefore humans have the ability to choose or be detached from it; b) the second section is the kitab in the form of ma'rifah which consists of natural law and human life such as death, the end of the world, etc.\n\nIn this context, it is necessary to understand that Shahrur did not join any Islamic institution, nor did he take any formal training or obtain a certificate in Islamic sciences. The works he has written, among others, are Al-Kitāb wa Al-Qur'ān–Qirā'ah Mu'āshirah (1990), Al-Daulah wa al-Mujtama'(1994), Al-Islām wa al-Īmān–Manzhūmah al- Qiyam-(1996), Nahw Ushl al-Jadīdah Li al-Fiqh al-Islāmy (2000), and Tajfīf Manābi' al-Irhāb (2008). Of these works, the ones that have received the most attention are Al-Kitāb wa Al-Qur'ān –Qirā'ah Mu'āshirah (Contemporary Study of the Book and Al-Quran) and Nahw Ushl al-Jadīdah Li al-Fiqh al-Islāmy (Contemporary Islamic Fiqh Methodology). His monumental work, Al Kitab wa Al Qur'an, Qira'ah Mu'ashirah (Contemporary Study of the Book and Al-Quran) is his greatest work.24\n\nHe often involved himself in issues of shari'a liberalization and deconstruction of the the Qur'anic commentary. Several Islamic laws and the rules of the science of commentary and ushul fiqh were deconstructed with technical knowledge and relying on their Arabic origins. His environmental background, both education and socialization, also influenced his way of thinking.\n\nThe term millennial commentary, of course, is not a term coined by Shahrur, but a term that the author attaches to Shahrur's thoughts on commentary. In my humble opinion, this term is appropriate after reading Shahrur's views on commentary, which are relevant to be applied with the millennial spirit of this era, an era where all forms of culture and lifestyle meet and influence each other. In this context, Shahrur himself agreed that legal products must be able to synergize with the socio-cultural context, including the times.\n\nShahrur came to the realization that the outcome of Islamic law is greatly influenced by the socio-cultural setting as a result of his language approach to the study of commentary. In order to bring the texts of the Qur'an—the foundation of fiqh—into line with the realities of society everywhere and at any time, Shahrur thought it necessary to reinterpret them. Shahrur mistrusted the Sunnah al-Nabawiyyah as a source of law due to his emphasis on the Qur'anic scriptures.\n\nHe believes that the Qur'an is sufficient since it contains guidelines for addressing life's realities in its verses. Shahrur created the Theory of Limits to implement his proposal (Nazariyyat al-Hudud). Shahrur attempts to integrate the muhkamat al-Qur'an texts into the reality of life with its constraints through this Theory of Limits. He asserts that the laws of the Qur'an are adaptable and can be employed in any situation, regardless of place or time. As long as it stays within certain bounds and does not go beyond them, the law permits it to be done regardless of the state of the community\n\nThe theory of limits consists of a lower limit (al-hadd al-adna/minimum) and an upper limit (al-hadd al-a'la/maximum). There are six forms of application of this theory of limits in the study of legal verses, namely as quoted by M. Amin Abdullah from Shahrur's thoughts (see Table 3):25\n\nThe six forms of the theory of limits proposed by Shahrur above have an impact on the istinbath of Islamic law. We take the example of the first theory of limits which only has a lower limit, namely regarding women's clothing and intimate parts. When interpreting QS. [24]: 31, \"Or children who are still unaware of women's intimate parts”.26 According to Shahrur, intimate parts are what make a person ashamed when seen, and intimate parts are not related to halal and haram, both from near and far.\n\nHe gave an example, “If someone is bald and doesn't like people seeing his bald head, then he will wear wigs, because he considers his bald head to be an intimate part.” Then he quoted the hadith of the Prophet, “Whoever covers the intimate parts of a believer, surely Allah will cover his intimate parts.” He commented, covering the intimate parts of the believer in the hadith, does not mean putting clothes on them so that they are not visible. Then he concluded that aurat (intimate parts) stems from shame, namely a person's dislike when something is seen, both from their body and behavior. Being shy according to him is relative, changing according to customs, times, and places.27\n\nTherefore, when there is a verse that tells to wear the hijab in the QS. [33]: 59, “O Prophet! Ask your wives, daughters, and believing women to draw their cloaks over their bodies. In this way it is more likely that they will be recognized ˹as virtuous˺ and not be harassed.”28 He interprets that this verse is in the form of teaching, not sharia, and was revealed in Medina which indicates that it must be understood temporally with the aim of security from two disturbances, namely natural or weather disturbances and social disturbances that adapt to local traditions so as not to invite ridicule.29\n\nSo Shahrur's conclusion for the hijab has a maximum and minimum limit. The maximum limit is to cover the entire body except the face and palms, while the minimum limit is that which only covers the juyūb which according to him includes the cleavage, body parts under the armpits, genitals, and buttocks. Apart from these, it does not include intimate parts and only adapts to community traditions.30\n\nNext, Shahrur also interpreted the verse, “Let them not show their adornments, except what normally appears” to mean there are two kinds of jewelry for women: object jewelry and place jewelry.31 Object jewelry is, for example, clothing and accessories, while place jewelry is the entire woman's body which is commonly seen as the abdomen, back, head, and legs. So, all parts of the body may be exposed based on the verse above. The hidden ones are the juyub (pubic area, buttocks, armpits, and breasts). In other words, a woman who only wears underwear out of the house is not considered to have violated Allah's provisions. Showing a stomach piercing is also permissible.\n\nMoreover, he stated that a woman's vital intimate parts (armpits, breasts, and genitals) may be revealed to the seven groups of men mentioned in the QS. [24]: 31, namely brothers, fathers, daughters of a sibling, sons of a sibling, parents of one’s wives and their children. His opinion states that a Muslim woman may be completely naked in front of these men. He said, “If parents see their daughter completely naked, then it is not said that it is haram, but only a disgrace.”32\n\nHe even said that the relationship between teenagers of the opposite sex without marriage, or living together is “halal”. Shahrur said that if it is in accordance with their will, without a contract, or without being accompanied by a sheikh or without permission, then it is lawful. He stated, “Read the Book of Allah, don't be afraid of it; all of you can do that without intermediaries and without teachers, and promiscuity is lawful, provided there is agreement between the two parties,” he said. He also stated that promiscuity between a man and a woman is a substitute for marriage, and without a written contract, is “halal, and in accordance with shar'i.”33\n\nThe second example of the theory of limits, which only has an upper limit, is regarding the verse of cutting off hands for thieves. Shahrur argued that the words qata'a could mean physical or non-physical cutting. By looking at the basis of the word qata'a, it turns out to have many meanings and not all meanings refer to physical cutting. In addition, in the Qur’an not all the words qata'a mean physical cutting. An example of qata'a which means physical cutting is found in QS Al-Maidah: 33,34 while the meaning of not physical cutting is in QS. Ali-Imran: 127,35 QS. Al-anfal: 7,36 and QS. Al-Baqarah: 27.37\n\nIt is at this stage that Shahrur then concludes that the words qata'a in the context of theft can be interpreted as physical or non-physical cutting. By looking at the maslahah (the aims and objectives in Islamic law) between physical and non-physical cutting, Shahrur considers that physical cutting in the verse is the maximum law (upper limit) that can be set, while non-physical cuts, for example, putting the perpetrator in prison. This means that in this verse the concept of hudud al-a'la (upper limit) applies and the human ijtihad is under the hudud al-a'la.\n\nFurther, the third example of the theory, which has both an upper and a lower limit, that is, the minimum and maximum limits have been set by the Qur’an, while ijtihad is in between the two minimum and maximum limits. For example: QS. An Nisa verse 11, concerning the Division of Inheritance. The maximum limit for men is twice that of women, while the minimum limit for women is 0.5 of men. Ijtihad moves between the two maximum and minimum limits by looking at the various aspects that exist.\n\nRegarding polygamy, Shahrur is very strict. With the Theory of Limits, there are two important limitations of terms, namely the limitation on quantity (al-Had al-Kamy), which is four wives, and the limitation on quality (al-Had al-Kalfy), namely the second, third, and fourth wives are widows who have children. Shahrur allows polygamy under two conditions, namely first, the second, third, and fourth wives are widows with children whose husbands left them. Second, the husband must have an uneasy feeling that he will not be able to deal justly with his children. If the two conditions above are not met, polygamy will fail. This means that the prospective wife must be a widow, not a virgin and must have children, as well as the prospective husband must be fair in all aspects, especially the social aspects of life/society. Shahrur applies these two conditions based on the structure of language norms in the Qur'an Surah an-Nisa verse 4. Shahrur takes these two conditions based on the “structure of language rules” in the word of Allah “And if you are afraid you shall not be able to deal justly with the orphans, then marry two, three or four women whom you like.” Shahrur also sees how Allah honors a widow by using the gentle words “ma tabalakum” (women you like) instead of “mashi'tum min an-nisa” which is respect for marriage.\n\nRegarding the law of adultery, which falls into in the fourth limit theory, the provisions of the lower and upper limits are at one point or there is no other alternative and there can be no more or less. This means that the provision of the maximum limit is also the minimum limit, so that ijtihad is not possible to take heavier and lighter laws. For example: QS. An-Nur: 2, regarding the punishment for adultery. In that verse the punishment for adultery is a maximum and a minimum limit at the same time, because in that verse there is an order not to do “ra'fah”, which means there is no waiver. Furthermore, regarding the fifth limit theory, a provision that has a lower and upper limit at the same time, but both cannot be exceeded; if exceeded it means violating God's rules, which applies to male and female relationships. If a man and a woman commit acts approaching adultery but have not committed adultery, then both of them have not fallen within the limits of Allah's hudud.\n\nFinally, the rule which has an upper and lower limit, where the upper limit is positive and cannot be exceeded, while the lower limit is negative and can be exceeded applies to material relationships among human beings, both men and women. The upper limit is positive in the form of usury, while the lower limit is negative in the form of zakat (alms). The upper limit that cannot be exceeded is usury, the lower limit that can be exceeded is zakat (zakat as a negative limit because it is the minimum limit for assets that must be paid). In this case, zakat can be exceeded by charity, while usury cannot be exceeded because it is an upper limit that cannot be exceeded.\n\nThis study is limitated as it has only discussed women based on Shahrur's theory of limits as tool of analysis, while the book Nahw Ushūl al-Jadīdah Li al-Fiqh al-Islāmy; Fiqh al-Mar’ah. This study limitation also raises opportunities for future researchers to conduct studies on other content such as inheritance (الإرث) and testament (وصية).\n\n\nConclusion\n\nThe term millennial commentary of Mohamammad Shahrur, in my humble opinion, is quite appropriate after reading Shahrur's views on commentary, which are relevant to be applied to the millennial spirit of this era, an era where all forms of culture and lifestyle meet and influence each other. In this context, Shahrur himself agreed that Islamic legal products must be able to synergize with the socio-cultural context, including the times. Shahrur finally came to the conclusion that the outcome of Islamic law is greatly dependent on the socio-cultural setting thanks to his study's language approach. In order to bring the texts of the Qur'an into alignment with the realities of society everywhere and at any time, Shahrur analyzes the need for reinterpreting the verses of the Qur'an that form the foundation of fiqh (Islamic Jurisprudence). Shahrur mistrusted the Sunnah al-Nabawiyyah as a source of law due to his emphasis on the Qur'anic scriptures. He believes that the Qur'an is sufficient since it contains guidelines for addressing life's realities in its verses. Shahrur created the Theory of Limits to implement his proposal (Nazariyyat al-Hudud).\n\nShahrur attempts to integrate the muhkamat al-Qur'an texts into the reality of life with its constraints through this Theory of Limits. He asserts that the laws of the Qur'an are adaptable and can be employed in any situation, regardless of place or time. The community's state falls within these bounds, and the law permits it to be done as long as it doesn't go beyond the predetermined.", "appendix": "Data availability\n\nHarvard dataverse: Data research of Saifuddin Herlambang, https://doi.org/10.7910/DVN/BRATPU, Harvard Dataverse, V4. 38\n\nThis project contains the following underlying data:\n\n‐ notes 1. pdf\n\n‐ notes 2. pdf\n\n‐ notes 3. pdf\n\nThis project contains the following extended data:\n\n‐ Komisi etik.pdf (Letter of research ethical commission from The Institute for Research and Community Service (Lembaga Penelitian dan Pengabdian Kepada Masyarakat/LP2M), Pontianak State Institute for Islamic Studies (in Indonesian))\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nAustgard K: Doing it the Gadamerian way–using philosophical hermeneutics as a methodological approach in nursing science. Scand. J. Caring Sci. 2012; 26(4): 829–834. Publisher Full Text\n\nLutfi Syaukani A: Tipologi dan Wacana Pemikiran Arab Kontemporer. Jurnal Paramadina. 1998; (2).\n\nAbdul Karim Soroush Menggugat Otoritas dan Tradisi Agama. Bandung:Mizan;2002.\n\nSaeed A: Interpreting the Qur’an: Towards a Contemporary Approach. Oxon:Routledge;2005.\n\nSaeed A: The Qur’an: An Introduction. London and New York:Routledge;2008.\n\nMubarok AZ: Pendekatan Strukturalisme Linguistik dalam Tafsir al-Qur’an Kontemporer “ala” M. Shahrur. Yogyakarta:Elsaq Press;2007.\n\nByrne M: Hermeneutics as a methodology for textual analysis. AORN J. 2001 May; 73(5): 968–970. PubMed Abstract \| Publisher Full Text\n\nArmayant H: Mengenal Shahrur dan Teori Batasnya. Kajian Timur Tengah. Desember 2010.Reference Source\n\nHerlambang S: Data research of Saifuddin Herlambang. Harvard Dataverse. 2022a; V4. Publisher Full Text\n\nHusein:Indonesian Women's Ulema Congress at the Kebon Jambu Al-Islamiy Babakan Islamic Boarding School, Ciwaringin Cirebon, Interview on Wednesday 26 April 2017. Jose Casanova. Public Religion in the Modern World. Chicago and London:The University of Chicago Press;1994.\n\nHerlambang S: Data research of Saifuddin Herlambang. Harvard Dataverse. 2022b; V4. Publisher Full Text\n\nCasanova J: Public Religion in the Modern World. Chicago and London:The University of Chicago Press;1994.\n\nMinistry of Religious Affaris of the Republic of Indonesia: Al-Qur’an dan Terjemahan. Madinah:Qadim Al-Haramain Al-Syarifain;1980.\n\nAbou El-Fadl KM: Atas Nama Tuhan; Dari Fiqh Otoriter ke Fiqh Otoritatif. Jakarta:Serambi Ilmu Semesta;2004.\n\nKhudori Soleh dkk:Muhammad Shahrur: Teori Batas. Pemikiran Islam Kontemporer. Yogyakarta:Jendela;2003.\n\nAmin Abdullah M: Neo Ushul Fiqih Menuju Ijtihad Kontekstual. Yogyakarta:Fakultas Syari’ah Press dan Forum Studi Hukum Islam;2004.\n\nMuḥammad ʻĀbid al-Jabiri: Bunyah al-Aql al-‘Arabi: Dirasah Tahliliyah Naqdiyah li Nudzum al-Ma’rifah fi al-Tsaqafah al-‘Arabiyah. Bayrūt:al-Markaz al-Tsaqafi al-Arabi;1991.\n\nMuḥammad ʻĀbid al-Jabiri: Takwīn al-ʻaql al-ʻArabī. Bayrūt:Markaz Dirāsāt al-Waḥdah al-‘Arabīyah;2014; vol. 1. .\n\nShahrur M: Al-Kitab wa al-Qur’an: Qira’ah Muasirah. Damaskus:Al-Ahaliy li at-Tabaah wa an-Nasyr wa at-Tawzi’;1990.\n\nShahrur M: Nahwa Usul Jadidah lil Fiqh Islami: Fiqh al-Mar’ah. Damaskus:Al-Ahali li-t-Tibaah;2000.\n\nClark P: The Shahrorur’s Phenomenon; A Liberal Islamic Voice From Syiria. Islam and Christian-Muslim Relation. 1996; VII(3).\n\nPaler ER: Hermeneutics: Theory of Interpretation in the Thoughts of Schleiermacher, Dilthey, Heidegger, and Gadamer. Translated by. Stephanus Aswar Herminarko. YogyakartaIRCiSoD;First Edition2022 July; p.92.\n\nMartin RC, editor.Islam dan Studi Agama: Sebuah Pengantar. Pendekatan Terhadap Islam dalam Studi Agama. Pustaka Pelajar;Yogyakarta:2001. Zakiyuddin Baidhawy (tran.).\n\nSyahrur M: Principles and Basis of Contemporary Al-Qur'an Hermeneutics. Sahiron Syamsuddin (translation)Yogyakarta: elSaq. Cet. Ke-I.2004; p. 65.\n\nUta: Masih Ada Diskriminasi Gender. Media Indonesia. 2018. Selasa, Okt.Reference Source\n\nSaputra Y: Kongres Ulama Perempuan: Meluruskan paham diskriminatif terhadap perempuan. Rappler. Com. 27 Apr 2017; Reference Source\n\n\nFootnotes\n\n1 Uta, ‘Masih ada Diskriminasi Gender [Gender Discrimination Still Exists].’, Media Indonesia (Tuesday, Oct 2018), http://mediaindonesia.com/read/detail/189401-masih-ada-diskriminasi-gender.\n\n2 Yuli Saputra, ‘Women's Ulema Congress: Straightening the Discrimination Against Women’, Rappler.Com (27 Apr 2017), https://www.rappler.com/indonesia/berita/168095-meluruskan-paham-diskriminatif-perempuan.\n\n3 Husein. Indonesian Women's Ulema Congress at the Kebon Jambu Al-Islamiy Babakan Islamic Boarding School, Ciwaringin Cirebon, Interview on Wednesday 26 April 2017.\n\n4 Ministry of Religious Affairs of the Republic of Indonesia, Al-Qur’an dan Terjemahan (Madinah: Qadim Al-Haramain Al-Syarifain, 1980).\n\n5 Husein. Indonesian Women's Ulema Congress at the Kebon Jambu Al-Islamiy Babakan Islamic Boarding School, Ciwaringin Cirebon, Interview on Wednesday 26 April 2017.\n\n6 Women's Ulema Congress: Straightening the Discrimination Against Women’.\n\n7 Richard C. Martin (ed.) Zakiyuddin Baidhawy (tran.), ‘Islam and Religious Studies: An Introduction’, in Approaches to Islam in Religious Studies (Yogyakarta: Pustaka Pelajar, 2001), p. 1.\n\n8 Jose Casanova, Public Religion in the Modern World (Chicago and London: The University of Chicago Press, 1994).\n\n9 Muḥammad ʻ Ā bid al-Jabiri, Takwīn al-ʻaql al-ʻArabī, vol. 1 (Bayrūt: Markaz Dirāsāt al-Waḥdah al-‘Arabīyah, 2014); Muḥammad ʻ Ā bid al-Jabiri, Bunyah al-Aql al-‘Arabi: Dirasah Tahliliyah Naqdiyah li Nudzum al-Ma’rifah fi al-Tsaqafah al-‘Arabiyah (Bayrūt: al-Markaz al-Tsaqafi al-Arabi, 1991).\n\n10 Khaled M. Abou El-Fadl, Atas Nama Tuhan; Dari Fiqh Otoriter ke Fiqh Otoritatif (Jakarta: Serambi Ilmu Semesta, 2004).\n\n11 Abdul Karim Soroush, Menggugat Otoritas dan Tradisi Agama [Challenging Religious Authority and Traditions] (Bandung: Mizan, 2002).\n\n12 Abdullah Saeed, Interpreting the Qur’an: Towards a Contemporary Approach (Oxon: Routledge, 2005); Abdullah Saeed, The Qur’an: An Introduction (London and New York: Routledge, 2008).\n\n13 Muhammad Shahrur, Nahwa Usul Jadidah lil Fiqh Islamy: Fiqh al-Mar’ah (Damascus: Al-Ahali li-t-Tibaah, 2000); Muhammad Shahrur, Al-Kitab wa al-Qur’an: Qira’ah Muasirah (Damascus: Al-Ahaliy li at-Tabaah wa an-Nasyr wa at-Tawzi’, 1990).\n\n14 Richard C. Martin (ed.) Zakiyuddin Baidhawy (tran.), ‘Islam dan Studi Agama: Sebuah Pengantar’.\n\n15 A Lutfi Syaukani, ‘Tipologi dan Wacana Pemikiran Arab Kontemporer’ [Typology and Discourse of Contemporary Arabic Thought], Jurnal Paramadina, no. 2 (1998).\n\n16 E. Paler, Richard. Hermeneutics: Theory of Interpretation in the Thoughts of Schleiermacher, Dilthey, Heidegger, and Gadamer. Translated by. Stephanus Aswar Herminarko. IRCiSoD, Yogyakarta: First Edition, July, 2022.p.92.\n\n17 E. Paler, Richard. Hermeneutics: Theory of Interpretation in the Thoughts of Schleiermacher, Dilthey, Heidegger, and Gadamer. Translated by. Stephanus Aswar Herminarko. IRCiSoD, Yogyakarta: First Edition, July, 2022.p.92.\n\n18 Byrne M. Hermeneutics as a methodology for textual analysis. AORN J. 2001 May;73(5):968-70. doi: 10.1016/s0001-2092 (06)61749-3. PMID: 11378953.\n\n19 Austgard, K. (2012). Doing it the Gadamerian way–using philosophical hermeneutics as a methodological approach in nursing science. Scandinavian Journal of Caring Sciences, 26(4), 829-834.\n\n20 Ibid.\n\n21 For a more complete explanation of Muhammad Shahrûr's biography, please refer directly to Shahrur's official website, namely: http://www.shahrour.org.\n\n22 Peter Clark, ‘The Shahrorur’s Phenomenon; A Liberal Islamic Voice From Syiria’, Islam and Christian-Muslim Relation, vol. VII, no. 3 (1996), p. 339.\n\n23 Syahrur, M. (2004). Principles and Basis of Contemporary Al-Qur'an Hermeneutics. Sahiron Syamsuddin (translation)Yogyakarta: elSaq. Cet. Ke-I, p. 65.\n\n24 Khudori Soleh dkk, ‘Mohammad Shahrur: Teori Batas’ [the Theory of Limits], in Pemikiran Islam Kontemporer (Yogyakarta: Jendela, 2003), p. 296.\n\n25 M. Amin Abdullah, Neo Ushul Fiqih Menuju Ijtihad Kontekstual (Yogyakarta: Fakultas Syari’ah Press dan Forum Studi Hukum Islam [Faculty of Shari'a Press and Islamic Law Study Forum], 2004), pp. 156–8.\n\n26 Ministry of Religious Affairs of the Republic of Indonesia, Al-Qur’an dan Terjemahan.\n\n27 Muhammad Shahrur, Nahwa Usul Jadidah lil Fiqh Islami: Fiqh al-Mar’ah, p. 370.\n\n28 Ministry of Religious Affairs of the Republic of Indonesia, Al-Qur’an dan Terjemahan.\n\n29 Muhammad Shahrur, Nahwa Usul Jadidah lil Fiqh Islami: Fiqh al-Mar’ah, pp. 372–3.\n\n30 Ibid., pp. 376–8; Muhammad Shahrur, Al-Kitab wa al-Qur’an: Qira’ah Muasirah, p. 607.\n\n31 Muhammad Shahrur, Al-Kitab wa al-Qur’an: Qira’ah Muasirah, p. 606.\n\n32 Ibid., p. 607.\n\n33 Harda Armayanti, ‘Mengenal Shahrur dan Teori Batasnya’, Kajian Timur Tengah [Mengenal Shahrur dan Teori Batasnya’, Kajian Timur Tengah] (Desember 2010), https://kajiantimurtengah.wordpress.com/2010/12/04/mengenal-Shahrur-dan-teori-batasnya/., yang ia kutip dari http://www.Hidayatullah.com publikasi Selasa, 29 Januari 2008.\n\n34 Verily, the recompense for those who fight against Allah and His Messenger and cause mischief in the earth is only that they are killed or crucified, or their hands and feet are cut off in exchange for reciprocity, or are banished from the land (where they live). That is (as) an insult to them in this world, and in the Hereafter they will have a great torment. Kementerian Agama Republik Indonesia [Ministry of Religion of the Republic of Indonesia], Al-Qur'an and its Translation, Al-Qur’an dan Terjemahan.\n\n35 (Allah helps you in the battle of Badr and gives reinforcements) to destroy a group of disbelievers, or humble the rest, causing them to withdraw in disapointment. Ibid.\n\n36 And (remember), when Allah promised you that one of the two groups (which you faced) was for you, while you wanted that which did not have the strength of a weapon was for you, and Allah wanted to justify the truth with His verses and destroy Unbelievers. Ibid.\n\n37 Who break the covenant of Allah after contracting it and sever that which Allah has ordered to be joined and cause corruption on earth. It is those who are the losers. Ibid.\n\n38 Herlambang, Saifuddin, 2022, “Data research of Saifuddin Herlambang”, https://doi.org/10.7910/DVN/BRATPU, Harvard Dataverse, V4" }	[ { "id": "177220", "date": "11 Jul 2023", "name": "Nur Zainatul Nadra Zainol", "expertise": [ "Reviewer Expertise Islamic Studies", "Quranic Interpretation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is well-constructed and carefully written to understand Muhammad Shahrur's interpretation on women issues. However, it requires some amendments for the paper to be accepted. The abstract should include a statement about interpretation on ayah muhkamat must along with fiqh mazahib.\nData interpretation on the 1st women issues; relationships between teenagers of the opposite sex without marriage or living together is \"halal\" if it follows their will, without a contract, being accompanied by syecih or permission - this is controversial and must do comparison with other opinions.\n\nThe references only have 2 in recent 5 years, requiring more to fit into the state-of-the-art literature. This paper is considered to be indexed after amendments 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? 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": [ { "c_id": "9925", "date": "08 Aug 2023", "name": "Saifuddin Herlambang", "role": "Author Response", "response": "Dear reviewer, thank you for your suggestion. This additional text written on the text on appropriate section. This article presents a study of interpretation in tafsir. Interpreters have been grouped into two categories: modern/progressive interpreters and conventional interpreters. Syahrur and Amena Wadud are prominent examples of progressive modern interpreters. It is important to clarify that this study remains independent of any specific madhhab, focusing solely on tafsir analysis All interpreters and scholars except Syahrur have agreed that musakanah (samen leven) are “haram”. Muhammad Kholid holds the view that Syahrur's methodology and epistemology are full of inconsistency and problems. This interpretation departs from the mainstream consensus of the majority of Muslim scholars. (abstract) In response to Abdul Aziz's dissertation on Syahrur's stance regarding the permissibility of sex outside of marriage, Deputy Chairman of the Indonesian Ulema Council (MUI), Yunahar Ilyas, asserted that such a view contradicts the teachings of the Qur'an. Syahrur's perspective suggests that the roles performed by slaves in ancient times served as a substitute for certain functions, including sexual relations, household assistance, and work relations. He draws support for the function of sexual relations from Surah Al-Mukminun verses 5 and 6, the function of household assistance from Surah An-Nuur verse 58, and the function of work relations from Surah An-Nahl verse 71. Hamka and Yusuf Qardhawi hold the belief that a woman's private parts encompass her entire body, with the exception of the face and palms. In contrast, Syahrur presents a distinction, dividing it into two categories: the lower limit comprises the concealed genitalia, causing embarrassment if exposed, while the upper limit includes the entirety of a woman's body, excluding the face and palms. On the subject of hijab, Quraish Shihab thinks that it is not obligatory but rather a recommended practice. Additional for State of the art: Rosyada's research focused on the subject of polygamy and justice according to Syahrur (2019). Meanwhile, Hidayat conducted a comparative analysis, examining Wahbah Az-Zuhaili's perspective alongside Syahrur's views on polygamy (2020). In addition, Hadi explored the concept of milkul yamin from the perspective of ushul fiqh, focusing on Syahrur's insights (2019). Building on this theme, Husna further investigated the boundaries of women's genitals, drawing from Syahrur's book (2021). Auliya and Gazali contributed to the discussion by providing a comprehensive review of the concept of female genitalia based on Syahrur's boundary theory (2020). Similarly, in 2021, Fathony and Hamid delve into the reconstruction of Syahrur's thoughts on women's private parts in the Indonesian Archipelago. Lastly, in 2022, Ramadana undertook a comparative study, analyzing the perspectives of Fatima Mernissi, Quraish Shihab, and Syahrur, offering insights into their perpectives." } ] } ]	1	https://f1000research.com/articles/12-39
https://f1000research.com/articles/12-193/v1	20 Feb 23	{ "type": "Case Report", "title": "Case Report: A case of a multivisceral echinococcosis with atypical localization", "authors": [ "Rania Kaddoussi", "Mohamed Jellazi", "Abdelkader Mizouni", "Ikram Chamtouri", "Mabrouk Abdelaaly", "Asma Migaou", "Hager Ben Brahim", "Nessrine Fahem", "Ahmed Ben Saad", "Sameh Joober", "Saoussen Cheikhmhamed", "Naceur Rouetbi", "Mohamed Jellazi", "Abdelkader Mizouni", "Ikram Chamtouri", "Mabrouk Abdelaaly", "Asma Migaou", "Hager Ben Brahim", "Nessrine Fahem", "Ahmed Ben Saad", "Sameh Joober", "Saoussen Cheikhmhamed", "Naceur Rouetbi" ], "abstract": "Hydatidosis is a pathology that is still common. The hydatid cyst commonly involves the liver and lung. Cases of multi visceral echinococcosis with atypical localization are rare. We report the case of a 53-year-old Tunisian farmer with a multiple organ hydatidosis that included 13 hydatid cysts: the lungs, the liver, the left heart ventricle, the left kidney, the abdomen cavity, muscles (psoas, adductors), and subcutaneous gluteal area. The majority of these cysts was already treated surgically, and some were due to be removed.", "keywords": [ "Hydtidosis", "multi visceral", "muscles" ], "content": "Background\n\nHydatidosis is a human disease caused by the larval form of Echinococcus spp., which live in the gut of dogs, wild canines and other carnivorous animals. Humans become the accidental intermediate hosts by ingesting Taenia spp. eggs. Echinococcus spp. are endemic in many countries where sheep, dogs and man live in close contact.\n\nAll organs in the human body may be affected by hydatid disease. The hydatid cyst from Echinococcus granulosus commonly involves the liver and lung but may also be found in other unusual organs, including the brain, heart and bones. Hydatid cysts rupture into left-sided cardiac chambers may cause systemic emboli, and if ruptured into right-sided cardiac chambers may cause pulmonary emboli.\n\nCases of multi visceral echinococcosis with atypical localization are rare. We report here the case of a male with 13 hydatid cysts including the lung, the heart, the muscles, the liver, the kidney and abdomen cavity.\n\n\nCase report\n\nThis is the case of a 53-year-old maghribian male farmer. This patient, with no personal or family history, was referred to the pulmonology department, for the management of a pulmonary Aspergilloma on a sequelary lung cavity following lung surgery.\n\nAt the time of the encounter the patient had no subjective complaints, expect for right lower limb paresthesia. The physical exam showed no abnormalities.\n\nThe patient was followed up in the abdominal surgery department for a multiple organ hydatidosis that included 13 hydatid cysts: the lungs, the liver (Figure 1), the left heart ventricle, the left kidney (Figure 2), the abdomen cavity, muscles (psoas, adductors), and subcutaneous gluteal area. The majority of these cysts was already treated surgically and some are still pending to be removed (Table 1). The patient has received oral Albendazole 400 mg twice-daily for 2 years.\n\nDuring a regular post-surgical follow up, a scannographic image of a fluid-density endo-bronchial material in the right superior lobe (lung cavity sequelary to the previous cystectomy) of the lung separated from the cavity wall by an airspace (“air crescent” sign) was found, this image is typical of pulmonary aspergilloma (Figure 3). Even though the Aspergillus serology showed doubtful results, the clinical context coupled to the CT scan findings were highly suggestive of a pulmonary aspergilloma. Blood work up showed high levels of IgE. A surgical resection of the cavity is programmed but not yet performed.\n\n\nDiscussion\n\nHydatid cyst remains an important issue in Tunisian health that affects both humans and animals, especially in rural areas.\n\nThe annual incidence of hydatidosis is 11.3 per 100000 inhabitant.1 Usually, hydatidosis presents as a single cyst usually of the liver or of the lungs, but in certain circumstances multiple organs may be affected. In our case we are reporting multiple atypical locations including heart, kidney, muscles and subcutaneous tissue. The conjunction of cysts in these locations simultaneously has not been described in the literature. We will not focus on the liver and the lung involvement given that they are a classic location of this parasitosis, and they are well commonly cited in the literature, instead we will discuss the other locations separately.\n\nHeart involvement is uncommon and accounts for less than 0.5% of the cases, it is usually part of a disseminated infection.2 This localization is potentially fatal without surgical treatment but fortunately with the improvement of surgical techniques, its morbidity has declined drastically. Our patient underwent open heart surgery to remove a left ventricular wall cyst without local recurrence and a post-surgical echocardiography without abnormalities.\n\nThe invasion of the myocardium usually occurs hematogeniously through the coronary arteries and since the majority of the population have a left dominant circulation, the left ventricle is the most commonly involved part of the heart (60%),3 other explanation is the dissemination from the lungs either following a pulmonary vein rupture and migration of the cysts4 or by a direct contact with hydatid cysts originating from the lung.5\n\nRenal involvement is also rare (2–3%) and it is usually associated to a disseminated disease, they are most commonly asymptomatic, like the case of our patient. The diagnosis was made by an abdominal CT which has a sensitivity of 98% to diagnose hydatid disease.6\n\nPsoas cysts is also uncommon, our patient presented with two psoas cysts, a finding never been described before in literature.\n\nThe patient has also presented with a 30-mm gluteal subcutaneous cyst, this involvement was described in rare cases in literature and usually the patient will have a painless palpable mass history of at least 3 months, and it is usually larger than 3 cm, which is the case in our patient.7 Subcutaneous cysts tend to involve trunk and limb roots, possibly due to the rich vascularization and relatively less muscle activity in these areas.8\n\nAnother intriguing finding in this case report is the discovery of an aspergilloma, on a lung cavity. Pulmonary aspergilloma occurs as a colonizer of pre-existing pulmonary cavity of any etiology such as sequelae tuberculosis, cavitary neoplasia or operated hydatid cyst and it is a saprophytic infection.9 Aspergilloma has rarely been described in operated hydatid cyst cavities in immunocompetent patients.10 For this patient, the aspergilloma was discovered two years after the lung surgery. A very similar case of a 56-year-old patient, who presented with an aspergilloma of the upper right lobe following cystectomy, have been described by M. El Hammoumi et al.10\n\nDespite the existence of multiple cysts, our patient is doing well with good tolerance and he is asymptomatic.\n\n\nConclusion\n\nMultiple hydatidosis is a rare condition which can endanger the vital and functional prognosis. Imaging is essential for the diagnosis and finds its place for the assessment of extension and detection of asymptomatic localization to ensure early treatment. Prevention remains the best treatment for hydatid cyst.\n\n\nAuthor contributions\n\nNF, AM and AM actively involved in data collection and processing. RK and MJ were involved in manuscript preparation. HB, AB, SJ, SCH, NR, and FM were involved in manuscript reviewing. All authors have read and approved the manuscript.\n\n\nConsent\n\nWritten informed consent was received 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\nAchour N, Dammak J, Zouari B, et al.: Epidemiology of hydatid cyst in Tunisia (apropos of 4124 cases of surgically treated patients 1977-1982). Tunis. Med. 1988; 66(1): 21–25. PubMed Abstract\n\nTekbas EO, Tekbas G, Atilgan ZA, et al.: Left ventricle hydatid cyst mimicking acute coronary syndrome. J. Infect. Dev. Ctries. 2012; 6(7): 579–583. PubMed Abstract\n\nShankarappa RK, Moorthy N, Bhat P, et al.: Left ventricular hydatid cyst: an uncommon cause of chest pain in young adults. Cardiol. Young. 2013; 23(3): 460–462. PubMed Abstract \| Publisher Full Text\n\nCacoub P, Chapoutot L, Du-Boutin LT, et al.: Hydatid cyst of the interventricular septum. Contribution of magnetic resonance imaging. Arch. Mal. Coeur Vaiss. 1991; 84(12): 1857–1860. PubMed Abstract\n\nAlper H, Yünten N, ScSener RN: Intramural hydatid cysts of pulmonary arteries: CT and MR findings. Eur. Radiol. 1995; 5(5): 666–668. Publisher Full Text\n\nMongha R, Narayan S, Kundu AK: Primary hydatid cyst of kidney and ureter with gross hydatiduria: A case report and evaluation of radiological features. Indian J. Urol. 2008; 24(1): 116–117. PubMed Abstract \| Publisher Full Text\n\nRamos Pascua L, Santos Sanchez JA, Samper Wamba JD, et al.: Atypical image findings in a primary subcutaneous hydatid cyst in the gluteal area. Radiography (London, England: 1995). 2017; 23(3): e65–e67. PubMed Abstract \| Publisher Full Text\n\nÖzdemir M, Kavak RP, Kavak N, et al.: Primary gluteal subcutaneous hydatid cyst. IDCases. 2020; 19: e00719. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKabiri H, Lahlou K, Achir A, et al.: Pulmonary aspergilloma: results of surgical treatment. Report of a series of 206 cases. Chirurgie. 1999; 124(6): 655–660. PubMed Abstract \| Publisher Full Text\n\nEl Hammoumi M, Traibi A, El Oueriachi F, et al.: Surgical treatment of aspergilloma grafted in hydatid cyst cavity. Rev. Port. Pneumol. 2013; 19(6): 281–283. PubMed Abstract \| Publisher Full Text" }	[ { "id": "164950", "date": "14 Mar 2023", "name": "Faisal Ahmed", "expertise": [ "Reviewer Expertise the discussion and case report sections need more revision." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral:\nI strongly encourage the authors to have a manuscript reviewed by a fluent English speaker and writer to improve its language contents before resubmission.\n\nAbstract:\nPlease add a piece of important information regarding postoperative therapy and the outcome.\n\nKeywords:\nPlease add a case report in your keywords.\n\nBackground:\nIt is inappropriate to have a background without a single reference. Please note that all statements must be supported by references.\n\nCase report:\nThis section should be structured according to the subsections included in the CARE Checklist of information to include when writing a case report. All the following subheadings should appear in this section, unless not applicable: Patient Information, Clinical Findings, Timeline of current episode, Diagnostic assessment, Diagnosis, Therapeutic interventions, and Follow-up and outcome of interventions.\n\nPlease start with the primary concerns and symptoms of the patient. Then, medical, family, and psycho-social history including relevant genetic information, and finally, Relevant past interventions with outcomes.\n\nSignificant History of contamination such as animal contact, water, etc., should be mentioned.\n\nDiagnostic testing such as CT scans, laboratory findings, etc., should be mentioned.\n\nPlease add all details regarding surgical intervention.\n\nThe follow-up period for your patient should be mentioned with details such as patient status, radiologic image result, recurrence, and recommended medications.\n\nDiscussion:\n\nFor individual cases, it is advisable to describe how the case is rare/unusual and the educational/scientific merit of its publication, followed by an overview of the topic and a comparison of your case with similar cases described in the literature.\n\nThere are some sentences that need citations. Please note that all statements must be supported by references.\n\n\"The conjunction of cysts in these locations simultaneously has not been described in the literature.\" I suggest revising this sentence to \"rarely reported in the literature\" There are a few mentioned cases such as Cai et al. (20191), Sachar et al. (20142) and Dasbaksi et al. (20153).\n\nPlease discuss the factors below and compared them with your case:\nA: Potential risk factors and predisposing factors of cystic echinococcosis. B: Radiologic and laboratory tests. C: Therapeutic options. D: Recommended medication on follow-up and the duration. E: Recurrence, and mortality. F: The correlation between aspergilloma and echinococcosis infection.\n\nReferences:\n\nI see you include old historical papers in references (1,4,5,7, and 9). It is not wrong; however, you fail to include recent articles in your review. Recent similar papers must be reviewed and compared to your case.\n\nThere are some references not mentioned in your manuscript such as references 3 and 4 (all references must be numbered consecutively).\n\nFigures:\nFigures 1 and 2: You can combine multiple images in a single panel. Please ensure you label the panel appropriately (A, B, C, etc.) in the image legend, and use the panel indicator to explain or describe the content of the image panel.\n\nFigure 2:\n\nThe photo of the kidney cyst should be reduced to one photo.\n\nPlease add a photo of peritoneal and muscle cysts.\n\nFigure ligands:\nYour ligands are so tall. Please reduce the legends to clearly describe the abnormalities.\n\nTable 1.\n\"Bilobed\" please mention the exact size.\n\n\"Parieto colic gutter\" please use the usual medical term.\n\nThe treatment column did not provide any information and I suggest deleting it from the table and mentioning the details in your therapeutic intervention section.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? 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": "170271", "date": "20 Apr 2023", "name": "Mohamed Ali Chaouch", "expertise": [ "Reviewer Expertise I am a visceral and digestive surgeon in a pandemic country of hydatid cyst." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you very much for the opportunity to review this paper. The subject is relevant and rare. However, some points of the manuscript should be re-addressed.\n1. Background:\nAdd some reference for the different informations provided. The first reference is mentioned in the discussion section.\n\nSwitch \"human disease\" by \"an anthropozoonosis\" because hydatid cyst is not an only-human infection.\n\nAdd a sentence highlighting the interest of medical treatment in case of multiple hydatid cyst in addition to the surgical management.\n\nAdd the aim of reporting this case to the end of the background.\n\n2. Case presentation:\nPrecisely which protocol of medical treatment was used?\n\nMention if the patient presented any immune deficiency.\n\n3. Discussion:\nSome citations were historical. Avoid citing articles published more than 20 years ago.\n\nAdd the citation of the uncommon location for the psoas muscle.\n\nAdd the citation of the different radiological signs suggesting the hydatid cyst origin of the lesions like the daugher cyst sign that is present in the kidney cyst in your case.\n\nAdd some details concerning the management of these multiple cysts, like the importance of medical treatment and a radical surgery, avoiding conservative surgery, to reduce the reccurence rate.\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? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-193
https://f1000research.com/articles/13-241/v1	02 Apr 24	{ "type": "Research Article", "title": "Post kidney transplant hematologic abnormalities and association of post-transplant anemia with graft function", "authors": [ "Sindhura Lakshmi Koulmane Laxminarayana", "Shreya Jayaram", "Shilna Muttickal Swaminathan", "Ravindra Prabhu Attur", "Dharshan Rangaswamy", "Indu Ramachandra Rao", "Mohan V Bhojaraja", "Srinivas Vinayak Shenoy", "Shankar Prasad Nagaraju", "Sindhura Lakshmi Koulmane Laxminarayana", "Shreya Jayaram", "Shilna Muttickal Swaminathan", "Ravindra Prabhu Attur", "Dharshan Rangaswamy", "Indu Ramachandra Rao", "Mohan V Bhojaraja", "Srinivas Vinayak Shenoy" ], "abstract": "Background Haematological abnormalities following renal transplantation are frequently observed and have a significant effect on survival and graft outcomes. The pattern of haematological abnormalities varies globally. Few studies have been conducted in Asian countries. We aimed to evaluate the patterns of haematological abnormalities in post-transplant recipients in our center during the first year after post-renal transplant and the association of post-transplant anemia with graft function.\n\nMethods This single-center retrospective study was conducted on renal transplantation recipients between 2014 and 2019. The study included all patients who received kidney transplants from live/cadaveric donors and had follow-up data collected up to 12 months after the transplant. The outcome studied was the prevalence of haematological abnormalities and the association between post-transplant anemia (PTA) and graft function in post-transplant recipients.\n\nResults A total of 106 renal transplant recipients were included in the study. The prevalence of PTA was 98% in the first week, 75% at one month, 35% at three months, 32% at six months, and 27% at 12 months. The other cytopenia cases were leukopenia (43.4%), thrombocytopenia (33.2%), and pancytopenia (15.1%). Post-transplant erythrocytosis was observed in 17.9% of patients. 18 patients with severe PTA in the first week of transplant had significant allograft dysfunction (p=0.04). Patients with and without PTA had similar graft functions at six and 12 months (p=0.50).\n\nConclusions Haematological abnormalities are common in renal transplant recipients. PTA is highly prevalent during the first week and improves over time. Other haematological abnormalities observed were leukopenia, thrombocytopenia, pancytopenia, and post-transplant erythrocytosis. Leucopenia was primarily drug-induced, and thrombocytopenia and pancytopenia were frequently caused by infections in our cohort. Additionally, severe PTA was significantly associated with graft dysfunction in the first week post-transplant, whereas similar graft function was observed at 6 and 12 months post-transplant, irrespective of the presence or absence of PTA.", "keywords": [ "chronic kidney disease", "renal transplantation", "post-transplant anemia", "renal allograft rejection", "post-transplant infections" ], "content": "Introduction\n\nChronic kidney disease (CKD) is recognized as a significant cause of morbidity and mortality and globally around 843.6 million individuals are affected by this condition1 End-stage kidney disease (ESKD) is a growing global health concern and has a substantial impact on the quality of life2; renal transplantation represents the ultimate treatment modality for patients with stage 5 CKD or ESRD3; however, renal transplantation improves the quality of life and is susceptible to various post-transplant complications such as metabolic disturbances, life-threatening infections, malignancy, and haematological disturbances. Haematological abnormalities are frequently observed in renal transplant recipients and can lead to severe complications in transplant recipients if not recognized early. Common post-transplant blood disorders include post-transplant anemia (PTA), post-transplant cytopenia (PTC), including leukopenia, thrombocytopenia, pancytopenia, post-transplant lymphoproliferative disorder (PTLD), and post-transplant erythrocytosis (PTE).4,5 A better understanding of the prevalence and etiology of haematological abnormalities may help effectively address and mitigate these complications in our day-to-day practice.\n\nAnemia is a frequently observed complication in CKD patients, and its prevalence is higher in renal transplant patients and varies with time after transplantation.6 Earlier studies have shown that in post-renal transplantation, there is a biphasic pattern of anemia, and the incidence rate is higher, about 76% at the time of transplantation, 21% in 1st year, and 36% in the 4th year of transplantation.7 Several factors are linked to PTA, such as infection, iron deficiency, declining renal function, recurrent transplantation, and administration of immunosuppressive medications. Furthermore, long-term follow-up studies (nearly 4 years) have demonstrated that baseline anemia serves as an effective predictor of mortality and graft failure in kidney transplant recipients, and anemia can be considered as an important risk factor for graft rejection/dysfunction in these patients.6,8\n\nOther common haematological abnormalities, such as leukopenia, thrombocytopenia, and pancytopenia, change with the type of induction agent, maintenance immunosuppressive drug, and dose used, which varies across centers. Over the past few decades, the implementation of CMV prophylaxis has led to a reduction in both its prevalence and associated haematological abnormalities. The estimated incidence of leukopenia in kidney transplant patients ranges from 10–55%.9 There is also a high rate of thrombocytopenia following renal transplantation in the first year, with the majority of recipients experiencing the lowest platelet counts within the first three months after the transplant10 which causes an oxygen deficit and immune system dysfunction that have a broad impact on the body.11 Post-transplant erythrocytosis is usually observed in 10–15% of patients12 and is typically evident within the first year of transplant. These haematological abnormalities can indicate various underlying causes, leading to a therapeutic dilemma in determining the most appropriate course of treatment. Against this backdrop, the present study aimed to evaluate haematological abnormalities in post-renal transplant patients. Additionally, we studied the association between the first week post-transplant severe anemia and graft dysfunction, and compared graft function at both early (6 months) and late (12 months) post-transplant anemia.\n\n\nMethods\n\nThis retrospective single-center observational study included 106 renal transplant recipients who underwent kidney transplantation at Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.\n\nThe study included all patients who underwent kidney transplants from live/cadaveric donors between January 2014 and December 2019 (Figure 1).\n\nRenal recipients below the age of 18 years and those without available follow-up data for a minimum of one year were excluded (Figure 1).\n\nThis was a retrospective case-record-based study. Medical records were reviewed and clinical and laboratory parameters were tabulated. The research conducted in this study adhered to the principles outlined in the Declaration of Helsinki and was approved by the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee (IEC 542/2019) on 6th September 2019. A waiver of consent was granted as per our institutional ethics committee due to the retrospective nature of the study. Baseline demographic data and laboratory data, including complete blood counts (CBC) and serum creatinine levels, were collected from the pre-transplant period (<1 week). The follow-up details of CBC and serum creatinine were collected at the post-transplant first week, one month, three months, six months, and 12 months and tabulated, and the prevalence of PTA was studied. The time taken for normalization of the hemoglobin level was also documented.\n\nOther haematological abnormalities including leukopenia, thrombocytopenia, and pancytopenia were also collected, and the type of immunosuppression was noted. The donor details were also collected. The association between the first week post-transplant severe anemia and graft dysfunction was analyzed, and graft function was compared at both early (six months) and late (12 months) post-transplant anemia.\n\nAnemia: “Hemoglobin level less than 12 g/dL in women and less than 13 g/dL in men according to the World Health Organization (WHO) criteria”.13 Severe anemia was defined as blood transfusion requirement of <8 g/dL.\n\nLeukopenia: WBC count less than 4000/μL.14\n\nThrombocytopenia: platelet count less than 150,000/μL.14\n\nAcute and chronic rejections were confirmed by biopsy. Delayed graft function was characterized by the need for at least one dialysis treatment during the first week following transplantation. Slow graft function was characterized by a 30% creatinine reduction ratio on day two and 70% creatinine reduction ratio on day 7.15\n\nThe primary outcome studied was the prevalence of the most common haematological abnormalities in post-renal transplant patients.\n\nThe secondary outcomes studied were the association between the first week post-transplant severe anemia and graft dysfunction and the comparison of graft function between patients with and without PTA at six months and 12 months post-transplant.\n\nDiscrete variables are represented as frequencies and percentages. Continuous data are shown as mean±SD. An unpaired T-test or Wilcoxon signed-rank test was performed to compare parameters between different time points. Normality was assessed using the Kolmogorov-Smirnov test. A chi-squared test was performed to assess the association between the parameters. Statistical significance was set at P<0.05. The data were analyzed using SPSS version 29.\n\n\nResults\n\nThe demographics and clinical characteristics of the renal transplant recipients are shown in Table 1 and in the underlying data.16,17 The mean age of the patients was 36.9±10.8 years, and male preponderance was observed in 85.8% of patients. Regarding donor type, most patients obtained organs from live individuals (85.8%) and 14.2% from cadaveric donors. The mean age of the donors was 46.6±10.3 years, and most donors were female (77.2%). The pre-transplant Hb and creatinine levels were 9.4±1.7% and 9.2±4.5, respectively. Basiliximab (79.2%) was the predominant choice for induction therapy, followed by antithymoglobulin (ATG) (20.7%). The dose of basiliximab used was 20 mg intravenously on 0 and 4th-day post-operation. The ATG dose used varied from to 1-3 mg/kg at the nephrologist’s discretion. All patients received 500 mg methylprednisolone along with induction therapy. All patients were treated with triple immunosuppression (Tacrolimus, Mycophenolate, and steroids) as per KDIGO guidelines.\n\na Mean±SD; BMI, Body mass index.\n\nThe haematological abnormalities of patients post-transplantation are shown in Table 2.\n\nPTA is highly prevalent in our study population and has improved over time. As shown in Figure 2, the prevalence of anemia showed a trend of 98% during the first week, 75% at one month, 35% at three months, 32% at six months, and 27% at 12 months post-transplantation. In the first week after transplantation, 50 patients (47.1%) had severe PTA.\n\nThe pre-transplant Hb level was 9.4±1.7, and post-transplant there was a significant improvement in the Hb levels at one month (10.6±2.2), six months (11.8±2.9), and 12 months (12.5±3.1), which was significant when compared to pre-transplant levels (p<0.001) (Figure 3).\n\nA total of 46 patients (43%) had leukopenia after renal transplantation. The mean leukocyte count was 3.2±1.2-10/microL. The primary cause was drug-induced (90%) due to mycophenolate, which improved with dose adjustment. The second most common cause was CMV infection (7%), followed by patients treated with ATG (3%).\n\nThrombocytopenia occurred in 31.2% of the patients in the overall study group. The mean platelet count was 70 ±12 10/microL. The majority of cases were attributed to bacterial infections (84.5%), followed by fungal infections (9.2%), and CMV infections (6.3%).\n\nWe observed that 15.1% of patients had pancytopenia. The major cause was drug-induced mycophenolate mofetil (79.2%), followed by CMV (18.6%) and bacterial infections (3%).\n\nNineteen patients (17.9%) had erythrocytosis. The incidence was higher in males (72%), and the mean hematocrit count was 56±13%.\n\nIn the first week post-transplant, slow or delayed graft function was observed in 11 recipients (22.3%), 19 patients (39.5%) had acute rejection. Specifically, 15 cases were diagnosed as cell-mediated rejection, while four cases were identified as antibody-mediated rejection on biopsy. Severe post-transplant anemia in the first week was significantly associated with allograft dysfunction (SGF, DGF, and acute rejection) (p=0.04) (Table 3).\n\nSGF: Slow graft function; DGF, Delayed graft function.\n\n* Statistically significant.\n\nAt six and 12 months, mean serum creatinine levels for patients with PTA were 1.6±0.6 mg/dl with eGFR 68.0±19.3 mL/min/1.73 m2 and 1.7+0.5 mg/dl with mean eGFR 74.2±22 mL/min/1.73 m2. While for patients without PTA, the mean serum creatinine levels were 1.4±0.5 mg/dl with eGFR 64.3±22 mL/min/1.73 m2 and 1.3±0.4 mg/dl with mean eGFR 64.8±21 mL/min/1.73 m2 at six and 12 months respectively. Although the serum creatinine level was slightly higher in patients who underwent PTA, it was not statistically significant and was comparable between the groups (p=0.50), implying that PTA did not have any effect on graft function in our cohort at six and 12 months after renal transplant.\n\n\nDiscussion\n\nFollowing renal transplantation, in addition to common metabolic and infectious complications, patients also encounter haematological abnormalities.18 In our study population, the most prevalent blood-related complication was PTA. Renal transplant patients experience anemia at various periods after transplantation, and the cause of anemia differs with time. post-transplant anemia is usually classified as early anemia, which occurs at or less than six months post-transplantation, with a prevalence rate of 50%, and late anemia, which occurs six months post-transplantation, with a prevalence rate of 23–35%.19 Few studies have defined PTA occurring in the first week of transplant as immediate post-transplant anemia.20\n\nIn our study, the prevalence of anemia was 98% in the first week, 75% at one month, 35% at three months, 32% at six months, and 27% at 12 months after transplantation, and there was a noticeable downward trend in prevalence over the study period. Similarly, Poesen et al.21 observed a 98% prevalence during the immediate post-transplant period, and Talwar et al.20 found that 100% of recipients had PTA in the first week and 76.7% in the third month post-transplantation. Additionally in a retrospective study by Gafter-Gvili et al.22 the prevalence of PTA at six months was 51.3% and at two years it was 36%. The notable differences in anemia prevalence may be attributed to various diagnostic criteria, varied causes, and different clinical practices across different healthcare centers worldwide,23 such as iron deficiency as a result of iron store depletion during pre-transplantation, perioperative blood loss, and malnutrition.24 Late PTA is usually associated with decreased graft function and occurrence of renal insufficiency.25\n\nIn the present study, there was a significant improvement in the hemoglobin level at post-transplant one, six and 12 months as compared to the pre-transplant and it was significant (p<0.001), which was consistent with Radoui et al.26 who reported the pre-transplant Hb improvement from 10.2 g/dl at one month to 12.8 g/dl at sixth month and then to 13.2 g/dl at one year.\n\nThe broad causes of cytopenia may be drug toxicity/interactions, immune reactions, or viral infections. In the present study, the prevalence of post-transplant leukopenia (PTL) is 43.4%, which was consistent with the findings of Smith et al.27 were reported 47.5%. In our study population, mycophenolate was identified as the primary agent associated with leukopenia, and a lower incidence was observed with ATG. This contrasts with findings from other studies that have reported higher incidence rates among those who received ATG.20,21 This disparity may be attributed to the lower ATG dosage used in our population (1-3 mg/kg). In contrast, Max et al. reported a 34% incidence of CMV infection, whereas our population exhibited a lower rate of 6.3%.16 This may be due to our patients being on CMV prophylaxis for six months post-transplant.\n\nIn our study, the prevalence of post-transplant thrombocytopenia (PTT) is 31.2%, which is in line with Xie et al.28 and Heaf et al.29 where the prevalence was found to be 33.9% and 30%, respectively within the first year of transplantation. Previous studies have implicated immunosuppression regimens, including Grafalon and ATG, as causative agents.20,30 In contrast, our observations indicated that infection was the primary trigger. ATG/Grafalon use was significantly lower in our patients. In addition, most of our patients with lower socioeconomic status were prone to infections.\n\nWe observed post-transplant pancytopenia (PTP) in 15.1% of the patients, and the major cause was infections, which is consistent with previous studies31,32 Erythrocytosis was reported in 17.9% and it had male predominance, which was consistent with reports from Friman et al. and Kessler.33,34\n\nIn the present study, 30 patients were identified with allograft dysfunction, including SGF/DGF and acute rejection. Among these, 19 graft rejections were observed, which aligns with the findings of previous studies.34,35 Compared with our report, Talwar et al. reported a lower incidence of DGF (only 6%). Furthermore, in our cohort, graft dysfunction was higher in patients with severe anemia in the first week after transplantation. Consistent with this, Chhabra et al. reported a significant association between graft loss and PTA at three months. PTA-mediated allograft rejection/dysfunction is caused by limited oxygen delivery to the tubular interstitium. Hypoxia generates reactive oxygen species that cause oxidative insult to the renal tissues and mediate the release of pro-inflammatory cytokines, leading to the recruitment of inflammatory cells to the interstitium.36\n\nTo assess graft function, we compared the early and late serum creatinine and eGFR levels in patients with post-transplant anemia at six and 12 months. Although patients with PTA had higher serum creatinine levels than the non-anemic group, the difference was not statistically significant and was similar in patients with and without PTA in our study. This was most likely due to the small sample size. In contrast, Molnar et al. studied 938 renal transplant recipients and showed a statistically significant reduction in renal function in patients with PTA.37\n\nThe major limitation of our study was the small sample size, and the post-transplantation follow-up was limited to one year. This was a retrospective single-center study. Furthermore, we did not analyze the association between PTA and mortality or the severity of anemia and graft failure. We did not perform iron studies or measure erythropoietin levels in our population.\n\n\nConclusions\n\nHaematological abnormalities are common in post-RT patients. PTA is the most frequent abnormality, and it improves over time. There was a significant improvement in hemoglobin levels at one, six, and 12 months post-transplant compared to pre-transplant. Leukopenia, thrombocytopenia, pancytopenia, and post-transplant erythrocytosis are other common haematological abnormalities. Leucopenia was primarily drug-induced (mycophenolate mofetil), and thrombocytopenia and pancytopenia were frequently observed in our cohort. Additionally, severe post-transplant anemia was significantly associated with graft dysfunction in the first week post-transplant. However, PTA was not associated with graft function six and 12 months after transplantation.", "appendix": "Data availability\n\nFigshare: This study contains the underlying data for ‘Post kidney transplant hematologic abnormalities and association of post-transplant anemia with graft function’ https://doi.org/10.6084/m9.figshare.25211441.v2. 16\n\nFigshare: Extended data for ‘Post kidney transplant hematologic abnormalities and association of post-transplant anemia with graft function’, https://doi.org/10.6084/m9.figshare.24441268.v1. 17\n\nThis project contains the following extended data:\n\n• Strobe checklist\n\n• Proforma\n\n• Protocol\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nJager KJ, Kovesdy C, Langham R, et al.: A single number for advocacy and communication—worldwide more than 850 million individuals have kidney diseases. Nephrol. Dial. Transplant. 2019 Nov 1; 34(11): 1803–1805. PubMed Abstract \| Publisher Full Text\n\nThurlow JS, Joshi M, Yan G, et al.: Global epidemiology of end-stage kidney disease and disparities in kidney replacement therapy. Am. J. Nephrol. 2021 Apr 15; 52(2): 98–107. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVernooij RW, Law W, Peters SA, et al.: The probability of receiving a kidney transplantation in end-stage kidney disease patients who are treated with haemodiafiltration or haemodialysis: a pooled individual participant data from four randomised controlled trials. BMC Nephrol. 2021 Dec; 22(1): 1–9. Publisher Full Text\n\nReindl-Schwaighofer R, Oberbauer R: Blood disorders after kidney transplantation. Transplant. Rev. 2014 Apr 1; 28(2): 63–75. Publisher Full Text\n\nGarewal G, Ahluwalia J, Kumar V, et al.: The utility of bone marrow examination in renal transplantation: nine years of experience from north India. Transplantation. 2006 May 15; 81(9): 1354–1356. PubMed Abstract \| Publisher Full Text\n\nLocatelli F, Pisoni RL, Combe C, et al.: Anaemia in haemodialysis patients of five European countries: association with morbidity and mortality in the Dialysis Outcomes and Practice Patterns Study (DOPPS). Nephrol. Dial. Transplant. 2004; 19(1): 121–132. PubMed Abstract \| Publisher Full Text\n\nVanrenterghem Y: Anaemia after renal transplantation. Nephrol. Dial. Transplant. 2004; 19(suppl_5): v54–v58. Publisher Full Text\n\nAugustine JJ, Knauss TC, Schulak JA, et al.: Comparative Effects of Sirolimus and Mycophenolate Mofetil on Erythropoiesis in Kidney Transplant Patients. Am. J. Transplant. 2004; 4(12): 2001–2006. PubMed Abstract \| Publisher Full Text\n\nZafrani L, Truffaut L, Kreis H, et al.: Incidence, risk factors and clinical consequences of neutropenia following kidney transplantation: a retrospective study. Am. J. Transplant. 2009 Aug; 9(8): 1816–1825. PubMed Abstract \| Publisher Full Text\n\nJafari A, Najivash P, Khatami MR, et al.: Cytopenia occurrence in kidney transplant recipients within early post-transplant period. J. Res. Pharm. Pract. 2017 Jan; 6(1): 31.\n\nNarang V, Sachdeva MU: Posttransplantation and pancytopenia. Blood. 2012 Nov 8; 120(19): 3872. Publisher Full Text\n\nKiberd BA: Post-transplant erythrocytosis: a disappearing phenomenon? Clin. Transpl. 2009 Nov; 23(6): 800–806. PubMed Abstract \| Publisher Full Text\n\nBaker SJ, DeMaeyer EM: Nutritional anemia: its understanding and control with special reference to the work of the World Health Organization. Am. J. Clin. Nutr. 1979 Feb 1; 32(2): 368–417. PubMed Abstract \| Publisher Full Text\n\nHenningsen M, Jaenigen B, Zschiedrich S, et al.: Risk factors and management of leukopenia after kidney transplantation: A single-center experience. Transplant. Proc. Elsevier; 2021 Jun 1; Vol. 53(5: pp. 1589–1598. PubMed Abstract \| Publisher Full Text\n\nMoore J, Shabir S, Chand S, et al.: Assessing and comparing rival definitions of delayed renal allograft function for predicting subsequent graft failure. Transplantation. 2010 Nov 27; 90(10): 1113–1116. PubMed Abstract \| Publisher Full Text\n\nNagaraju SP: Post kidney transplant hematologic abnormalities and association of post-transplant anemia with graft function-Data. [Dataset]. figshare. 2024. Publisher Full Text\n\nNagaraju SP: Extended data. figshare. 2024. Publisher Full Text\n\nMekraksakit P, Leelaviwat N, Benjanuwattra J, et al.: A systematic review and meta-analysis of posttransplant anemia with overall mortality and cardiovascular outcomes among kidney transplant recipients. Prog. Transplant. 2023 Mar; 33(1): 78–89. PubMed Abstract \| Publisher Full Text\n\nSchechter A, Gafter-Gvili A, Shepshelovich D, et al.: Post renal transplant anemia: severity, causes and their association with graft and patient survival. BMC Nephrol. 2019 Dec; 20: 1–1. Publisher Full Text\n\nTalwar S, Nair R, Sreedharan S, et al.: Prevalence of posttransplant anemia in patients undergoing renal transplantation at a tertiary care center in Kerala - A prospective observational study. Indian J. Transplant. 2021 Apr 1; 15(2): 93–98.\n\nPoesen R, Bammens B, Claes K, et al.: Prevalence and determinants of anemia in the immediate postkidney transplant period. Transpl. Int. 2011 Dec; 24(12): 1208–1215. PubMed Abstract \| Publisher Full Text\n\nGafter-Gvili A, Gafter U: Posttransplantation anemia in kidney transplant recipients. Acta Haematol. 2019 May 15; 142(1): 37–43. PubMed Abstract \| Publisher Full Text\n\nKasiske BL, Vazquez MA, Harmon WE, et al.: Recommendations for the outpatient surveillance of renal transplant recipients. J. Am. Soc. Nephrol. 2000 Oct 1; 11(suppl_1): S1–S86. Publisher Full Text\n\nZheng S, Coyne DW, Joist H, et al.: Iron deficiency anemia and iron losses after renal transplantation. Transpl. Int. 2009 Apr [cited 2023 Oct 14];22(4): 434–40. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLorenz M, Kletzmayr J, Perschl A, et al.: Anemia and iron deficiencies among long-term renal transplant recipients. J. Am. Soc. Nephrol. 2002 Mar 1; 13(3): 794–797. PubMed Abstract \| Publisher Full Text\n\nRadoui A, Skalli Z, Haddiya I, et al.: Prevalence and predictive factors of anemia after renal transplantation: a Moroccan report. Transplant. Proc. Elsevier; 2010 Nov 1; 42(9): 3542–3549.\n\nSmith A, Couvillion R, Zhang R, et al.: Incidence and management of leukopenia/neutropenia in 233 kidney transplant patients following single dose alemtuzumab induction. Transplant. Proc. Elsevier; 2014 Dec 1; 46(10): 3400–3404. PubMed Abstract \| Publisher Full Text\n\nXie L, He S, Fu L, et al.: The Prevalence and Risk Factors of Thrombocytopenia After Living-Related Renal Transplantation in Chinese Adult Recipients. Transplant. Proc. 2013 Jan 1; 45(1): 197–199. Publisher Full Text\n\nHeaf J: Bone marrow function during quadruple immunosuppressive therapy after renal transplantation. Clin. Nephrol. 1993 Dec 1; 40(6): 332–338. PubMed Abstract\n\nGierczak V, Jouve T, Malvezzi P, et al.: Impact of immunosuppressive strategies on post–kidney transplantation thrombocytopenia. Transplant. Proc. Elsevier; 2021 Apr 1; 53(3): 941–949.\n\nMarinella MA: Hematologic abnormalities following renal transplantation. Int. Urol. Nephrol. 2010 [cited 2023 Oct 14]; 42(1): 151–164. Publisher Full Text Reference Source\n\nCharfeddine K, Zaghdane S, Yaich S, et al.: Factors predisposing to post-renal transplant erythrocytosis: a retrospective study. Saudi J. Kidney Dis. Transpl. 2008; 19(3): 371–377. PubMed Abstract\n\nFriman S, Nyberg G, Blohme I: Erythrocytosis after renal transplantation; treatment by removal of the native kidneys. Nephrol. Dial. Transplant. 1990 Jan 1; 5(11): 969–973. Publisher Full Text\n\nKamar N, Rostaing L: Negative impact of one-year anemia on long-term patient and graft survival in kidney transplant patients receiving calcineurin inhibitors and mycophenolate mofetil. Transplantation. 2008 Apr 27; 85(8): 1120–1124. PubMed Abstract \| Publisher Full Text\n\nChhabra D, Grafals M, Skaro AI, et al.: Impact of anemia after renal transplantation on patient and graft survival and on rate of acute rejection. Clin. J. Am. Soc. Nephrol. 2008 Jul; 3(4): 1168–1174. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nde Bhailís ÁM , Chrysochou C, Kalra PA: Inflammation and oxidative damage in ischaemic renal disease. Antioxidants. 2021 May 25; 10(6): 845. Publisher Full Text\n\nMolnar MZ, Czira M, Ambrus C, et al.: Anemia is associated with mortality in kidney-transplanted patients—a prospective cohort study. Am. J. Transplant. 2007 Apr 1; 7(4): 818–824. PubMed Abstract \| Publisher Full Text" }	[ { "id": "281377", "date": "11 Jun 2024", "name": "Abraham Cohen-Bucay", "expertise": [ "Reviewer Expertise kidney transplantation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 single-center retrospective study examines the incidence of hematologic abnormalities in the first year post-transplant. Although not entirely novel, as some of the results are well-known (e.g., the high incidence of anemia, leukopenia, and thrombocytopenia), this report still contributes valuable information to the transplant community. However, several points should be addressed to enhance the manuscript:\n\nBaseline Anemia Data: It would be beneficial to provide baseline anemia data pre-transplant. Although the mean hemoglobin level is provided, the percentage of patients with anemia is not. Given the post-transplant anemia incidence of 98% at one week, it is likely that the pre-transplant anemia incidence is similarly high Anemia Definition and stratification: The study defines anemia as hemoglobin levels <12 g/dL in women and <13 g/dL in men. However, this definition is unrealistic for early post-transplant patients, given the target on dialysis is only >10 g/dL with erythropoietin treatment. Therefore, It would be informative to stratify the incidence of anemia severity: <10 g/dL, 10-12/13 g/dL, and no anemia (>12/13 g/dL) Details on leukopenia: Further details regarding leukopenia would be informative. Specifically, distinguishing between lymphopenia and neutropenia, the number of patients with neutropenia, and whether any required G-CSF treatment for neutropenia Timing of cytopenia definition: Please clarify if leukopenia and thrombocytopenia were defined at specific time points during follow-up or if any cytopenia (even transient) qualified a patient as having these conditions. Valganciclovir and trimethoprim/sulfamethoxazole are known to cause leukopenia and bone marrow suppression. How many patients were on these medications, and were any of these medications needed to be discontinued due to leukopenia or other cytopenias? Did any patients have thrombotic microangiopathy, which could explain the observed thrombocytopenia and anemia (hemolysis)? Limitations: I concur with the limitations noted by the authors. Additionally, the young recipient age in your study may limit the generalizability to other populations. Causes of cytopenias: The manuscript notes that most cytopenias were attributed to mycophenolate use rather than ATG, due to the low ATG dose. How did you reach the diagnosis of mycophenolate-induced cytopenia? How were other potential causes ruled out? Was the diagnosis of mycophenolate-induced cytopenia made by the treating clinician, or were hematology consultations sought? Mycophenolate dosing: Please provide the initial dose of mycophenolate used at the study's outset, and detail any dose adjustments made due to cytopenias/anemia, including the extent of such reductions.\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": "12369", "date": "26 Sep 2024", "name": "Shankar Prasad Nagaraju", "role": "Author Response", "response": "We thank the editorial team of F1000 research for bringing in expert reviewers to provide valuable feedback. We are also extremely grateful to the reviewers for their valuable comments. We have revised our manuscript to incorporate the changes suggested by reviewers. Comment 1: Baseline Anemia Data: It would be beneficial to provide baseline anemia data pre-transplant. Although the mean hemoglobin level is provided, the percentage of patients with anemia is not. Given the post-transplant anemia incidence of 98% at one week, it is likely that the pre-transplant anemia incidence is similarly high Response: Dear Sir, Many thanks for your suggestion to improve our manuscript. We have incorporated the percentage of pre-transplant anaemia as suggested in the result section. (Page No.9, Line No.119) Comment 2: Anemia Definition and stratification: The study defines anemia as hemoglobin levels <12 g/dL in women and <13 g/dL in men. However, this definition is unrealistic for early post-transplant patients, given the target on dialysis is only >10 g/dL with erythropoietin treatment. Therefore, It would be informative to stratify the incidence of anaemia severity: <10 g/dL, 10-12/13 g/dL, and no anaemia (>12/13 g/dL) Response: Thank you for bringing this to our attention. Based on your feedback, we have revised manuscript to more accurately reflect the clinical context of PTA. Specifically, we have categorized the severity of PTA in Table 3 as suggested into three distinct groups as no anaemia (>12/13 g/dL) <10 g/dL, mild anaemia 10-12/13 g/dL, and severe (<10 g/dL). (Page No.10, Line No.127) Comment 3: Details on leukopenia: Further details regarding leukopenia would be informative. Specifically, distinguishing between lymphopenia and neutropenia, the number of patients with neutropenia, and whether any required G-CSF treatment for neutropenia Response: Many thanks for the suggestion. We have added information regarding neutropenia and number of patients who required G-CSF treatment for neutropenia in the result section (Page No.11, Line No.164-168) Comment 4: Timing of cytopenia definition: Please clarify if leukopenia and thrombocytopenia were defined at specific time points during follow-up or if any cytopenia (even transient) qualified a patient as having these conditions Response: Sincere thanks for your suggestion. The presence or absence of leukopenia and thrombocytopenia were defined at post-transplant time points of <6 months and >6 months. The same has been defined in the methods section (Page No.8, Line No.79-80). The same has been added in the results section too (Page No.11, Line No.164). Comment 5: Valgancyclovir and trimethoprim/sulfamethoxazole are known to cause leukopenia and bone marrow suppression. How many patients were on these medications, and were any of these medications needed to be discontinued due to leukopenia or other cytopenia? Response: Dear Sir, Thank you for the valuable input. Our patients were on Valgancyclovir prophylaxis until first 6 months and the trimethoprim sulfamethoxazole up to 12 months after kidney transplantation. They were also stopped during leukopenia. So we have revised the section on leukopenia in the manuscript with the details and as suggested instead of implying that mycophenolate mofetil as cause of leukopenia we have mentioned it as drug induced leukopenia (Page No.12, Line No.180-186). Comment 6: Did any patients have thrombotic microangiopathy, which could explain the observed thrombocytopenia and anemia (hemolysis)? Response: Dear Sir, Many thanks for the suggestion. None of our patients had TMA As indicated, we have incorporated the same in the result section in the manuscript (Page No.9, Line No.124-125). Comment 7: I concur with the limitations noted by the authors. Additionally, the young recipient age in your study may limit the generalizability to other populations. Response: Dear Sir, Thank you for the input. The same has been added in the limitation section as suggested (Page No.14, Line No.274-275) Comment 8: Causes of cytopenia: The manuscript notes that most cytopenias were attributed to mycophenolate use rather than ATG, due to the low ATG dose. How did you reach the diagnosis of mycophenolate-induced cytopenia? How were other potential causes ruled out? Was the diagnosis of mycophenolate-induced cytopenia made by the treating clinician, or were hematology consultations sought? Response: Dear Sir, Thank you for the valuable suggestions and insights to improve the manuscript. ATG may have a superimposed impact in patients where it has been administered. Additionally, when pancytopenia was present, other medications like Valgancyclovir and trimethoprim sulfamethoxazole were also stopped. All patients were tested for CMV RNA PCR during the pancytopenia episodes. The manuscript has been revised and mentioned as drug induced cytopenia as suggested instead of mycophenolate induced cytopenia. We thank the reviewer for bringing this into our notice and guiding us in revising the manuscript. The decision was made by Nephrologist and clinical hematology consultation was not sought due to non-availability of haematologist at our institute during the study period. (Page No.12, Line No.180 and 187). Comment 9: Mycophenolate dosing: Please provide the initial dose of mycophenolate used at the study's outset, and detail any dose adjustments made due to cytopenias/anemia, including the extent of such reductions Response: The mycophenolate dose used varied from 1.5-2.00 gm as induction based on the body weight and nephrologist clinical decision. The dose was reduced to 0.5-1.0 g per day after the cytopenia episodes and was adjusted further on follow-up on case to case basis as per etiology. The same has been incorporated in the manuscript (Page No.8, Line No.105-109)" } ] }, { "id": "281382", "date": "15 Jul 2024", "name": "Dr Sonia Sharma", "expertise": [ "Reviewer Expertise Clinical Nephrology", "Paediatric Nephrology", "Kidney Transplantation MMF AUC work", "Nephrotic syndrome", "Tubular disorders" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGood work done by the author. The research topic is important, and data from Asian countries are surely lacking.\nThe study design is appropriate, and sufficient details are given in the method section. However, in the result section, some details are required to make it more informative for indexing:\n1. High prevalence shown at one month and in the subsequent time period. It is required, therefore, if there were any associated ongoing etiologies. Related discussions and comments on previous data are also required later in the relevant section (discussion part). 2. What was the severity of anemia at three months, six months, and one year? 3. About Leukopenia and thrombocytopenia: At what stage of transplant were both noted? For Leukopenia, 90% of study patients were shown to have mycophenolate mofetil association. What dose of mycophenolate was given if there were other side effects of the drug at the same time. 4. Were there any differences in parameters between cadaveric and live donors?\n\nMinor: 1. The text and tables provide almost similar information. Either must be modified to avoid repetition, and better informative tables are required. 2. Figure 3. Clarity of message is required related to the proportion of patients. 3. Correction is required for the last line of the conclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "12370", "date": "26 Sep 2024", "name": "Shankar Prasad Nagaraju", "role": "Author Response", "response": "We would like to thank the editorial team of F1000 research for bringing in expert reviewers to provide valuable feedback. We are also extremely grateful to the reviewers for their valuable comments. We have revised our manuscript incorporating the changes suggested by reviewers Comment 1: High prevalence shown at one month and in the subsequent time period. It is required, therefore, if there were any associated ongoing etiologies. Related discussions and comments on previous data are also required later in the relevant section (discussion part) Response: Dear Madam, Thank you for your valuable input on improving our manuscript. Since most PTA are due to surgical blood loss, we didn’t evaluate in detail for PTA in all patients. As suggested we have included and discussed the causes for post-transplant anaemia in discussion section. Comment 2: What was the severity of anemia at three months, six months, and one year? Response: Thank you for the suggestion, which helped us refine our manuscript. We have stratified PTA severity at each time points into three categories (severe, mild, no anemia) in Table 3 (Page No.10, Line No.127) Comment 3: About Leukopenia and thrombocytopenia: At what stage of transplant were both noted? For Leukopenia, 90% of study patients were shown to have mycophenolate mofetil association. What dose of mycophenolate was given if there were other side effects of the drug at the same time Response: Sincere thanks for your suggestion. The presence or absence of leukopenia and thrombocytopenia were defined at post-transplant time points of <6 months and >6 months. The same has been defined in the methods section. (Page No.8, Line No.105-109). During the pancytopenia episodes Valgancyclovir and/or trimethoprim/sulphamethoxozole were also stopped in addition to mycophenolate mofetil. ATG was given to 20.7% of patients as induction. Hence, as suggested by both the reviewers we have revised the manuscript. Instead of implying that the cytopenia was due to mycophenolate mofetil alone, we have mentioned that it is drug induced cytopenia. We sincerely thank both the reviewers for bringing this to our notice and helping us improving the manuscript. Comments 4: Were there any differences in parameters between cadaveric and live donors? Response: Dear Madam, Thank you for this query. As 85.8% of the recipients received the kidney from live donors, the difference in the parameters between the cadaveric and live donors was not analysed. Minor Comment 5: The text and tables provide almost similar information. Either must be modified to avoid repetition, and better informative tables are required Response: Dear Madam, Thank you for the suggestion. The text has been suitably modified. Comment 6: Figure 3. Clarity of message is required related to the proportion of patients. Response: Sincere thanks for the suggestion. We have revised the graph incorporating the proportion of patients (Page No.11, Figure 3). Comment 7: Correction is required for the last line of the conclusion Response: Thank you for bringing this to our notice. This part has been modified (Page No.14, Line No.285-286)." } ] } ]	1	https://f1000research.com/articles/13-241
https://f1000research.com/articles/12-604/v1	05 Jun 23	{ "type": "Systematic Review", "title": "COVID-19 vaccinations and their side effects: a scoping systematic review", "authors": [ "Hind Monadhel", "Ayad Abbas", "Athraa Mohammed", "Ayad Abbas", "Athraa Mohammed" ], "abstract": "Introduction: The COVID-19 virus has impacted people worldwide, causing significant changes in their lifestyles. Since the emergence of the epidemic, attempts have begun to prepare a vaccine that can eliminate the virus and restore balance to life in the entire world. Over the past two years, countries and specialized companies have competed to obtain a license from the World Health Organization for the vaccines that were discovered. After the appearance of vaccines in the health community, comparisons and fears of their side effects began, but people don’t get an answer to the question of which is the best vaccine. Methods: IEEE Xplore, ScienceDirect, the New England Journal of Medicine, Google Scholar, and PubMed databases were searched for literature on the COVID-19 vaccine and its side effects. we surveyed the literature on the COVID-19 vaccine’s side effects and the sorts of side effects observed after vaccination. Depending on data from the literature, we compared these vaccines in terms of side effects, then we analyzed the gaps and obstacles of previous studies and made proposals to process these gaps in future studies. Results: Overall, 17 studies were included in this scoping systematic review as they fulfilled the criteria specified, the majority of which were cross-sectional and retrospective cross-sectional studies. Most of the side effects were mild, self-limiting, and common. Thus, they usually resolve within 1–3 days after vaccination. Factors associated with higher side effects included advanced age, allergic conditions, those taking other medications (particularly immunosuppressive ones), those with a history of type II diabetes, heart disease, hypertension, COVID-19 infection, and female sex. Our meta‐analyses also found that mRNA vaccines looked to be more effective, while inactivated vaccinations had fewer side effects. Conclusion: This review shows that the COVID-19 vaccine is safe to administer and induces protection.", "keywords": [ "COVID-19 Vaccine", "Machine learning", "side effects", "Statistical methods", "Adverse reactions", "Data Processing and Analysis", "Data Mining." ], "content": "Introduction\n\nCOVID-19 is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was initially detected in December 2019 in Wuhan, China. It belongs to the same group of ribonucleic acid (RNA) viruses that cause Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) (Mahendra 2020). Corona-viruses are a large family of viruses that infect many different species, including humans. In humans, the coronavirus can cause a variety of diseases, from minor respiratory tract infections like the common cold to fatal infections (Weiss & Navas-Martin 2005).\n\nThe virus might be transferred by close touch or simply droplets, between people, when the mucosal membranes of healthy individuals are exposed to secretions generated by the carriers (Sharma 2020). Symptoms of COVID-19 might vary from person to person. Some of them may exhibit no signs or symptoms of infection, such as breathing difficulties, or they may succumb to the sickness (Sahin 2020).\n\nEven though several therapeutic compounds and medications have been proposed and reused in the battle against COVID-19, they have remained supportive therapy choices; however, vaccines remain the most efficient and effective way to protect people from this disease (Tavilani et al. 2021).\n\nThe development of vaccinations has made significant advances; the first mass vaccination program started in early December 2020 in Europe, with priority given to individuals who are at high risk of severe COVID-19 infection, such as the elderly, and those who are at high risk of viral exposure and transmission, such as front-line medical staff (Paules et al. 2020). 7,952,750,402 vaccine doses have been provided globally through December 6, 2021 (WHO 2021c).\n\nHowever, no vaccine is entirely free from complications or adverse reactions. Any vaccination can have early adverse reactions, including local ones like pain, swelling, and redness, as well as systemic ones like headache, chills, nausea, fatigue, myalgia, and fever (Al Khames et al. 2021). Following the SARS-CoV-2 vaccination, there have been several recorded occurrences of side effects; in addition, there have been a small number of deaths (Varsavsky 2021). This has been recorded with COVID-19 vaccinations, and it has been observed in people with pre-existing health conditions like diabetes and high blood pressure, as well as people who have had allergic reactions to the vaccine. The extent to which they are linked to vaccines, however, is unknown and under investigation (Hussien 2019).\n\nIn this systematic review, we aim to make reference to the wide range of possible reactions that can occur after vaccinations, so that healthcare providers can better understand these patients. The purpose of this scoping systematic review is to summarize and integrate the results of studies on the side effects of the COVID-19 vaccination and then determine the gaps in these studies. This paper is organized in the following manner: Section 1 is an introduction to COVID-19 viruses and vaccination, Section 2 is Background, section 3 is the methods, Section 4 is a review of the Conducted Studies, Section 5 the results, section 6 discusses the results & gaps in the literature studies, section 7 concludes the most important points of this paper and section 8 represent study strengths and limitations.\n\nWhat are the rates of side effects of COVID-19 vaccines, and which symptoms are the most common?\n\n\nBackground\n\nA vaccine is a biologics that provides Active-Adaptive immunity against a particular disease. In vaccination development, the micro-organisms that cause the disease are utilized in either attenuated or killed form or involve using their toxins or surface proteins. in order to activate the immunological system against foreign bodies, Vaccines are administered nasally, orally, or by injection (intramuscularly, subcutaneously, or intradermally) (Dai et al. 2019). To develop immunity, the body produces antibodies (immunoglobulins) against microorganisms, thus generating the body’s defense mechanism. The antibodies produced by the immune system in response to re-exposure to the same microorganism prevent or lower disease severity (WHO 2020; Dai et al. 2019).\n\nAny unwanted and unintended or harmful reactions following the administration of a medicine, vaccine, or combination of vaccinations are known as adverse reactions. It may be a known adverse event or previously unrecognized (Salisbury et al. 2006). The COVID-19 vaccinations contain genetic blueprints for producing spike (S) proteins that sit on the coronavirus’s surface and allow it to enter human cells. Upon receiving these instructions, human cells produce copies of the spike (S) protein. In fact, since cells only produce a portion of the virus and not the whole pathogen, we are not infected. While foreign spikes cannot cause disease, they can activate the immune system exactly as it is supposed to do. As a result of the strong immune response triggered by vaccines, a wide range of symptoms can be triggered, including fever, fatigue, chills, inflammation, and reactions at the injection site. The innate immune system response to the COVID-19 vaccine causes the reactions (Marsa 2021).\n\nMessenger RNA\n\nThese vaccines involve using synthetically manufactured Messenger RNA (mRNA), that infects host cells and produces a component of the spike protein. After the body degrades it, the protein triggers the production of antibodies. These immunoglobulins (antibodies) prepare the body to deal with any infection in the future with a minimal risk of side effects. This mechanism is used by the Pfizer and Moderna vaccines (CDC 2021a). The BNT162b2 developed by Pfizer/BioNTech produces an immunological response by eliciting IgG, IgA, CD8+ cells, or CD4+ cells, whereas mRNA-1273 developed by Moderna stimulates CD8 T cells (Goyal et al. 2021).\n\nViral vector-based vaccines\n\nThey are altered versions of a virus belonging to a different genus that is utilized as a vector. Through its interaction with immune cells, it helps them recognize and outwit pathogenic viruses. The immune cells of the body recognize the presence of foreign antigens as soon as they are injected into the body, and activate an immune response by releasing antibody-producing B cells and T cells that search down infected cells and destroy them. T cells function by examining the storage of proteins that are expressed on the cell’s surfaces. When they encounter a foreign protein, they trigger an immune response against the cell storing it because they are able to identify the body’s own proteins as “self” (WHO 2021a). This mechanism is used by Janssen/Johnson & Johnson, Sputnik V, and AstraZeneca vaccines (CDC 2021b).\n\nWhole virus or inactivated virus vaccines\n\nAn age-old and common vaccine, there are currently two types: live-attenuated and inactivated. Chemicals, heat, and radiation are used to destroy the virus’s genetic material in order to prepare inactivated vaccinations. Because these vaccines are versions of weak natural pathogens, the immune system activates a wide range of defense mechanisms in response, including killer T cells that destroy the infected cells, helper T cells that help produce antibodies, and antibodies-producing B cells that attack pathogens (WHO 2021b). When they are introduced into the body, they induce antibody-mediated responses that are weak and relatively short-lived. Therefore, they are administered along with an adjuvant, and often booster doses are required. The live attenuated vaccines, in contrast, use a weakened version of the virus inside the body. These viruses can grow and reproduce once they are inside the body, yet they do not cause symptomatic disease in the host (NIAID 2021). This inactivated mechanism is used by Sinopharm, Covaxin, Sinovac, and Corovac vaccines. The live attenuated mechanism is used in the Covivac vaccine (Shahzamani et al. 2021).\n\nTable 1 depicts a comparison of the COVID-19 vaccines that were included in the research studies; moreover.\n\n\n\n1. Have a severe allergic reaction after a previous dose of the vaccine.\n\n2. Individuals who developed myocarditis or pericarditis following the first dose of vaccine.\n\n3. Have a severe allergic reaction to any of the ingredients.\n\n\n\n1. Have a severe allergic reaction to any of the ingredients.\n\n2. Anyone with a fever (body temperature over 38.5°C).\n\n\n\n1. Have a severe allergic reaction to any of the ingredients.\n\n2. Individuals who have had Thrombosis with thrombocytopenia (TTS) after the first dose.\n\n\n\n1. Have anaphylaxis to any of the ingredients.\n\n2. Anyone with a fever (body temperature over 38.5°C).\n\n1. Have anaphylaxis to any of the ingredients.\n\n2. Cases with acute PCR-confirmed COVID-19.\n\n3. Anyone with a fever (body temperature over 38.5°C).\n\n4. People with bleeding disorders.\n\n\n\n1. Chills\n\n2. Tiredness\n\n3. Headache\n\n4. Pain (at the injection site)\n\n5. Swelling\n\n6. Readiness (at the injection site).\n\n\n\n1. Chills\n\n2. Tiredness\n\n3. Headache\n\n4. Pain (at the injection site)\n\n5. Swelling\n\n6. Readiness (at the injection site).\n\n\n\n1. Tiredness\n\n2. Headache\n\n3. Nausea\n\n4. Pain, Readiness, Bruising, or Warmth at the injection site\n\n5. Vomiting\n\n6. Chills\n\n\n\n1. Pain, Swelling, and Readiness at the injection site.\n\n2. Fatigue\n\n3. Headache\n\n4. Fever or Chills\n\n\n\n1. Pain, Swelling, or both at the injection site.\n\n2. Fever\n\n3. Irritability\n\n4. Headache\n\n\n\n1. Based on the availability of the product, either of the WHO EUL COVID-19 vectored vaccinations (Janssen or AstraZeneca Vaxzervria/COVISHIELD) may be used as a second dose after a first dose of the Moderna vaccine.\n\n2. A second dose of the Moderna vaccination may be given following any of the WHO COVID-19 inactivated vaccinations (Sinopharm, Sinovac, Bharat) or vectored vaccinations (Janssen Vaxzervria/COVISHIELD).\n\n3. A booster dose of Moderna can be given after any other COVID-19 vaccine.\n\n\n\n1. Based on the availability of the product, either of the WHO EUL COVID-19 vectored vaccinations (Janssen or AstraZeneca Vaxzervria/COVISHIELD) may be used as a second dose after a first dose of the Pfizer vaccine.\n\n2. A second dose of the Pfizer vaccination may be given following any of the WHO COVID-19 inactivated vaccinations (Sinopharm, Sinovac, Bharat) or vectored vaccinations (Janssen Vaxzervria/COVISHIELD).\n\n3. A booster dose of Pfizer can be given after any other COVID-19 vaccine.\n\n\n\n1. Based on the availability of the product, either of the mRNA COVID-19 vaccines (Pfizer or Moderna) may be used as a second dose after a first dose of the AstraZeneca vaccine.\n\n2. A second dose of the Astra-Zeneca vaccination may be given following any of the WHO COVID-19-inactivated vaccinations (Sinopharm, Sinovac, or Bharat).\n\n\n\n1. Based on the availability of the product, Either of the WHO EUL COVID-19 mRNA vaccines (Pfizer or Moderna) or vectored vaccines (AstraZeneca Vaxzervria/COVISHIELD or Janssen) may be used as a second dose after a first dose of the Sinopharm vaccine.\n\n\n\n1. Based on the availability of the product, Either of the WHO EUL COVID-19 mRNA vaccines (Pfizer or Moderna) or vectored vaccines (AstraZeneca Vaxzervria/COVISHIELD or Janssen) may be used as a second dose after a first dose of the Bharat vaccine.\n\n\nMethods\n\nThe PRISMA guidelines for systematic reviews and meta-analyses were followed in this research (Moher et al. & PRISMA Group*. 2009).\n\nInclusion criteria\n\nResearch studies, whose focus is COVID-19 vaccines and their side effects, were included.\n\nExclusion criteria\n\n• Abstracts papers, Preprints, grey literature.\n\n• Book chapters, non-English studies, Case reports, and Unrelated studies.\n\nWe searched through the databases of IEEE Xplore, ScienceDirect, the New England Journal of Medicine, Google Scholar, and PubMed to find studies about COVID-19 and the side effects of COVID-19 vaccinations. from 2019 to 2022 to select eligible research publications. The searches were performed without time filters, and backward snowballing was used to find articles that weren’t found in the initial search by screening relevant studies and their references (Figure 4). These databases had been selected based on several collected journals & conferences about emerging topics, including the Coronavirus disease (COVID-19) and the side effects related to the COVID-19 vaccine.\n\nOur keyword search will be based on the following combination of Medical Subject Headings: (COVID-19 OR SARS-CoV-2 OR 2019-nCoV OR coronavirus OR MERS-CoV OR SARS-CoV) AND (Vaccines OR Vaccination OR COVID-19 vaccine OR SARS-CoV-2 vaccine OR MERS-CoV vaccine OR mRNA vaccine OR Moderna vaccine OR Pfizer-BioNTech COVID-19 vaccine OR mRNA-1273 vaccine OR ChAdOx1covid-19 vaccine OR AZ1222 covid-19 vaccine OR Johnson & Johnson covid-19 vaccination OR Ad26 covid-19 vaccine OR BIBP-CorV vaccine OR BIBP vaccine OR CDC-approved COVID-19 vaccines OR Sinopharm vaccine OR AstraZeneca-Oxford vaccine OR BNT162b2 COVID-19 Vaccine) AND (Toxicity OR harmful impact OR side effects OR adverse events OR negative reactions) as shown in Table 2.\n\nThis section classifies articles according to criteria such as the year of publication and publishing house or journal. Figure 1 below shows the trend of article publications in various databases (i.e., IEEE Xplore, ScienceDirect, the New England Journal of Medicine, Google Scholar, and PubMed) from 2019 to 2022. Annual increases in publication rates are observed. Therefore, COVID-19 vaccines have in recent years gained increasing interest among researchers. Thus, further studies are expected to be conducted in the future.\n\nFigure 2 illustrates how research articles are distributed based on their orientation: survey or review papers, learning-based studies, and statistical and analytical studies. It is noticeable that a large portion of the papers is statistical since our paper attempts to investigate the side effects of vaccines. In the systematic literature review, there are three categories of research studies: survey and review studies, studies that apply machine learning, and studies that use statistics and analytical methods. The New England Journal of Medicine has published 14 articles in the statistics and analytical methods category. IEEE has published 12 articles. Two of them are survey and review studies, and the other 10 are about statistics and analytical methods. In ScienceDirect 11 articles have been published as follows: survey and review studies (3), statistics & analytical studies (8). In Google Scholar and PubMed, 19 articles have been published as follows: survey and review studies (3), machine learning studies (4), and statistics and analytical studies (12).\n\nTo gain a better understanding of COVID-19 vaccines and predict and analyze their side effects, several studies were conducted between 2020 and 2021. We highlight a few of these studies in this section, which presents the categories of relevant research papers based on their classification (see Figure 4).\n\nPrediction of the COVID-19 vaccine that is associated with a higher percentage of side effects using machine learning methods In (Abdulrahman et al. 2021) demonstrate how the clustering techniques utilized in the instance of COVID-19 vaccine side effects datasets help to give accuracy for clustering the COVID-19 vaccine side effects datasets. Using the WEKA tool, this paper compared four clustering techniques. It also describes the datasets in terms of multiple-precision factors, cluster case, number of iterations, and time, the findings of these algorithms, the clustering methods employed, and their accuracy. The clustering algorithm k-means was discovered to be frequently used in several types of COVID-19 vaccine side effects datasets with great accuracy.\n\nPrediction of side effects associated with the COVID-19 vaccines and their severity using machine learning methods In (Ahamad 2020) the authors aim to categorize and define patients at risk of such responses using patient data and discover probable common reasons for such side effects to find treatments that lower patient risk. They examined patient medical records and data on the impacts and consequences of immunization. The data was analyzed using a collection of machine learning (ML) classification methods. In most cases, similar traits were shown to be closely connected to negative patient reactions. They included prior infections, hospitalizations, and SARS-CoV-2 reinfection. Medical history-based ML classifiers also could determine which patients were most likely to receive a vaccination with no side effects reliably. In (Hatmal et al. 2021) the authors evaluated the side effects and perceptions of the COVID-19 vaccines in Jordan. An online poll was distributed to Jordanians who had received any COVID-19 vaccines as part of a cross-sectional investigation. Data were statistically examined, and machine learning (ML) algorithms were utilized to predict the severity of side effects. Despite significant differences in the presence and severity of side effects among these vaccines, statistical analysis revealed that they provide comparable protection against COVID-19 infection. The current paper confirmed that the CDC-approved COVID-19 vaccines are safe and that vaccination makes people feel safer. However, severe cases may necessitate additional medical care or perhaps hospitalization.\n\nTable 3 compares the results of studies based on machine learning techniques about the COVID-19 side effects. Evaluation of Machine Learning Models Eq. (1) was used to evaluate ML models by calculating their accuracies (Grandini et al. 2020).\n\nA variety of statistical methods have been used to assess the side effects after vaccinations (Jayadevan 2021) aim to evaluate the initial reaction to the COVID-19 vaccine’s first dosage and to investigate the range of post-vaccination symptom profiles for different vaccinations. A cross-sectional online survey was conducted in India that included questions about the immediate post-vaccination experience. Over a week, from January 29 to February 4, 5396 persons replied to the poll. Overall, 65.9% of respondents said they had had one post-vaccination symptom. 79% of those who reported symptoms did so within the first 12 hours. 472 people reported COVID-19 out of 5396 (or 8.7%). Their symptom profile was similar to those who had no prior experience. In (El-Shitany 2021) the authors obtained their data using a Google Form questionnaire (online survey). The results were based on the responses of 455 people, all of whom live in Saudi Arabia. After the first and second doses, the vaccine’s side effects were documented. The most common complaints were injection site pain, headaches, flu-like symptoms, fever, and tiredness. Fast heartbeat, generalized aches, difficulty breathing, joint discomfort, cold, and exhaustion whereas some of the less common side effects. Lymph node enlargement and pain, as well as Bell’s palsy, are uncommon side effects. Recipients who had previously been infected reported more difficulty breathing than those who had never been infected with the coronavirus.\n\nZahid (2021) looked into the most common side effects associated with these four vaccines’ first and second doses. 311 people who had two doses of one of these four vaccinations completed an online questionnaire, which was used to collect data. The findings of this paper demonstrated that the second dose of the vaccine caused higher side effects, independent of the vaccine’s identification. Overall, vaccination recipients (Sinopharm) experienced the fewest side effects among the four vaccines examined. The most important conclusion of the paper is that the post-vaccination side effects of the first and second doses were modest and predictable, with no hospitalizations; this information can help reduce vaccine fear.\n\nAs for comparing the side effects of the COVID-19 vaccines (Andrzejczak-Grządko et al. 2021) compared the AstraZeneca and Pfizer vaccines’ side effects. The survey results suggest that side effects from the AstraZeneca vaccine’s first dose are more common than those from the Pfizer vaccine’s first and second doses. In this survey, most respondents reported at least one side effect after receiving the AstraZeneca and Pfizer vaccines, but these reactions were less common after receiving the Pfizer vaccine. A survey was made available on the internet. It was done on patients who had been immunized with Pfizer or AstraZeneca vaccines. The respondents were asked about the side effects of the vaccines after the first and second doses. In (Almufty et al. 2021) the authors highlighted probable side effects from covid19 vaccines, a comparison of the three COVID-19 vaccines now available in Iraq, and risk factors for severe side effects (Sinopharm, AstraZeneca-Oxford, and Pfizer- BioNTech). A standardized questionnaire platform was used to collect information about the Iraqi people. The majority of the symptoms ranged from mild to moderate in severity. With P values less than 0.0001, both residencies in Iraq’s Kurdistan Region and the AstraZeneca vaccine were statistically significant risk factors for experiencing severe symptoms.\n\nIn regards to young age groups and side effects Alamer et al. (2021) looked into the early side effects of the Pfizer-BioNTech (BNT162b2) mRNA vaccine in Saudi Arabian youngsters aged 12 to 18. A cross-sectional study using a self-administered online survey was done to examine the side effects in children in this age range after receiving one or two doses of the Pfizer-BioNTech (BNT162b2) mRNA vaccine. After vaccination, general and demographic information was acquired, and vaccine-related side effects were examined.\n\nAs the safety assessment of the COVID-19 vaccines is necessary, in Dziedzic et al. (2021). The goal was to see if the ChAdOx1 n-COV-19 vaccine was safe in terms of systemic and local side effects on patients 48 hours after injection. This paper report has three (3) particular aims. First, the paper report assesses and analyzes the safety of the first and second doses of the ChAdOx1 n-COV-19 vaccinations 48 hours after administration. Second, the paper examines the side effects of the ChAdOx1 n-COV-19 vaccination among people younger than 40 years and people older than 40 years following delivery over a two-day (48-hour) period to evaluate and compare the vaccine’s safety by age and sex.\n\nTo analyze the side effects from different aspects in Azimi et al. (2021), the authors aimed to determine the frequency, intensity, and degree of side effects linked with the COVID-19 vaccination (ChAdOx1 nCoV-19 vaccine or AstraZeneca) among Kabul University of Medical Sciences employees. A retrospective observational, interview-based study was undertaken among the Kabul University of Medical Science’s faculty and instructors in Kabul, Afghanistan, from April 4 to April 20, 2021, to examine the COVID-19 vaccine’s side responses (ChAdOx1 nCoV-19 vaccine or AstraZeneca). Participants were questioned after the first AstraZeneca vaccination dosage was given out. They were instructed to report any negative reactions to the vaccination within 8–10 days of getting it. Klugar et al. (2021) aimed to assess the post-vaccination side effects of the various vaccines approved in Germany. An online questionnaire that has been validated and evaluated for a priori dependability was used in a cross-sectional survey. Demographic information, medical and COVID-19-related anamneses, and local, systemic, oral, and skin-related side effects following COVID-19 immunization were all asked about in the survey. Additionally, (Riad et al. 2021) conducted a cross-sectional survey-based study in the Czech Republic to gather data on the COVID-19 vaccine’s side effects among healthcare workers. The researchers used a validated questionnaire containing twenty-eight multiple-choice items about demographics, medical anamneses, COVID-19-related, and general, oral, and skin-related side effects. The most often used drugs with side effects were antihistamines, demanding a greater investigation. Overall, people who took two doses experienced more side effects. The manufacturer’s figures matched the distribution of side effects among Czech healthcare personnel, especially their link with younger age groups and the second dosage.\n\nAlso, Kitagawa et al. (2022) conducted an online survey of people who had self-reported side effects after receiving two doses of BNT162b2 or mRNA-1273 immunization. The incidence of adverse effects was investigated after each dose of vaccination. The incidence of side effects following the second dose of the BNT162b2 and mRNA-1273 vaccines was compared using propensity score matching.\n\nTo examine the duration of side effects’ appearances, a study conducted by Alhazmi et al. (2021) aimed to see how long it took for post-vaccination adverse effects to appear. An online questionnaire was used to perform cross-sectional, retrospective research among COVID-19 immunization participants in Saudi Arabia. General and demographic data were collected after at least one immunization dose, and vaccine-related side effects were examined. The side effects described by their paper participants after receiving the Oxford-AstraZeneca and Pfizer-BioNTech vaccines are similar to those reported in clinical trials, showing that both vaccines have safe profiles.\n\nIn terms of reducing vaccine hesitancy Saeed et al. (2021) aimed to gather data on Sinopharm’s COVID-19 vaccine’s side effects. Between January and April 2021, a cross-sectional survey paper was done to gather data on the effects of the COVID-19 vaccine among UAE residents. The response of persons who refused to take the COVID-19 vaccine was reported, as demographic data, vaccination, and the reasons people did not want to take the COVID-19 vaccine. The post-vaccination side effects of the first and second doses were modest and predictable, with no hospitalizations; this knowledge can assist in reducing vaccine fear. Moreover, Kadali et al. (2021) looked at the side effects of the mRNA 1273 vaccine by going over all of the organ systems in depth an impartial online survey tool was used in a randomized, cross-sectional investigation to collect responses from HCWs. The bulk of the symptoms did not appear to be life-threatening. This vaccination appears to have a better level of acceptability, despite the wide variety of self-reported effects.\n\n\nResults\n\nAccording to the search strategy, 391 papers were identified. A total of 170 papers were screened for eligibility by full-text review after titles and abstracts were screened. Following a thorough full-text screening, 114 papers were deemed unacceptable for the reasons listed in (Figure 3). The remaining 17 papers (Table 5) were included in this scoping systematic review as they fulfilled the criteria specified. The majority of studies were designed as randomized cross-sectional studies (n = 2), survey-based studies (n = 3), retrospective cross-sectional studies (n = 5), cross-sectional studies (n = 5), and research article studies (n = 2) (Figure 5A).\n\nThe final analysis of the studies, included 38680 individuals who experienced at least 1 or more side effects were involved from twelve countries representing three regions of the world, representing as North America (n = 1), South & Western Asia (n = 9), and Central Eastern European region (n=2). A detailed description of the studies (Abdulrahman et al. 2021; Ahamad, 2020; Ma’mon, 2021; Grandini et al. 2020; Jayadevan, 2021; El-Shitany, 2021; Zahid, 2021; Andrzejczak-Grządko et al. 2021; Almufty et al. 2021; Alamer et al. 2021; Dziedzic et al. 2021; Azimi et al. 2021; Klugar et al. 2021; Riad et al. 2021; Kitagawa et al. 2022; Alhazmi et al. 2021; Saeed et al. 2021; Kadali et al. 2021) is provided in Table 5. Among the Vaccine platforms included in the systematic review were DNA (2), inactivated (2), and mRNA (2). There were seven (7) studies in which healthcare workers were the study population, while twelve (12) studies featured a majority of female participants. Among the cases reported, most side effects were reported in women and age groups between 20 and 30 (Figure 5B & C). The max number of participants in Kitagawa’s study was around 12109 and the min number of participants in Dziedzic’s study was only 247 participants. Participants in the studies were all adults and adolescents aged 18 or older. Except for Alamer’s study, participants were between 12 and 18 years old (Table 5).\n\nLocal side effects were more prevalent than systemic side effects, and the reported side effects were significantly higher among females than males. Most of participants, however, experienced mild and short-term side effects. Severe reactions or anaphylactic reactions may occur in rare cases. The most reported local and systemic side effects for the vaccines were pain at the site of the injection and tiredness, respectively (Figure 5D). Adenovirus Viral vector COVID-19 vaccines had a higher incidence of side effects than other COVID-19 vaccines in most of the studies. Max side effects of injection site pain reported in Riad’s study around 89.8%. Max side effects of Tiredness reported in Alhazmi’s study was around 83.5% (Table 4). It was reported in half of the studies that side effects lasted between 1-3 days.\n\nA total of 533 cases of oral and skin side effects have been reported in three studies following vaccination with COVID-19. The most common oral side effects were vesicles (6.3%), bleeding gingiva (4.3%), oral paraesthesia (2.2%), dysgeusia (2.4%), blisters (36%), and halitosis (25.4%) (Figure 6). While rash and urticaria (other than at the site of the injection) were the most reported skin-related side effects (Figure 7). Three-fourths (75.1%) of the oral side effects appeared within the first week following vaccination. The most affected sites for skin-related side effects were the upper limb, face, chest (trunk), lower limb, and back.\n\nThe association between patients’ medical histories and side effects was only looked at in some studies (Ahamad 2020). According to the results, patient medical histories are strongly correlated with the incidence of side effects, some of which can be severe and even fatal. Patients with advanced age, allergic conditions, and those taking other meds (particularly immunosuppressive ones) are most likely to experience side effects after vaccination, as well as those with a history of type II diabetes, heart disease, hypertension, or COVID-19 infection. Also, the study found that severe reactions are mostly associated with symptoms such as hospitalization duration, headache, dyspnea (shortness of breath), fever/pyrexia, chills, fatigue/tiredness, dizziness, different kinds of pain, rash, and physical disability.\n\nIn addition, females were associated with higher D-dimer levels (p-value = 0.05), In which six women who received AstraZeneca vaccines, one of whom was over 50 years old, had elevated D-dimer levels, and three developed petechiae and hematomas. one of whom was hospitalized for thromboembolism treatment (Almufty et al. 2021).\n\n\nDiscussion\n\nVaccines play a vital role in reducing global rates of infections and diseases (Lombard et al. 2007). The original assumption of vaccinations, dating back to the 11th century, was to expose a human to a small amount of disease to foster protection and immunity against exposure to a larger amount of the same pathogen. This method was 1st recorded in Chinese literature that ingesting a small amount of poison could prevent death from a larger dose of poison (Plotkin 2005).\n\nVaccines induce a strong immune-response that triggers a wide range of reactions, including fever, chills, fatigue, inflammation, and swelling at the site of injection (Marsa 2023). An “adverse event following immunization” (AEFI) is defined by the World Health Organization (WHO) as any unintended medical event that occurs after the vaccination, and which does not necessarily indicate a causal relationship with the vaccine. Symptoms, abnormal laboratory findings, or diseases that are not desirable or unintended are called adverse events (WHO 2023).\n\nA systematic evaluation of existing vaccination candidates was required to investigate their safety, effectiveness, immunogenicity, undesired events, and limitations. The review was conducted by scanning online resources, and 17 studies were ultimately chosen. Several types of vaccine candidates with different methods against the COVID-19 virus, including inactivated, mRNA-based, recombinant, and nanoparticle-based vaccines, are being developed and marketed, according to our findings. Depending on data from the literature, we compared these vaccines in terms of side effects. We discovered that mRNA vaccines looked to be more effective, Adenovirus Viral vector COVID-19 vaccines had a higher incidence of side effects, while inactivated vaccinations had fewer side effects.\n\nPain at the injection site was the most commonly reported side effect, which conformed with the Fact sheets for post-vaccine trials (Pfizer-BioNTech COVID-19 vaccine side effects, 2023; Moderna COVID-19 vaccine side effects, 2023; Sinopharm COVID-19 vaccine side effects, 2023; AstraZeneca COVID-19 vaccine side effects, 2023; Bharat Biotech COVID-19 vaccine side effects, 2023); localized pain has been the most common side effect in numerous other injectable vaccine trials conducted previously (Nichol et al. 1996). In addition, tiredness, headaches, and fever were the most commonly reported systemic side effects by the participants. In contrast, the other effects weren’t much-repeated, but it was individual states (Figure 6D).\n\nAlthough there were no serious side effects reported in most of the studies, facial paralysis and Bell’s palsy were also observed in a few cases, which resulted in life-threatening adverse reactions (El-Shitany 2021; Ahamad 2020). Additionally, tachycardia, lymphadenopathy, and anaphylaxis were reported in a few patients (Riad et al. 2021; Almufty et al. 2021; Dziedzic et al. 2021). Anaphylaxis (an acute allergic reaction) following vaccinations can occur due to vaccination antigens, preservatives, and stabilizers in the vaccine formulation, or residual nonhuman proteins (Kim et al. 2021).\n\nAmong the included studies, three studies reported the incidence of oral and skin-related side effects. The most common oral side effects were vesicles (6.3%), bleeding gingiva (4.3%), oral paraesthesia (2.2%), dysgeusia (2.4%), blisters (36%), and halitosis (25.4%). While rash and urticaria (other than at the site of the injection) were the most reported skin-related side effects. There was a higher incidence of oral reactions in those who received only one vaccine dose (mRNA or viral vector-Based) and young age participants. While the prevalence was similar among males & females.\n\nSkin-related side effects were more prevalent among females (22.6%), those who received two vaccine doses (mRNA or viral vector-Based), and participants aged ≤ 43 > 43 years. In general, the viral vector-Based vaccines were associated with the highest risk of oral and skin-related side effects, while an mRNA vaccine is associated with the lowest. Three-fourths (75.1%) of the oral side effects appeared within the first week following vaccination. The most affected sites for skin-related side effects were the upper limb, face, chest (trunk), lower limb, and back. As for oral-related side effects, the most commonly affected areas were the lips, labial, tongue, palate, and gingiva.\n\nMost studies didn’t report delayed side effects, but Alhazmi’s study showed that delayed side effects were reported in 1% of the participants, with onset occurring at ≥ three days after vaccination (Alhazmi et al. 2021). It was observed that, in general, these reactions began on the first day after getting a vaccination, regardless of the dosage and most of these side effects resolve within one-three days. Fewer than 1% of studies participants required hospitalization. We discovered that mRNA vaccines looked to be more effective, while inactivated vaccinations had fewer side effects. The vaccine’s effectiveness far surpasses any concerns regarding side effects.\n\nFor studies that are based on the machine learning approach: Because there was no input data to train from and the model was learning from raw data without any prior knowledge, utilizing unsupervised learning in Abdulrahman et al. (2021) resulted in a less accurate outcome. This is time-consuming because the algorithm’s learning phase, which analyzes and calculates all options, might take a long. Although supervised learning is used in studies (Ahamad 2020; Hatmal et al. 2021) and obtains higher accuracy, it is not really considered high accuracy because they work on small datasets.\n\nAs for studies based on a statistical approach: There were many problems that were observed, the most important of which is the small sample size, as in the studies (Jayadevan 2021; Azimi et al. 2021). The most apparent problem in studies related to the side effects of vaccines is that the number of vaccinators of one sex exceeds the other in the sample of studies (Riad et al. 2021; Zahid 2021; Andrzejczak-Grządko et al. 2021; Kadali et al. 2021; Dziedzic et al. 2021), and this makes the results inaccurate. As is the case for the paper (Alhazmi et al. 2021), which was limited to a certain age group, namely young people, and ignored the rest of the age groups that constitute a large part of the community. Among the other gaps that were noted is not specifying which dose led to the emergence of the offending effects, as in the paper (Klugar et al. 2021), or relying on short-term effects in analyzing the side effects, as in the papers (Alamer et al. 2021; Kitagawa et al. 2022). “Table 5” below explains these studies in detail.\n\nAs far as the authors are aware, this is the first study to analyze various kinds of side effects of COVID-19 vaccines. Furthermore, this study pointed out possible factors that might contribute to these effects.\n\nThis study has some limitations. Despite not restricting language in the search process, we used only English-language databases, so publications in other languages have been missed, leading to publication bias. Studies did not provide information about certain groups, such as pregnant women. Furthermore, some of the participants in the analyzed studies may have reported side effects in a biased way. This could be related to the disparity in their educational levels. Therefore, the reliability of reported side effects may be affected by reporting bias in the included studies.\n\n\nConclusion and future works\n\nIn conclusion, this scoping systematic review investigated the side effects associated with COVID-19 approved vaccines including Pfizer BioNTech (Comirnaty), Moderna (mRNA-1273), Sinopharm (BBIP CorV), and AstraZeneca (ChAdOx1), as well as Bharat Biotech (Covaxin). Most of the side effects were mild, self-limiting, and common. Thus, they usually resolve within 1–3 days after vaccination. Currently, all types of vaccines that are approved still outweigh the possible risks of these vaccines, and the vaccinations are strongly recommended when it is available.\n\nIn future works, it is necessary to study the side effects more accurately, and that is done through the correct selection of the study community, which begins with the selection of the study population. The study sample must ensure appropriate representation of men and women, as gender bias was a major loophole in the studies we adopted and had a significant impact on the real results obtained.\n\nFigshare: PRISMA-P checklist for ‘COVID-19 vaccinations and their side effects: A scoping systematic review’. https://doi.org/10.6084/m9.figshare.22722592.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Data availability statement\n\nAll data supporting the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nAbdulrahman L, Abdulazeez M, Hasan D: COVID-19 World Vaccine Adverse Reactions Based on Machine Learning Clustering Algorithm. Qubahan Academic J. 2021; 1(2): 134–140. Publisher Full Text\n\nAhamad M: Adverse effects of COVID-19 vaccination: machine learning and statistical approach to identify and classify incidences of morbidity and post-vaccination reactogenicity. medRxiv. 2020. Publisher Full Text\n\nAl Khames Aga QA, Alkhaffaf WH, Hatem TH, et al.: Safety of COVID-19 vaccines. J. Med. Virol. 2021; 93(12): 6588–6594. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlamer E, Alhaffar A, Alrashed H, et al.: Side Effects of COVID-19 Pfizer-BioNTech mRNA Vaccine in Children Aged 12–18 Years in Saudi Arabia. Vaccines. 2021; 9(11): 1297. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlhazmi A, Alharbi O, Aljohani N, et al.: Evaluation of Side Effects Associated with COVID-19 Vaccines in Saudi Arabia. Vaccines. 2021; 9(6): 674. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlmufty H, Jasim HM, Al-Hadithi TS: Potential adverse effects of COVID19 vaccines among Iraqi population; a comparison between the three available vaccines in Iraq; a retrospective cross-sectional study. Diabetes Metab. Syndr. 2021; 15(5): 102207. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAndrzejczak-Grządko S, Czudy Z, Donderska M: Side effects after COVID-19 vaccinations among residents of Poland. Eur. Rev. Med. Pharmacol. Sci. 2021; 25: 4418–4421. PubMed Abstract \| Publisher Full Text\n\nAstraZeneca COVID-19 vaccine side effects: European Medicines Agency.[cited 2023 Jan 21]. Reference Source\n\nAzimi M, Ahmadi A, Jamshidi N, et al.: Adverse Effects of the COVID-19 Vaccine Reported by Lecturers and Staff of Kabul University of Medical Sciences, Kabul, Afghanistan. Infect. Drug Resist. 2021 Oct 4 [cited 2022 Apr 15]; 14: 4077–4083. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nBharat Biotech COVID-19 vaccine side effects: Bharat Biotech.[cited 2023 Jan 21]. Reference Source\n\nCenters for Disease Control and Prevention: Understanding mRNA COVID-19 vaccines.2021a [cited 2023 Jan 20]. Reference Source\n\nCenters for Disease Control and Prevention: Understanding viral vector COVID-19 vaccines.2021b [cited 2023 Jan 22]. Reference Source\n\nCovaxin COVID-19 vaccine: What to know about side effects: Medical News Today.[cited 2023 Jan 23]. Reference Source\n\nCOVID-19 vaccine: World Health Organization.[cited 2023 Jan 22]. Reference Source\n\nDai X, Xiong Y, Li N, et al.: Vaccine types. Vaccines-the History and Future. IntechOpen; 2019.\n\nDziedzic A, Bozek A, Jaroszynski A, et al.: Self-Reported Adverse Events of COVID-19 Vaccines in Polish Healthcare Workers and Medical Students. Cross-Sectional Study and Pooled Analysis of CoVaST Project Results in Central Europe. J. Clin. Med. 2021; 10(22): 5338. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEl-Shitany N: Minor to Moderate Side Effects of Pfizer-BioNTech COVID-19 Vaccine Among Saudi Residents: A Retrospective Cross-Sectional Study. Int. J. Gen. Med. 2021; 14: 1389–1401. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoyal K, Goel H, Baranwal P, et al.: Immunological mechanisms of vaccine-induced protection against SARS-CoV-2 in humans. Immuno. 2021; 1(4): 442–456. Publisher Full Text\n\nGrandini M, Bagli E, Visani G: Metrics for Multi-Class Classification: An Overview. arXiv:2008.05756v1 [stat.ML].August 13, 2020.\n\nHatmal MM, Al-Hatamleh MAI, Olaimat AN, et al.: Side Effects and Perceptions Following COVID-19 Vaccination in Jordan: A Randomized, Cross-Sectional Study Implementing Machine Learning for Predicting Severity of Side Effects. Vaccines. 2021; 9(6): 556. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHussien M: A systematic review for enabling of develop a blockchain technology in healthcare application: Taxonomy, substantially analysis, motivations, challenges, recommendations and future direction. J. Med. Syst. 2019; 43(10): 320. PubMed Abstract \| Publisher Full Text\n\nJayadevan R: Survey of symptoms following COVID-19 vaccination in India. medRxiv. 2021. Publisher Full Text\n\nKadali R, Janagama R, Peruru S: Non-life-threatening adverse effects with COVID-19 mRNA-1273 vaccine: A randomized, cross-sectional study on healthcare workers with detailed self-reported symptoms. J. Med. Virol. 2021; 93(7): 4420–4429. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim MA, Lee YW, Kim SR, et al.: COVID-19 vaccine-associated anaphylaxis and allergic reactions: consensus statements of the KAAACI Urticaria/Angioedema/Anaphylaxis Working Group. Allergy Asthma Immunol. Res. 2021; 13(4): 526–544. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKitagawa H, Kato H, Miyakawa K: Adverse reactions to the BNT162b2 and mRNA-1273 mRNA COVID-19 vaccines in Japan. J. Infect. Chemother. 2022; 28(4): 576–581. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKlugar M, Riad A, Karch A: Side Effects of mRNA- Based and Viral Vector-Based COVID-19 Vaccines among German Healthcare Workers. Biology. 2021; 10(8): 752. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLombard M, Pastoret PP, Moulin AM: A brief history of vaccines and vaccination. Revue Scientifique et Technique-Office International des Epizooties. 2007; 26(1): 29–48. Publisher Full Text\n\nMahendra P: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2): An Update. Cureus. 2020; 12(3): e7423. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarsa L: Why vaccine side effects really happen, and when you should worry. National Geographic; 2021 May 13 [cited 2022 Nov 11]. Reference Source\n\nMarsa L: Why do vaccine side effects really happen, and when you should worry. National Geographic; [cited 2023 Jan 22]. Reference Source\n\nModerna COVID-19 vaccine side effects: US Food and Drug Administration.[cited 2023 Jan 22]. Reference Source\n\nMoher D, Liberati A, Tetzlaff J, et al.: Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med. 2009; 6(7): e1000097. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNational Institute of Allergy and Infectious Diseases: Vaccine types.2021 [cited 2023 Jan 22]. Reference Source\n\nNichol KL, Margolis KL, Lind A, et al.: Side effects associated with influenza vaccination in healthy working adults: a randomized, placebo-controlled trial. Arch. Intern. Med. 1996; 156(14): 1546–1550. Publisher Full Text\n\nPaules CI, Marston HD, Fauci AS: Coronavirus infections-more than just the common cold. JAMA. 2020; 323(8): 707–708. PubMed Abstract \| Publisher Full Text\n\nPfizer-BioNTech COVID-19 vaccine side effects: US Food and Drug Administration.[cited 2023 Jan 22]. Reference Source\n\nPlotkin SA: Vaccines: past, present and future. Nat. Med. 2005; 11(Suppl 4): S5–S11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRiad A, Pokorná A, Attia S, et al.: Prevalence of COVID-19 Vaccine Side Effects among Healthcare Workers in the Czech Republic. J. Clin. Med. 2021; 10(7): 1428. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaeed BQ, Al-Shahrabi R, Alhaj SS, et al.: Side effects and perceptions following Sinopharm COVID-19 vaccination. Int. J. Infect. Dis. 2021; 111: 219–226. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSahin A: 2019 novel coronaviruses (COVID-19) outbreak: a review of the current literature. Eur. J. Med. Oncol. 2020; 4: 1–7. Publisher Full Text\n\nSalisbury D, Ramsay M, Noakes K: Immunisation Against Infectious Diseases. The Stationery Office; 2006.\n\nSerious AEFI - World Health Organization (WHO): World Health Organization.[cited 2023 Jan 22]. Reference Source\n\nShahzamani K, Mahmoudian F, Ahangarzadeh S, et al.: Vaccine design and delivery approaches for COVID-19. Int. Immunopharmacol. 2021 Jul; 100: 108086. Epub 2021 Apr 20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharma A: severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): a global pandemic and treatment strategies. Int. J. Antimicrob. Agents. 2020; 56: 106054. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSinopharm COVID-19 vaccine side effects: Food and Drug Administration Philippines.[cited 2023 Jan 22]. Reference Source\n\nTavilani A, Abbasi E, Ara FK, et al.: COVID-19 vaccines: Current evidence and considerations. Metab Open. 2021; 12: 100124. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVaccine Characteristics: VIEW-HUB.[cited 2023 Jan 23]. Reference Source\n\nVarsavsky T: Detecting COVID-19 infection hotspots in England using large-scale self-reported data from a mobile application: a prospective, observational study. Lancet Public Health. 2021; 6(1): e21–e29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWeiss SR, Navas-Martin S: Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiol. Mol. Biol. Rev. 2005; 69(4): 635–664. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWHO Collaborating Centre for Vaccine Safety: How do vector vaccines work?2021a [cited 2023 Jan 20]. Reference Source\n\nWorld Health Organization: How do vaccines work? Body’s response to vaccines—29 December 2020. World Health Organization.Reference Source\n\nWHO Collaborating Centre for Vaccine Safety: How do inactivated vaccines work [Internet]. 2021b [cited 2023 Jan 22]. Reference Source\n\nWorld Health Organization: COVID-19 vaccines [Internet]. 2021c. Reference Source\n\nZahid M: Unfolding the Mild to Moderate Short-Term Side Effects of Four COVID-19 Vaccines Used in Bahrain: A Cross-Sectional Study. Vaccines (Basel). 2021; 9(11). PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "218626", "date": "24 Nov 2023", "name": "Yongbin Wang", "expertise": [], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript performs a scoping systematic review to explore the COVID-19 vaccinations and their side effects, this topic is very interesting and has important guiding significance for evaluating the effectiveness of vaccines. Although this paper did a good job, the current version needs to be further improved by a minor revision.\nTitle: The title is concise and summarizes the content of the article.\n\nAbstract: The abstract is concise and effectively outlines the research's objectives, which include evaluating the COVID-19 vaccinations and their side effects. However, several minor points need to be revised:\nResults need to provide figures to support the findings instead of something like a conclusion. Conclusion should give a summary of adverse reactions of the vaccine.\n\nIntroduction: The introduction provides adequate context for understanding the research problem and the primary hypotheses. Also, some minor points need to be revised:\nParagraph 1 should summarize the severity of the impact of COVID-19, including the number of cases and deaths. Paragraph 4 should provide the recent figures regarding the vaccine doses, this data is available on the WHO website. It should be highlighted that the duration of application of COVID-19 vaccines is short, and adverse effects are inconsistent due to different types of vaccines.\n\nBackground: This part is well-written, particularly the method used in this study, giving an adequate description. Here just needs a very minor revision:\n“A brief overview of the vaccine” should be removed. Check \"from 2019 to 2022 to select eligible research publications.\"\n\nResults: The results are also adequate. Factors associated with side effects of COVID-19 vaccines can provide a summary in Table or Figure.\n\nDiscussion: The discussion also gives a full comparison with other studies. But some minor points should be addressed:\nIn the discussion, can the authors explain the causes of adverse reactions of different vaccines from the mechanism level? Some new research results have been published recently, and the discussion needs to be supplemented and fully compared.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "12473", "date": "26 Sep 2024", "name": "Hind Monadhel", "role": "Author Response", "response": "Dear Dr. Wang, Thank you for your thoughtful and constructive feedback on our manuscript. We have carefully considered your comments and made the necessary revisions to improve the paper. We sincerely appreciate your insightful suggestions, which have significantly contributed to strengthening the manuscript" } ] }, { "id": "309618", "date": "23 Aug 2024", "name": "Bekir Kocazeybek", "expertise": [ "Reviewer Expertise Microbiology", "immunology" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nCOVID-19 VACCINATIONS AND THEIR SIDE EFFECTS: A SCOPING SYSTEMATIC REVIEW It was evaluated according to the PRISMA 2020 Checklist. The article needs major revision before indexing. My recommendations: Is the Grandini et al.2020 study included in the 17 selected studies? If so, it is not included in Table 5, where all studies are shown. It is mentioned as if Hatmal et al.2021 was included in the study. Although it has an explanation and evaluation, its name is not in Table 5 and the list of studies. It is recommended that notifications be made in accordance with PRISMA 8- “Indicate the methods used to decide whether a study meets the criteria for inclusion in the review, including how many reviewers screened each record and whether each report was worked on independently and, if appropriate, details of the automation tools used in the process.” It is recommended to make notifications in accordance with PRISMA 9- “Specify the methods used to collect data from reports, how many reviewers collected data from each report, whether they worked independently, the process for obtaining or approving data from study investigators, and details of automation tools used in the process, if any.” It is recommended to add a study in accordance with PRISMA 16-b “Cite studies that may appear to meet the inclusion criteria but were excluded and explain why they were excluded.” PRISMA 17- “Cite each included study and provide its characteristics.” Ma’mon,2021 is mentioned in the study but its description is not included in the Review of the conducted studies section. It is recommended to make notifications in accordance with PRISMA 18- “Provide assessments of risk of bias for each included study.” It is recommended to make notifications in accordance with PRISMA 22- “Provide assessments of precision (or reliability) as evidence for each outcome assessed.”\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Partly", "responses": [ { "c_id": "12474", "date": "26 Sep 2024", "name": "Hind Monadhel", "role": "Author Response", "response": "Dear Dr. Bekir Kocazeybek, Thank you for your thoughtful and detailed comments. I appreciate the opportunity to clarify and address the points you raised. Regarding Grandini et al. (2020): I would like to clarify that Grandini et al. (2020) is cited as a reference for the equation used in the analysis but is not included among the 17 studies reviewed. Therefore, it is not listed in Table 5. I appreciate your attention to this detail, and I hope this resolves any confusion. Regarding Hatmal et al. (2021): You are correct that Hatmal et al. (2021) is mentioned in the manuscript. This study is included among the 17 studies in Table 5, but it was mistakenly cited under the name M. Ma'mon et al. I have now corrected this citation discrepancy to ensure consistency throughout the document. I hope this resolves the concern. PRISMA 18 - Risk of Bias: The recommendation to assess the risk of bias for each included study has already been addressed in the \"Gaps in Conducted Studies\" section, where I discuss limitations in study design, sample size, and methodological weaknesses that indicate potential bias. PRISMA 22 - Assessments of Precision: In line with PRISMA 22, I have now included assessments of precision (or reliability) for some outcome, which can be found in the discussion section of the manuscript. Once again, I sincerely appreciate your valuable feedback and your effort to ensure the rigor of the manuscript. I hope these revisions address your concerns, and I look forward to any further comments you may have." } ] } ]	1	https://f1000research.com/articles/12-604
https://f1000research.com/articles/13-813/v1	18 Jul 24	{ "type": "Systematic Review", "title": "Exploring the landscape of digital servitization: A systematic review", "authors": [ "Hendri Ginting", "Hamidah Nayati Utami", "Riyadi Riyadi", "Benny Hutahayan", "Hamidah Nayati Utami", "Riyadi Riyadi", "Benny Hutahayan" ], "abstract": "Background Digital servitization is a strategic transformation where companies adopt a service-focused approach in response to the prevailing trend of digitalization. Utilizing digital technology, businesses manage product and service operations and develop new value propositions. Further research into digital servitization is essential for maintaining competitiveness and meeting evolving market demands globally. This study aims to comprehend the evolution of digital services from theoretical and practical viewpoints and examines how these challenges are tackled.\n\nMethods Utilizing a systematic literature review methodology, the study adopts the PRISMA approach to identify 26 pertinent articles from a pool of 340 papers obtained through a SCOPUS database search. These papers were published between 2019 and 2024 and were retrieved using the keywords (‘digitalization OR digital AND servitization OR servitization’). The selection process involved scrutinizing titles, abstracts, and keywords based on predefined criteria.\n\nResults The findings reveal that current digital servitization research emphasizes five determinant variables: digitization, servitization, manufacturing servitization, process innovation, and product innovation. Additionally, response variables influenced by digital servitization were identified, including firm competitiveness, firm performance, financial performance, firm profitability, and sustainable performance.\n\nDiscussion The results of this review point to inconsistencies, underscoring the necessity for additional research into the factors influencing digital servitization across companies beyond the manufacturing sector. This highlights the importance of gaining a deeper understanding of digital servitization strategies and their impacts across various industries. By expanding the scope of research to include a broader range of sectors, researchers can provide more comprehensive insights into the complexities and nuances of digital servitization adoption. This broader perspective enables a more thorough examination of the challenges and opportunities associated with implementing digital servitization strategies, ultimately contributing to a richer understanding of its implications for businesses across diverse industries.", "keywords": [ "Digital Servitization", "Systematic Literature Review", "PRISMA", "Determinants" ], "content": "1. Introduction\n\nIn the ever-evolving digital era, companies across various industry sectors face significant pressure to adapt to the rapidly changing business landscape. One of the notable transformations in business strategies is the shift from product-centric models towards digitally-oriented services. Digitalization is compelling many organizations to explore ways of shifting their focus away from a product-centered approach and towards offering services that are digitally oriented (Kohtamäki et al., 2020; Kowalkowski et al., 2017). By leveraging digital technology, these organizations aim to generate value in their processes and provide improved customer experiences. This effort has led to the emergence of a new concept in servitization literature, known as digital servitization (Coreynen et al., 2020; Gebauer et al., 2020; Paschou et al., 2020).\n\nDigital servitization involves the use of digital technology to integrate services into existing products, creating added value for customers, and improving operational efficiency. Digital servitization represents a strategic transformation where companies are required to transition from a preplanned, product-centric mindset to a collaborative, service-focused approach in order to adapt to new production methods and collaboration models in the digital age (Vargo & Lusch, 2017; Chen et al., 2023). In the realm of digitalization, organizations utilize digital technology to efficiently manage their product and service operations, creating innovative value propositions such as intelligent products, services, and solutions (Vendrell-Herrero et al., 2017). When viewed from the servitization perspective, companies incorporate customer-centric services into their existing product offerings.\n\nEngaging in the digital ecosystem, digital servitization links internal entities and external partners to build a service framework facilitated by technology, ongoing interaction, and procedural collaboration (Bustinza et al., 2018). In this context, digital products serve as boundary objects within the service system, enabling the integration of resources and activities between service providers and users, which in turn enhances their interaction and collaboration. Through the digital servitization transformation, sophisticated business models are developed through process innovation (Hilbolling et al., 2022) and collaboration with diverse stakeholders in a more advanced, interactive manner, thereby embedding themselves within the digital ecosystem.\n\nThe digital servitization process involves a simultaneous and dynamic interaction between business models and digital technologies (Chen et al., 2021). This transition is intricate and demands that companies cultivate fresh capabilities and foundational elements at a micro level to facilitate the change (Chirumalla et al., 2023). The shift towards digital servitization requires organizations to adapt their structures, processes, and cultures to accommodate the new business model (Sklyar et al., 2019).\n\nDigital servitization results in the creation of digital product service systems, amalgamations of physical products and intangible services tailored to meet the specific requirements of individual customers (Lerch & Gotsch, 2015). Yet, the body of literature concerning digital servitization remains constrained, primarily concentrating on select digital technologies and particular industries (Paschou et al., 2020). Hence, additional research is warranted to delve into the potential advantages and areas of application for digital servitization.\n\nHowever, despite the significant potential associated with digital servitization, numerous challenges must be addressed, such as technology integration, complex data management, information security, and cultural changes within organizations. Therefore, a deeper understanding of this concept through systematic and comprehensive research is required.\n\nIn this context, systematic literature research on digital servitization can be a highly valuable tool. It can help identify trends, developments, and weaknesses in the existing literature, as well as provide a clear view of the extent to which this concept has been studied and applied across various industry sectors. Based on this, the Research Questions (RQ) to be answered in this study are as follows:\n\nRQ1: What are the definitions of digital servitization based on previous literature?\n\nRQ2: In which industries is digital servitization extensively researched?\n\nRQ3: What are the determinants variable of digital servitization?\n\nRQ4: What are the factors influenced by digital servitization?\n\nThis paper conducts a systematic literature review (SLR) on digital servitization, as SLRs offer a comprehensive summary of prior research on the topic and help identify knowledge gaps, thereby highlighting areas for future investigation. The primary objective of this paper is to enrich the current body of literature on digital servitization in two key ways: first, by presenting a thematically organized classification of existing research, and second, by using the SLR findings to propose detailed factors that influence digital servitization for future research.\n\n\n2. Literature review\n\nThe resource-based view (RBV) assumes that a company is an entity that maximizes profits guided by rational managers operating in a specific market, reaching a level that can be predicted and moving towards equilibrium (Bromiley & Papenhausen, 2003; Leiblein, 2003). RBV emerged to comprehend how combinations of valuable, rare, inimitable, non-substitutable, and organized resources (VRIN/O) can yield competitive advantages for a company (Barney, 1991; Penrose, 1959). Resources need to be rearranged to capitalize on new business opportunities, such as digital servitization (Kohtamäki et al., 2019).\n\nResources are tangible and intangible assets of an organization, where the organization can accumulate resources from external sources that are treated as crucial assets in the production process (Kraja, 2018). The RBV theory suggests that organizations should focus on managing resources that can generate higher value and disregard some resources with lower opportunities to enhance value propositions (Wernerfelt, 2014). Huikkola and Kohtamäki (2017) pinpointed essential resources and strategic procedures that establish strategic competencies and competitive edges. These competencies encompass fleet administration, technological advancement, mergers and acquisitions, value evaluation, project oversight, supplier network administration, and cooperative value generation.\n\nThe digital aspect of digital servitization presents opportunities for enhancing process and capability development, resulting in enhanced value creation and capture, improved efficiency in customization, and more streamlined order fulfillment processes. It also facilitates effective resource restructuring as companies venture into new business prospects, including untapped customer markets, innovative projects, and smart solutions (Kohtamäki et al., 2019). Overall, a company’s readiness to adapt to digital servitization will hinge on its history and its capability to restructure both its internal operations and external resource pool (Sklyar et al., 2019).\n\n\n3. Methods\n\nThis article seeks to offer profound insights into digital servitization, identifying emergent key concepts, and delineating the challenges and opportunities encountered by firms considering this approach. Through a systematic literature review, a more comprehensive comprehension of how digital servitization has reshaped corporate operations and customer interactions in the constantly evolving digital age can be attained.\n\nThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) approach was used in this systematic literature review (Farisyi et al., 2022; Liberati et al., 2009; Moher et al., 2015). The PRISMA approach ensures transparency and clarity in reporting systematic literature reviews by using an evidence-based checklist (Ginting, 2024b) connected to a four-phase flowchart. By applying the PRISMA approach, one may reduce bias, lessen the impact of chance, and improve the quality of data analysis.\n\nThe information search was carried out on a comprehensive academic research database, specifically Elsevier (SCOPUS), which houses extensive collections of scholarly literature. The search included articles published between 2019 and 2024 to ensure the literature used in the research analysis remains current and up-to-date. The search was completed on January 15, 2024.\n\nTwo sets of keywords associated with the concepts of servitization and digitalization were chosen and utilized in tandem. The selected keywords for this research are as follows: ‘digitalization OR digital AND servitization OR servitisation’. The Inclusion Criteria (IC) employed as guidelines in conducting the Systematic Literature Review are outlined below:\n\nIC1: Articles are original documents that have undergone a peer-review process and were published between 2019-2024.\n\nIC2: Articles are original documents written in the English language.\n\nIC3: Research that employs quantitative methods.\n\nIC4: Studies aimed at identifying factors influenced by digital servitization.\n\nIn detailing the Inclusion Criteria (IC), IC1 emphasizes that only articles that are original documents and peer-reviewed, published between 2019-2024, will be considered. Furthermore, IC2 indicates that the selected articles must be in the English language. This is because research conducted in English generally provides the most current information for that period, ensuring more accurate updates. IC3 ensures that only research using a quantitative approach will be taken into account in this study. Quantitative methods are used to collect numerically measurable data, providing a more structured framework for analyzing relationships between variables and identifying indicators in measuring digital servitization. Meanwhile, IC4 underscores that the studies focused on in this research must have a specific aim of identifying factors influenced by digital servitization. Furthermore, articles that were not fully accessible were excluded from the study.\n\nThe subsequent step involved identifying publications and conducting practical screening, resulting in the identification of 340 papers. Following screening with IC1 and IC2, 310 studies were excluded, and the remaining studies were moved to the screening phase. At this stage, the titles, abstracts, and keywords of the 310 collected papers were scrutinized for relevance to the research objectives, resulting in 62 studies. Subsequently, the full text of the remaining 62 publications was meticulously reviewed, with only articles deemed capable of contributing to answering the research questions being selected. Ultimately, based on the predefined criteria, namely IC3 and IC4, 26 papers were chosen and analyzed to compile knowledge in this research field and identify potential knowledge gaps and future research directions.\n\nThe information gleaned from each article is outlined systematically, encompassing details such as the publication year, authors, country of origin and sample size, research aims, variables examined, aspects affected by digital servitization, and findings concerning its influence on dependent variables. Figure 1 provides a comprehensive depiction of the stages involved in this systematic literature review (Figure 1 also uploaded in Ginting (2024a)).\n\nEach study was independently assessed by four authors. To ensure objectivity and reduce the likelihood of bias in the evaluation process, the authors worked independently. Any discrepancies between the authors’ assessments were resolved through discussion and consensus.\n\nTo determine the degree of information completeness in accomplishing the research objectives, data was gathered from all of the chosen papers. A more thorough summary of the studies that need to be studied and how they can particularly answer the research questions is also provided by the extraction process. These actions are predicated on the previously mentioned selection procedure. After extraction, the data is sorted and entered into a worksheet. Cruzes & Dyba (2011) suggest using thematic synthesis to synthesize the findings. Additionally, an integrated synthesis process technique is used to guarantee that all study goals are met.\n\n\n4. Results\n\nThe SCOPUS database search using the keywords (‘digitalization OR digital AND servitization OR servitization’) produced 340 papers published between 2019 and 2024 in English. These papers underwent examination and selection based on IC2 and IC3 criteria, focusing on titles, abstracts, and keywords, resulting in 62 articles remaining. One article remained inaccessible or uncategorized among those excluded or not researched. Ultimately, 26 articles were left for further analysis after this procedure. Selected articles are uploaded in Ginting (2024c) using Figshare.\n\nNumerous journal publications on digital servitization are issued each year, with a notable increase observed in 2019. These journals utilize a combination of qualitative and quantitative methodologies. This trend underscores the ongoing relevance of research on digital servitization in recent years, as illustrated in Figure 2 below.\n\nBetween 2019 and 2024, numerous countries, including China, Finland, France, Germany, Italy, Norway, Spain, Sweden, Switzerland, and the United Kingdom, contribute to journals addressing digital servitization. Recent data indicate the ongoing relevance of research on digital servitization in these countries, as illustrated in Figure 3.\n\nBased on an analysis of reputable international journals, the percentage data of articles published in 18 major fields of study over the last five years is presented in Figure 4. 35% of the articles focus on business, management, and accounting. Engineering and computer science represent 17% and 13% of the total scholarly publications. The dominance of publications in applied fields such as business, engineering, and computer science reflects the dynamic needs of the industrial world for innovations in business models, technology, and digital solutions in the current era of the Industrial Revolution. Meanwhile, the smaller proportion of articles in decision sciences and other fields indicates the limited scope of multidisciplinary studies and fundamental research in addressing the complex challenges faced by modern society.\n\nAdditionally, a qualitative synthesis was conducted on the 26 chosen articles, as illustrated in Table 1.\n\nBuilding upon the analysis of the 26 selected articles, determinants of digital servitization are further scrutinized utilizing the following additional criteria:\n\n1. Digital servitization is used as an independent and dependent variable.\n\n2. Digital servitization is assessed or quantified in diverse forms, serving as both an independent and dependent variable.\n\n3. Determinants and response included as research outcomes are those examined in at least two articles and used as dependent and response variables.\n\nConsidering the criteria above, Table 2 presents the determinants, items, result, conclusion, and references related to digital servitization.\n\nApart from examining digital servitization as a dependent variable, this research also considers it as an independent variable. Table 3 below presents the variable responses, items, results, conclusions, and references related to digital servitization as an independent variable.\n\n\n5. Discussion\n\nDigital servitization is a multifaceted and continuous procedure, given its amalgamation of servitization and digitalization (Chen et al., 2021). As businesses increasingly integrate digital technologies and reshape their business models, they must confront the challenges and opportunities inherent in this transition, including adjusting to more dynamic and interconnected markets (Chen et al., 2021). Digital servitization can occur within ecosystems, where companies work together to create value-creating and capturing systems (Kohtamäki et al., 2019).\n\nEmploying digital technologies like big data and cloud computing empowers companies to gather and analyze extensive datasets, offering valuable insights and stimulating innovation (Hacioglu, 2019). Digital servitization frequently entails adopting novel business models centered around offering packages comprising products, services, and digital tools like IoT, big data, and cloud computing (Hacioglu, 2019). Digital servitization enables connectivity between products, services, and customers, allowing for better monitoring, control, and optimization (Chen et al., 2021).\n\nDigital servitization, as defined by Parate et al. (2022), encompasses leveraging digital technology to elevate existing business models or devise new ones. In order to further develop this idea, Paschou et al. (2020) present a digital servitization maturity model that includes elements like strategy, business procedures, customer experience, and organizational culture. In their contribution to this conversation, Tronvoll et al. (2020) identify three critical turning points that are essential for successful digital servitization: moving from hierarchy to partnership, from scarcity to abundance, and from planning to discovery. Finally, Lerch & Gotsch (2015) examines the fusion of digitalization with service innovation, underscoring the potential ramifications for service provision.\n\nResearch Question 2 (RQ2) delves into the industries where digital servitization has been extensively researched. A review of the literature indicates that, in the context of digital servitization, a wide range of industries have garnered substantial scholarly attention. Digital servitization study finds a dominant domain in the manufacturing industry. Several research papers examine the incorporation of digital technology into conventional manufacturing processes, delving into the ways in which this transition to service-oriented business models impacts the performance, sustainability, and innovation of firms. Another notable industry is the information technology (IT) sector, given its intrinsic connection to digital technologies. Research in this domain often focuses on how IT firms leverage digitalization to offer innovative service solutions, enhance customer experiences, and drive competitive advantage. Additionally, the automotive industry garners considerable attention, with studies exploring how automotive companies embrace digital technologies to offer value-added services alongside traditional product offerings. The healthcare sector is also a significant area of research interest, particularly regarding the adoption of telemedicine, remote patient monitoring, and personalized healthcare solutions. Moreover, the financial services, retail, energy, and telecommunications industries all feature prominently in digital servitization research, reflecting the widespread adoption and impact of digital technologies on business models, value propositions, and customer experiences across diverse sectors. Understanding the nuances of digital servitization within specific industries is crucial for practitioners and policymakers navigating the evolving landscape of service-driven economies.\n\nResearch Question 3 (RQ3) aims to discern the determinants variables of digital servitization as elucidated in Table 2. Each determinant variable of digital servitization, in a more complex and comprehensive manner, can be elucidated within the following subsections:\n\n5.3.1 Digitalization\n\nDigitalization plays a pivotal role in driving the adoption of digital servitization, as digitally mature companies possess the capabilities and infrastructure essential for implementing such business models. In other words, companies actively employing digital technology are more prepared and inclined to adopt digital servitization strategies (Vendrell-Herrero et al., 2017). A study conducted by Kohtamäki et al. (2020) on the relationship between digitization and servitization concluded that the level of adoption of digital technology by a manufacturing company significantly affects its ability to implement the digital servitization business model. This is consistent with earlier findings indicating the positive role of operational digitization and digital infrastructure in enabling servitization in the manufacturing industry (Kohtamäki et al., 2020).\n\n5.3.2 Servitization\n\nServitization pertains to the extent to which services are integrated into the product offerings of a manufacturing company. Coreynen et al. (2020) define servitization as the transformation of a business model from a product-focused approach to a solution-focused one by integrating product-service bundles. The higher the adoption of a hybrid product-service business model, the greater the likelihood of the company implementing digital servitization strategies. Both Bortoluzzi et al. (2022) and Rakic et al. (2022) identified a significant positive correlation between the extent of servitization in manufacturing firms and the adoption of digital servitization. This aligns with a longitudinal study by Coreynen et al. (2020), which concluded that as a company’s age increases, it is typically accompanied by an increase in the complexity of product-service offerings, thereby driving the adoption of digital solutions to integrate and manage these offerings.\n\n5.3.3 Manufacturing servitization\n\nManufacturing servitization, refers to the degree of integrating services into the manufacturing operations and product offerings of an industrial company. Neely (2008) defines manufacturing servitization as a phenomenon where manufacturing companies offer additional services related to their products. As the proportion of a company’s revenue derived from services increases, so does the level of manufacturing servitization, providing an opportunity to implement digital servitization to facilitate the delivery of these service values (Neely, 2008; Visnjic et al., 2018). Agarwal et al. (2022) and Chen and Zhang (2021) both concluded that companies embracing a high degree of manufacturing servitization are also inclined to adopt digital platforms and solutions. The aim is to integrate and present product-service offerings effectively. Put simply, there exists a correlation between a high degree of manufacturing servitization and the adoption of digital technology to streamline and improve efficiency in delivering products and services. Consistent with a study conducted by Visnjic et al. (2018), it is concluded that manufacturing servitization creates new opportunities for implementing digital technology to support the operationalization of business models.\n\n5.3.4 Process innovation\n\nProcess innovation, refers to the development and introduction of new production, distribution, or management methods by manufacturing companies that significantly enhance the quality and efficiency of their internal processes (Garcia & Calantone, 2002). The more successful process innovations implemented, the higher the flexibility and operational capabilities of the company to adopt the digital servitization business model to enhance service quality for customers (Raddats et al., 2014; Valtakoski, 2017). Opazo-Basáez et al. (2022) and Vendrell-Herrero et al. (2023) found that a higher level of process innovation positively influences the ability of manufacturing companies to implement digital servitization strategies. The transformation and improvement of internal production processes through automation serve as a crucial foundation for adopting the digital servitization business model to enhance the value proposition to consumers (Martín-Peña et al., 2018).\n\n5.3.5 Product innovation\n\nProduct innovation entails a company’s creation and introduction of new products or services that represent a significant improvement over previous offerings, based on its performance (Schumpeter & Swedberg, 2021). The more innovative products are introduced, the greater the incentive for manufacturing companies to implement digital servitization strategies to support the delivery of value from these innovative products to consumers (Frank et al., 2019). Opazo-Basáez et al. (2022) and Vendrell-Herrero et al. (2023) found a positive impact of the number of product innovations on the ability of companies to implement the digital servitization business model. The success of developing smart/connected products requires supporting digital service offerings to integrate and optimize the value of the products for consumers (Rymaszewska et al., 2017; Kohtamäki et al., 2020).\n\nResearch Question 4 (RQ4) aims to understand the variables that can be influenced by digital servitization as described in Table 3. Each variable that can be influenced by digital servitization is discussed in a more complex and comprehensive manner in the following subsections:\n\n5.4.1 Firm competitiveness\n\nDeveloping a unique value proposition that differentiates a business from its rivals is one way to become competitive (Porter, 1997; Chen et al., 2023). Gebauer and Fleisch (2007) claim that servitization enables businesses to make five times as much money from services as they do from products, guaranteeing a consistent flow of income regardless of volatility in the economy and boosting competitiveness. Therefore, businesses can obtain a competitive edge by providing long-term, comprehensive, and high-quality services that are focused on products or customers (Chen et al., 2023). Furthermore, servitization in the manufacturing sector has a big effect on business performance and global competitiveness. Leading manufacturing companies that implement servitization strategies usually hold onto essential components like production, design, and R&D, which allows them to react quickly to needs from around the world (Huang et al., 2024).\n\n5.4.2 Firm performance\n\nAccording to Miao et al. (2023), servitization plays a mediating role in industrial digitalization’s enhancement of firm performance. By harnessing the advantages of servitization, digitalization eventually boosts business performance. According to Martín-Peña et al. (2020), servitization improves customer interactions, lowers costs, increases efficiency, and provides integrated packages by augmenting digitalization. In a similar vein, Bortoluzzi et al. (2022) found that servitization and firm success were positively correlated. But regardless of a company’s level of technical maturity, Rakic et al. (2022) discovered that only Big Data-based digital solutions had a favorable and meaningful impact on business performance. However, in order to fully comprehend the effects of digital servitization, it is important to recognize a number of services that have a detrimental and significant influence on the performance of the firm. Examples of these services include software development, digital solutions, and PRS (Product-Related Services) in low-tech companies.\n\n5.4.3 Financial performance\n\nA company’s ability to create income, turn a profit, and increase its market value is referred to as its financial performance (Westerman et al., 2014). A competitive advantage and maybe better financial performance can result from strategic adjustments made to a business model to make it more customer-centric (by servitization) and data-driven (via digitalization) (Abou-Foul et al., 2021). According to Abou-Foul et al. (2021), there is a possibility for digitalization and data-driven solutions to improve financial performance and servitization. This might lead to the development of more effective market offerings. To realize the benefits of digitalization and attain positive performance effects, manufacturing organizations may need to invest in portfolios of sophisticated services, as digitalization alone may not be sufficient to produce favorable financial performance effects (Kohtamäki et al., 2020). To maximize the benefits of digitalization and improve the financial performance of manufacturing firms, servitization is a prerequisite (Kohtamäki et al., 2020).\n\n5.4.4 Firm profitability\n\nBy offering unique product-service combinations, sustainable business models and servitization-related competencies have the potential to increase a company’s competitive edge and profitability (Kohtamäki et al., 2024). According to Kohtamäki et al. (2024), a focus on sustainability has a direct negative effect on a company’s profitability. However, servitization plays a positive moderating influence, highlighting its importance in producing profits from this concentration on sustainability. Additionally, Vendrell-Herrero et al. (2023) contend that dual innovation enterprises have higher profitability when they use digital service innovation.\n\n5.4.5 Sustainable performance\n\nIn today’s rapidly evolving business environment, digital servitization emerges as a pivotal strategy for firms aiming to enhance their sustainable performance (Paiola et al., 2021). By offering value-added services aligned with customer needs, organizations can align their objectives, leading to heightened customer satisfaction and overall performance. Through servitization, firms can cultivate enduring customer relationships, fostering a sustainable revenue stream crucial for sustained performance. Moreover, servitization propels product enhancement efforts, as companies continuously strive to improve their offerings to meet evolving customer demands (Behl et al., 2024). Achieving sustainable performance necessitates companies to adapt to market dynamics and prioritize delivering solutions that address customer needs. Behl et al. (2024) argue that digital servitization positively influences a firm’s sustainable performance.\n\nPham and Vu (2022) define sustainable-oriented organizational performance as an organization’s capacity to efficiently and effectively utilize available resources to understand the interconnectedness of ecological, social, and economic dimensions of sustainability. They illustrate how digital servitization is becoming increasingly vital to organizational success in a sustainable manner by outlining its impact on sustainable-oriented organizational performance. Undoubtedly, a focused approach on these opportunities would enhance operational efficiency (Coreynen et al., 2017).\n\n\n6. Implications\n\nFor business practitioners, the findings underscore the critical importance of adopting digital technologies and transitioning to service-centric business models to enhance operational efficiency and customer value. Companies should invest in IoT, big data, and cloud computing to create intelligent products and services while developing capabilities related to digitization, servitization, and innovation. This strategic transformation can improve customer experience through better monitoring, control, and optimization of services, leading to higher customer satisfaction and loyalty. Additionally, integrating digital and service-oriented strategies can help businesses achieve sustainable competitive advantages, enhancing their long-term profitability and market position.\n\nFor policymakers, the study highlights the need to create and implement regulations that support the adoption of digital servitization. Developing legal frameworks that ensure transparency, efficiency, and investor confidence is crucial. Policymakers should provide incentives for businesses to invest in digital technologies and service-oriented models, such as tax breaks, grants, and other financial support mechanisms. Investing in necessary digital infrastructure, improving internet connectivity, data security, and digital literacy, is also essential. Encouraging collaboration between the public and private sectors can foster innovation and effective implementation of digital servitization strategies by facilitating partnerships and networks that promote knowledge sharing and resource pooling.\n\nThe study contributes to the expansion of knowledge by highlighting the need for broader research on digital servitization beyond the manufacturing sector. Future studies should explore its application in various industries to provide a comprehensive understanding of its impacts and potential. An interdisciplinary approach, incorporating insights from business management, engineering, and information technology, can enhance the theoretical framework of digital servitization. This can lead to a more holistic understanding of the concept.\n\nMethodologically, the study suggests the inclusion of qualitative and mixed-methods research to capture the experiential and contextual nuances of digital servitization, providing richer, more detailed insights that quantitative methods alone might miss. Longitudinal studies are also recommended to understand the long-term effects and evolution of digital servitization strategies, identifying trends, challenges, and best practices over time. Conceptually, the identification of key determinant and response variables contributes to the theoretical development of digital servitization. Future research should build on these findings to refine and expand the theoretical constructs associated with digital servitization. Exploring the causal relationships between digital servitization and various performance metrics can deepen theoretical insights, strengthening the theoretical foundation of the field.\n\n\n7. Conclusions\n\nIn conclusion, adhering to the established inclusion and exclusion criteria, a total of 26 studies were selected and identified. The primary analysis revealed that research related to digital servitization identified five determinant variables: digitization, servitization, manufacturing servitization, process innovation, and product innovation, as well as five response variables: firm competitiveness, firm performance, financial performance, firm profitability, and sustainable performance.\n\nCompared to other studies, the results of this research offer unique perspectives through in-depth comparative analysis and better classification, leading to more detailed and specific understandings of achieving legal harmonization in the context of municipal bond issuance. These findings contribute to the existing body of knowledge by highlighting the importance of legal harmonization in enhancing the effectiveness and transparency of regional development financing, thereby supporting sustainable development through the adoption of proven legal frameworks.\n\nIn summary, these findings underscore the significance of comprehending the role of digital servitization in today’s business landscape. The results of this analysis provide valuable insights for business practitioners, policymakers, and researchers interested in developing effective business strategies in the face of digitization and servitization changes. Thus, this research makes a significant contribution to expanding our understanding of digital servitization and its impact on various aspects of company performance.\n\nThe limitations of this study lie in its exclusive focus on quantitative methods, leading to the exclusion of qualitative and mixed-methods research. By limiting the scope to quantitative approaches, the review may overlook the contextual nuances and experiential dimensions inherent in the phenomenon of digital servitization. Qualitative data, with its emphasis on in-depth exploration and understanding of individual experiences, organizational contexts, and socio-cultural factors, could offer valuable insights that quantitative analysis alone might miss. Therefore, the absence of qualitative and mixed-methods research in this review may result in a less comprehensive understanding of digital servitization and its implications.\n\nFurthermore, future research could further explore the causal relationships between these variables and consider different industry and geographical contexts. In conclusion, digital servitization is a phenomenon that plays a crucial role in the modern business era, and a better understanding of the influencing factors and their impacts will continue to be an interesting and relevant research area.", "appendix": "Data availability statement\n\nNo data associated with this article.\n\nFigshare: Biblio Information in Systematic Literature Review in Digital Servitization, https://doi.org/10.6084/m9.figshare.25833901.v1 (Ginting, 2024c).\n\nThis project contains the following data:\n\n• Biblio Information SLR Digital Servitization.csv.\n\nFigshare: PRISMA 2020_Checklist Hendri Ginting SLR, https://doi.org/10.6084/m9.figshare.25894162.v1 (Ginting, 2024b).\n\nThis project contains the following data:\n\n• PRISMA 2020_Checklist Hendri Ginting SLR\n\nData are available under the terms of the Creative Commons “No Rights Reserved” license (CC0)\n\nPRISMA checklist and flowchart for “Exploring the Landscape of Digital Servitization: A Systematic Review”. https://doi.org/10.6084/m9.figshare.25894162.v1.\n\n\nAcknowledgements\n\nWe gratefully acknowledge all those who supported and contributed to the completion of this article.\n\n\nReferences\n\nAbou-Foul M, Ruiz-Alba JL, Soares A: The impact of digitalization and servitization on the financial performance of a firm: an empirical analysis. Prod. Plan. Control. 2021; 32(12): 975–989. Publisher Full Text\n\nAgarwal GK, Simonsson J, Magnusson M, et al.: Value-capture in digital servitization. J. Manuf. Technol. Manag. 2022; 33(5): 986–1004. Publisher Full Text\n\nBarney J: Firm resources and sustained competitive advantage. J. Manag. 1991; 17(1): 99–120. Publisher Full Text\n\nBehl A, Sampat B, Gaur J, et al.: Can gamification help green supply chain management firms achieve sustainable results in servitized ecosystem? An empirical investigation. Technovation. 2024; 129: 102915. Publisher Full Text\n\nBortoluzzi G, Chiarvesio M, Romanello R, et al.: Servitisation and performance in the business-to-business context: the moderating role of Industry 4.0 technologies. J. Manuf. Technol. Manag. 2022; 33(9): 108–128. Publisher Full Text\n\nBromiley P, Papenhausen C: Assumptions of Rationality and Equilibrium in Strategy Research: The Limits of Traditional Economic Analysis. Strateg. Organ. 2003; 1(4): 413–437. Publisher Full Text\n\nBustinza OF, Gomes E, Vendrell-Herrero F, et al.: An organizational change framework for digital servitization: Evidence from the Veneto region. Strateg. Chang. 2018; 27(2): 111–119. Publisher Full Text\n\nChen L, Dai Y, Ren F, et al.: Data-driven digital capabilities enable servitization strategy——From service supporting the product to service supporting the client. Technol. Forecast. Soc. Chang. 2023; 197: 122901. Publisher Full Text\n\nChen S, Zhang H: Does digital finance promote manufacturing servitization: Micro evidence from China. Int. Rev. Econ. Financ. 2021; 76: 856–869. Publisher Full Text\n\nChen Y, Visnjic I, Parida V, et al.: On the road to digital servitization – The (dis) continuous interplay between business model and digital technology. Int. J. Oper. Prod. Manag. 2021; 41(5): 694–722. Publisher Full Text\n\nChirumalla K, Leoni L, Oghazi P: Moving from servitization to digital servitization: Identifying the required dynamic capabilities and related microfoundations to facilitate the transition. J. Bus. Res. 2023; 158(January): 113668. Publisher Full Text\n\nCoreynen W, Matthyssens P, Van Bockhaven W: Boosting servitization through digitization: Pathways and dynamic resource configurations for manufacturers. Ind. Mark. Manag. 2017; 60: 42–53.\n\nCoreynen W, Matthyssens P, Vanderstraeten J, et al.: Unravelling the internal and external drivers of digital servitization: A dynamic capabilities and contingency perspective on firm strategy. Ind. Mark. Manag. 2020; 89(December 2018): 265–277. Publisher Full Text\n\nCruzes DS, Dyba T: Recommended steps for thematic synthesis in software engineering. 2011 International Symposium on Empirical Software Engineering and Measurement. IEEE; 2011, September; pp. 275–284.\n\nFarisyi S, Musadieq MA, Utami HN, et al.: A systematic literature review: Determinants of sustainability reporting in developing countries. Sustainability. 2022; 14(16): 10222. Publisher Full Text\n\nFrank AG, Mendes GHS, Ayala NF, et al.: Servitization and Industry 4.0 convergence in the digital transformation of product firms: A business model innovation perspective. Technol. Forecast. Soc. Chang. 2019; 141(July 2018): 341–351. Publisher Full Text\n\nGao J, Zhang W, Guan T, et al.: Influence of digital transformation on the servitization level of manufacturing SMEs from static and dynamic perspectives. Int. J. Inf. Manag. 2023; 73: 102645. Publisher Full Text\n\nGarcia R, Calantone R: A critical look at technological innovation typology and innovativeness terminology: a literature review. Journal of Product Innovation Management: An International Publication of the Product Development & Management Association. 2002; 19(2): 110–132. Publisher Full Text\n\nGebauer H, Fleisch E: An investigation of the relationship between behavioral processes, motivation, investments in the service business and service revenue. Ind. Mark. Manag. 2007; 36(3): 337–348. Publisher Full Text\n\nGebauer H, Gustafsson A, Witell L: Service transition in manufacturing companies: a capabilities perspective. J. Bus. Strateg. 2020; 41(3): 51–58.\n\nGinting H: Flowchart illustrating the process of literature selection reviewed using PRISMA. figshare. Media. 2024a. Publisher Full Text\n\nGinting H: PRISMA 2020_Checklist Hendri Ginting SLR. Dataset. figshare. 2024b. Publisher Full Text\n\nGinting H: Biblio Information SLR Digital Servitization.csv. Dataset. figshare. 2024c. Publisher Full Text\n\nHacioglu U: Handbook of research on strategic fit and design in business ecosystems. IGI Global; 2019.\n\nHilbolling S, Deken F, Berends H, et al.: Process-based temporal coordination in multiparty collaboration for societal challenges. Strateg. Organ. 2022; 20(1): 135–163. Publisher Full Text\n\nHuang G, Ma L, Xietian Z, et al.: Servitization of manufacturing and China’s power status upgrading of global value network. Struct. Chang. Econ. Dyn. 2024; 68: 313–328. Publisher Full Text\n\nHuikkola T, Kohtamäki M: Solution providers’ strategic capabilities. In. J. Bus. Ind. Mark. 2017; 32(5): 752–770. Publisher Full Text\n\nJiang S, Hu X, Li S: Effect of manufacturing service transformation management on technological innovation. J. Innov. Knowl. 2023; 8(4): 100404. Publisher Full Text\n\nKohtamäki M, Bhandari KR, Rabetino R, et al.: Sustainable servitization in product manufacturing companies: The relationship between firm’s sustainability emphasis and profitability and the moderating role of servitization. Technovation. 2024; 129: 102907. Publisher Full Text\n\nKohtamäki M, Parida V, Oghazi P, et al.: Digital servitization business models in ecosystems: A theory of the firm. J. Bus. Res. 2019; 104(June): 380–392. Publisher Full Text\n\nKohtamäki M, Parida V, Patel PC, et al.: The relationship between digitalization and servitization: The role of servitization in capturing the financial potential of digitalization. Technol. Forecast. Soc. Chang. 2020; 151(July 2019): 119804. Publisher Full Text\n\nKowalkowski C, Gebauer H, Kamp B, et al.: Servitization and deservitization: Overview, concepts, and definitions. Ind. Mark. Manag. 2017; 60: 4–10. Publisher Full Text\n\nKraja YB: The impact of tangible and intangible assets on the SMEs’ success: the Albanian case. Entrepreneurship in Post-Communist Countries: New Drivers Towards a Market Economy. 2018; 135–145. Publisher Full Text\n\nKumar M, Raut RD, Mangla SK, et al.: Moderating ESG compliance between industry 4.0 and green practices with green servitization: Examining its impact on green supply chain performance. Technovation. 2024; 129: 102898. Publisher Full Text\n\nLalic B, Marjanovic U, Rakic S, et al.: Big data analysis as a digital service: evidence form manufacturing firms. Proceedings of 5th International Conference on the Industry 4.0 Model for Advanced Manufacturing: AMP 2020. 2020; pp. 263–269. Publisher Full Text\n\nLeiblein MJ: The choice of organizational governance form and performance: Predictions from transaction cost, resource-based, and real options theories. J. Manag. 2003; 29(6): 937–961. Publisher Full Text\n\nLerch C, Gotsch M: Digitalized product-service systems in manufacturing firms: A case study analysis. Res. Technol. Manag. 2015; 58(5): 45–52. Publisher Full Text\n\nLiberati A, Altman DG, Tetzlaff J, et al.: The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: explanation and elaboration. Ann. Intern. Med. 2009; 151(4): W-65.\n\nMartín-Peña ML, Díaz-Garrido E, Sánchez-López JM: The digitalization and servitization of manufacturing: A review on digital business models. Strateg. Chang. 2018; 27(2): 91–99. Publisher Full Text\n\nMartín-Peña ML, Sánchez-López JM, Díaz-Garrido E: Servitization and digitalization in manufacturing: the influence on firm performance. J. Bus. Ind. Mark. 2020; 35(3): 564–574. Publisher Full Text\n\nMiao Y, Shi Y, Jing H: Effect of servitization on performance in manufacturing firms: A mediating effect model of digitalisation moderated by ESG performance. Heliyon. 2023; 9(10): e20831. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMishra V, Bisoyi B, Das B, et al.: Supply Chain Transformation Through Digital Servitization in Manufacturing Sector. Recent Advances in Thermofluids and Manufacturing Engineering: Select Proceedings of ICTMS 2022. Springer; 2022; pp. 571–579.\n\nMoher D, Shamseer L, Clarke M, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst. Rev. 2015; 4: 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNeely A: Exploring the financial consequences of the servitization of manufacturing. Oper. Manag. Res. 2008; 1(2): 103–118. Publisher Full Text\n\nOpazo-Basáez M, Vendrell-Herrero F, Bustinza OF: Digital service innovation: a paradigm shift in technological innovation. J. Serv. Manag. 2022; 33(1): 97–120. Publisher Full Text\n\nPaiola M, Schiavone F, Grandinetti R, et al.: Digital servitization and sustainability through networking: Some evidences from IoT-based business models. J. Bus. Res. 2021; 132: 507–516. Publisher Full Text\n\nParate V, Hiremath BV, Tailor RK: Digital servitization: An effective tool of attracting customers in modern business world. J. Manag. Res. Anal. 2022; 9(4): 207–209. Publisher Full Text\n\nPaschou T, Rapaccini M, Adrodegari F, et al.: Digital servitization in manufacturing: A systematic literature review and research agenda. Ind. Mark. Manag. 2020; 89: 278–292. Publisher Full Text\n\nPenrose ET: The Theory of the Growth of the Firm. Oxford: Oxford University Press; 1959.\n\nPham HQ, Vu PK: Unravelling the Potential of Digital Servitization in Sustainability-Oriented Organizational Performance—Does Digital Leadership Make It Different? Economies. 2022; 10(8): 185. Publisher Full Text\n\nPorter ME: Competitive strategy. Meas. Bus. Excell. 1997; 1(2): 12–17. Publisher Full Text\n\nRaddats C, Burton J, Zolkiewski J, et al.: Servitization capabilities for advanced services: a multi-actor perspective. Second Spring Servitization Conference. 2014; pp. 126–132.\n\nRakic S, Pero M, Sianesi A, et al.: Digital servitization and firm performance: Technology intensity approach. Inzinerine Ekonomika. 2022; 33(4): 398–413.\n\nRymaszewska A, Helo P, Gunasekaran A: IoT powered servitization of manufacturing – an exploratory case study. Int. J. Prod. Econ. 2017; 192: 92–105. Publisher Full Text\n\nSchumpeter JA, Swedberg R: The theory of economic development. Routledge; 2021. Publisher Full Text\n\nSklyar A, Kowalkowski C, Tronvoll B, et al.: Organizing for digital servitization: A service ecosystem perspective. J. Bus. Res. 2019; 104(October 2017): 450–460. Publisher Full Text\n\nTronvoll B, Sklyar A, Sörhammar D, et al.: Transformational shifts through digital servitization. Ind. Mark. Manag. 2020; 89(February): 293–305. Publisher Full Text\n\nUpadhayay NB, Rocchetta S, Gupta S, et al.: Blazing the trail: The role of digital and green servitization on technological innovation. Technovation. 2024; 130(December): 102922. Publisher Full Text\n\nValtakoski A: Explaining servitization failure and deservitization: A knowledge-based perspective. Ind. Mark. Manag. 2017; 60: 138–150. Publisher Full Text\n\nVargo SL, Lusch RF: Service-dominant logic 2025. Int. J. Res. Mark. 2017; 34(1): 46–67. Publisher Full Text\n\nVendrell-Herrero F, Bustinza OF, Opazo-Basaez M, et al.: Treble innovation firms: Antecedents, outcomes, and enhancing factors. Int. J. Prod. Econ. 2023; 255: 108682. Publisher Full Text\n\nVendrell-Herrero F, Bustinza OF, Parry G, et al.: Servitization, digitization and supply chain interdependency. Ind. Mark. Manag. 2017; 60: 69–81. Publisher Full Text\n\nVisnjic I, Neely A, Jovanovic M: The path to outcome delivery: Interplay of service market strategy and open business models. Technovation. 2018; 72-73(February): 46–59. Publisher Full Text\n\nWang J, Wang W, Wu H, et al.: Exploring the effects of manufacturing servitization on enterprise energy conservation and emissions reduction moderated by digital transformation. Energy Econ. 2023; 122: 106706. Publisher Full Text\n\nWen H, Wen C, Lee C-C: Impact of digitalization and environmental regulation on total factor productivity. Inf. Econ. Policy. 2022; 61: 101007. Publisher Full Text\n\nWernerfelt B: On the role of the RBV in marketing. J. Acad. Mark. Sci. 2014; 42(1): 22–23. Publisher Full Text\n\nWesterman G, Bonnet D, McAfee A: Leading digital: Turning technology into business transformation. Harvard Business Press; 2014.\n\nZhao S, Peng D, Wen H, et al.: Does the digital economy promote upgrading the industrial structure of Chinese cities? Sustainability. 2022; 14(16): 10235. Publisher Full Text\n\nZhou D, Wu Q, Lee S, et al.: Unpacking the mechanism linking digital servitization and manufacturing firm performance: the role of the service networks and slack resources. J. Bus. Ind. Mark. 2023." }	[ { "id": "307042", "date": "07 Aug 2024", "name": "João Reis", "expertise": [ "Reviewer Expertise Industrial Engineering", "Digital Transformation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 was kind of excited to read the article titled “Exploring the Landscape of Digital Servitization: A Systematic Review.”\nThis article is particularly important due to its relevance and the increasing interest it has gained in the academic community. It holds the potential to provide a comprehensive view of digital servitization within the context of fundamental sciences. However, several improvements are needed to improve its quality.\nFirstly, it is crucial to update the references during the revision process. Since the submission of the manuscript, several relevant articles on digital servitization have been published, such as:\n\nSoellner, S., et al. (2024). [Ref-1]. Leocádio, D., et al., (2024). [Ref-2].\n\nIt is understandable that the references are not up-to-date as of 2024 due to the research date and the often lengthy review process. However, updating these references before indexing can enhance the article's relevance.\nAdditionally, the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) currently includes 3 phases, not 4 as indicated in Figure 1. This needs to be corrected, and I recommend consulting the official website: https://www.prisma-statement.org\nThe figures in the article require a more professional layout. For example, Figure 2 is barely visible and should be improved.\nThe discussion section would benefit from continuous text and fewer bullet points. Excessive bullet points disrupt the logical flow, making the content seem fragmented. A coherent chain of ideas, transitioning from the most general to the most specific, is more effective (I believe).\nThe article's structure, which currently includes 7 headings, feels overly fragmented. Adopting the IMRaD (Introduction, Method, Results, and Discussion) format, which is well-established in the academic community, can provide a clearer and more cohesive structure to your article.\nFurthermore, the article needs extensive English proofreading with a focus on scientific writing. While I agree that using AI tools for proofreading is acceptable, human refinement is still essential in this context to ensure the writing meets scientific standards.\nAlthough my recommendations might seem broad at this stage, they are intended to help the authors develop a more robust article. If the authors agree to revise their article, I am willing to provide more detailed feedback before final approval.\nThe authors are not obliged to cite the articles above, as long as they cite current articles that are strictly related to the topic\nGood luck and have good work!\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? 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": "12467", "date": "25 Sep 2024", "name": "Hendri Ginting", "role": "Author Response", "response": "the reference has been updated using the most recent references: \"The concept of servitization spans a range between pure providers of tangible goods and pure providers of services. Within this spectrum, manufacturing companies are moving in the direction of service providers … (Soellner, S., et al., 2024).\" (page 2) the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) currently includes 3 phases, not 4 as indicated in Figure 1. This needs to be corrected, and I recommend consulting the official website: https://www.prisma-statement.org --> Revised on Page 6 and the picture is also attached on separated file The figures in the article require a more professional layout. For example, Figure 2 is barely visible and should be improved. --> revised on Page 7 and the picture is also attached on separated file The discussion section would benefit from continuous text and fewer bullet points. Excessive bullet points disrupt the logical flow, making the content seem fragmented. A coherent chain of ideas, transitioning from the most general to the most specific, is more effective (I believe) --> The discussion section revised into continous text The article’s structure has been simplified into 4 sections adopting the IMRaD (Introduction, Method, Results, and Discussion) This paper has passed the English grammar check using AI tools and also has been checked by human" } ] } ]	1	https://f1000research.com/articles/13-813
https://f1000research.com/articles/12-1402/v1	24 Oct 23	{ "type": "Software Tool Article", "title": "A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data", "authors": [ "Charlotte Hutchings", "Charlotte S. Dawson", "Thomas Krueger", "Kathryn S. Lilley", "Lisa M. Breckels", "Charlotte Hutchings", "Charlotte S. Dawson", "Thomas Krueger", "Kathryn S. Lilley" ], "abstract": "Background: Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system.\nMethods: Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilizes open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quantified using label-free quantitation (LFQ).\nResults: The workflow explains the software infrastructure before focusing on data import, pre-processing and quality control. This is done individually for TMT and LFQ datasets. The application of statistical differential expression analysis is demonstrated, followed by interpretation via gene ontology enrichment analysis.\nConclusions: A comprehensive workflow for the processing, analysis and interpretation of expression proteomics is presented. The workflow is a valuable resource for the proteomics community and specifically beginners who are at least familiar with R who wish to understand and make data-driven decisions with regards to their analyses.", "keywords": [ "Bioconductor", "QFeatures", "proteomics", "shotgun proteomics", "bottom-up proteomics", "differential expression", "mass spectrometry", "quality control", "data processing", "limma" ], "content": "Introduction\n\nProteins are responsible for carrying out a multitude of biological tasks, implementing cellular functionality and determining phenotype. Mass spectrometry (MS)-based expression proteomics allows protein abundance to be quantified and compared between samples. In turn, differential protein abundance can be used to explore how biological systems respond to a perturbation. Many research groups have applied such methodologies to understand mechanisms of disease, elucidate cellular responses to external stimuli, and discover diagnostic biomarkers (see Refs. 1–3 for recent examples). As the potential of proteomics continues to be realised, there is a clear need for resources demonstrating how to deal with expression proteomics data in a robust and standardised manner.\n\nThe data generated during an expression proteomics experiment are complex, and unfortunately there is no one-size-fits-all method for the processing and analysis of such data. The reason for this is two-fold. Firstly, there are a wide range of experimental methods that can be used to generate expression proteomics data. Researchers can analyse full-length proteins (top-down proteomics) or complete an enzymatic digestion and analyse the resulting peptides. This proteolytic digestion can be either partial (middle-down proteomics) or complete (bottom-up proteomics). The latter approach is most commonly used as peptides have a more favourable ionisation capacity, predictable fragmentation patterns, and can be separated via reversed phase liquid chromatography, ultimately making them more compatible with MS.4 Within bottom-up proteomics, the relative quantitation of peptides can be determined using one of two approaches: (1) label-free or (2) label-based quantitation. Moreover, the latter can be implemented with a number of different peptide labelling chemistries, for example, using tandem mass tag (TMT), stable-isotope labelling by amino acids in cell culture (SILAC), isobaric tags for relative and absolute quantitation (iTRAQ), among others.5 MS analysis can also be used in either data-dependent or data-independent acquisition (DDA or DIA) mode.6,7 Although all of these experimental methods typically result in a similar output, a matrix of quantitative values, the data are different and must be treated as such. Secondly, data processing is dependent upon the experimental goal and biological question being asked.\n\nHere, we provide a step-by-step workflow for processing, analysing and interpreting expression proteomics data derived from a bottom-up experiment using DDA and either LFQ or TMT label-based peptide quantitation. We outline how to process the data starting from a peptide spectrum match (PSM)- or peptide- level .txt file. Such files are the outputs of most major third party search software (e.g. Proteome Discoverer, MaxQuant, FragPipe). We begin with data import and then guide users through the stages of data processing including data cleaning, quality control filtering, management of missing values, imputation, and aggregation to protein-level. Finally, we finish with how to discover differentially abundant proteins and carry out biological interpretation of the resulting data. The latter will be achieved through the application of gene ontology (GO) enrichment analysis. Hence, users can expect to generate lists of proteins that are significantly up- or downregulated in their system of interest, as well as the GO terms that are significantly over-represented in these proteins.\n\nUsing the R statistical programming environment8 we make use of several state-of-the-art packages from the open-source, open-development Bioconductor project9 to analyse use-case expression proteomics datasets10 from both LFQ and label-based technologies.\n\nIn this workflow we make use of open-source software from the R Bioconductor9 project. The Bioconductor initiative provides R software packages dedicated to the processing of high-throughput complex biological data. Packages are open-source, well-documented and benefit from an active community of developers. We recommend users to download the RStudio integrated development environment (IDE) which provides a graphical interface to R programming language.\n\nDetailed instructions for the installation of Bioconductor packages are documented on the Bioconductor Installation page. The main packages required for this workflow are installed using the code below.\n\nAfter installation, each package must be loaded before it can be used in the R session. This is achieved via the library function. For example, to load the QFeatures package one would type library(\"QFeatures\") after installation. Here we load all packages included in this workflow.\n\n\nThe use-case: exploring changes in protein abundance in HEK293 cells upon perturbation\n\nAs a use-case, we analyse two quantitative proteomics datasets derived from a single experiment. The aim of the experiment was to reveal the differential abundance of proteins in HEK293 cells upon a particular treatment, the exact details of which are anonymised for the purpose of this workflow. An outline of the experimental method is provided in Figure 1.\n\nBriefly, HEK293 cells were either (i) left untreated, or (ii) provided with the treatment of interest. These two conditions are referred to as ‘control’ and ‘treated’, respectively. Each condition was evaluated in triplicate. At 96-hours post-treatment, samples were collected and separated into cell pellet and supernatant fractions containing cellular and secreted proteins, respectively. Both fractions were denatured, alkylated and digested to peptides using trypsin.\n\nThe supernatant fractions were de-salted and analysed over a two-hour gradient in an Orbitrap Fusion™ Lumos™ Tribrid™ mass spectrometer coupled to an UltiMate™ 3000 HPLC system (Thermo Fisher Scientific). LFQ was achieved at the MS1 level based on signal intensities. Cell pellet fractions were labelled using TMT technology before being pooled and subjected to high pH reversed-phase peptide fractionation giving a total of 8 fractions. As before, each fraction was analysed over a two-hour gradient in an Orbitrap Fusion™ Lumos™ Tribrid™ mass spectrometer coupled to an UltiMate™ 3000 HPLC system (Thermo Fisher Scientific). To improve the accuracy of the quantitation of TMT-labelled peptides, synchronous precursor selection (SPS)-MS3 data acquisition was employed.11,12 Of note, TMT labelling of cellular proteins was achieved using a single TMT6plex. Hence, this workflow will not include guidance on multi-batch TMT effects or the use of internal reference scaling. For more information about the use of multiple TMTplexes users are directed to Refs. 13, 14.\n\nThe cell pellet and supernatant datasets were handled independently and we take advantage of this to discuss the processing of TMT-labelled and LFQ proteomics data. In both cases, the raw MS data were processed using Proteome Discoverer v2.5 (Thermo Fisher Scientific). While the focus in the workflow presented below is differential protein expression analysis, the data processing and quality control steps described here are applicable to any TMT or LFQ proteomics dataset. Importantly, however, the experimental aim will influence data-guided decisions and the considerations discussed here likely differ from those of spatial proteomics, for example.\n\nThe files required for this workflow can be found deposited to the ProteomeXchange Consortium via the PRIDE15,16 partner repository with the dataset identifier PXD041794, Zenodo at http://doi.org/10.5281/zenodo.7837375 and at the Github repository https://github.com/CambridgeCentreForProteomics/f1000_expression_proteomics/. Users are advised to download these files into their current working directory. In R the setwd function can be used to specify a working directory, or if using RStudio one can use the Session -> Set Working Directory menu.\n\n\nThe infrastructure: QFeatures and SummarizedExperiments\n\nTo be able to conveniently track each step of this workflow, users should make use of the Quantitative features for mass spectrometry, or QFeatures, Bioconductor package.17 Prior to utilising the QFeatures infrastructure, it is first necessary to understand the structure of a SummarizedExperiment18 object as QFeatures objects are based on the SummarizedExperiment class. A SummarizedExperiment, often referred to as an SE, is a data container and S4 object comprised of three components: (1) the colData (column data) containing sample metadata, (2) the rowData containing data features, and (3) the assay storing quantitation data, as illustrated in Figure 2. The sample metadata includes annotations such as condition and replicate, and can be accessed using the colData function. Data features, accessed via the rowData function, represent information derived from the identification search. Examples include peptide sequence, master protein accession, and confidence scores. Finally, quantitative data is stored in the assay slot. These three independent data structures are neatly stored within a single SummarizedExperiment object.\n\nFigure reproduced from the SummarizedExperiment package18 vignette with permission.\n\nA QFeatures object holds each level of quantitative proteomics data, namely (but not limited to) the PSM, peptide and protein-level data. Each level of the data is stored as its own SummarizedExperiment within a single QFeatures object. The lowest level data e.g. PSM, is first imported into a QFeatures object before aggregating upward towards protein-level (Figure 3). During this process of aggregation, QFeatures maintains the hierarchical links between quantitative levels whilst allowing easy access to all data levels for individual proteins of interest. This key aspect of QFeatures will be exemplified throughout this workflow. Additional guidance on the use of QFeatures can be found in Ref. 17. For visualisation of the data, all plots are generated using standard ggplot functionality, but could equally be produced using base R.\n\nFigure modified from the QFeatures17 vignette with permission.\n\n\nProcessing and analysing quantitative TMT data\n\nFirst, we provide a workflow for the processing and quality control of quantitative TMT-labelled data. As outlined above, the cell pellet fractions of triplicate control and treated HEK293 cells were labelled using a TMT6plex. Labelling was as outlined in Table 1.\n\nThe first processing step in any MS-based proteomics experiment involves an identification search using the raw data. The aim of this search is to identify which peptide sequences, and therefore proteins, correspond to the raw spectra output from the mass spectrometer. Several third-party software exist to facilitate identification searches of raw MS data but ultimately the output of any search is a list of PSMs, peptides and protein identifications along with their corresponding quantification data.\n\nThe use-case data presented here was processed using Proteome Discoverer 2.5 and additional information about this search is provided in an appendix in the GitHub repository https://github.com/CambridgeCentreForProteomics/f1000_expression_proteomics. Further, we provide template workflows for both the processing and consensus steps of the Proteome Discoverer identification runs. It is also possible to determine several of the key parameter settings during the preliminary data exploration. This step will be particularly important for those using publicly available data without detailed knowledge of the identification search parameters. For now, we simply export the PSM-level .txt file from the Proteome Discoverer output.\n\nData cleaning, exploration and filtering at the PSM-level is performed in R using QFeatures. The function readQFeatures is used to import the PSM-level .txt file. As the cell pellet TMT data we will use is derived from one TMT6plex, only one PSM-level .txt file needs to be imported. This file should be stored within the users working directory.\n\nThe columns containing quantitative data also need to be identified before import. To check the column names we use names and read.delim (the equivalent for a .csv file would be read.csv). In the current experiment the order of TMT labels was randomised in an attempt to minimise the effect of TMT channel leakage. For ease of grouping and simplification of downstream visualisation, samples are re-ordered during the import step. This is done by creating a vector containing the sample column names in their correct order. If samples are already in the desired order, the vector can be created by simply indexing the quantitative columns.\n\nNow that the necessary file and its quantitative data columns have been identified, we can pass this to the readQFeatures function and provide these two pieces of information. We also specify that the file is tab-delimited by including sep = “\\t” (similarly you would use sep = “,” for a .csv file). Of note, the readQFeatures function can also take fnames as an argument to specify a column to be used as the row names of the imported object. Whilst previous QFeatures vignettes used the “Sequence” or “Annotated.Sequence” as row names, we advise against this because of the presence of PSMs matched to the same peptide sequence with different modifications. In such cases, multiple rows would have the same name forcing the readQFeatures function to output a “making assay row names unique” message and add an identifying number to the end of each duplicated row name. These sequences would then be considered as unique during the aggregation of PSM to peptide, thus resulting in two independent peptide-level quantitation values rather than one. Therefore, we do not pass a fnames argument and the row names automatically become indices. Finally, we pass the name argument to indicate the type of data added.\n\nAs outlined above, a QFeatures data object is a list of SummarizedExperiment objects. As such, an individual SummarizedExperiment can be accessed using the standard double bracket nomenclature, as demonstrated in the code chunk below.\n\nA summary of the data contained in the slots is printed to the screen. To retrieve the rowData, colData or assay data from a particular SummarizedExperiment within a QFeatures object users can make use of the rowData, colData and assay functions. For plotting or data transformation it is necessary to convert to a data.frame or tibble.\n\nHaving imported the data, each sample is first annotated with its TMT label, sample reference and condition. As this information is experimental metadata, it is added to the colData slot. It is also useful to clean up sample names such that they are short, intuitive and informative. This is done by editing the colnames. These steps may not always be necessary depending upon the identification search output.\n\nAs well as cleaning and annotating the data, it is always advisable to check that the import worked and that the data looks as expected. Further, preliminary exploration of the data can provide an early sign of whether the experiment and subsequent identification search were successful. Importantly, however, the names of key parameters will vary depending on the software used, and will likely change over time. Users will need to be aware of this and modify the code in this workflow accordingly.\n\nWe can see that the original data includes 48832 PSMs across the 6 samples. It is also useful to make note of how many peptides and proteins the raw PSM data corresponds to, and to track how many we remove during the subsequent filtering steps. This can be done by checking how many unique entries are located within the “Sequence” and “Master.Protein.Accessions” for peptides and proteins, respectively. Of note, searching for unique peptide sequences means that the number of peptides does not include duplicated sequences with different modifications.\n\nHence, the output of the identification search contains 48832 PSMs corresponding to 25969 peptide sequences and 5040 master proteins. Finally, we confirm that the identification search was carried out as expected. For this, we print summaries of the key search parameters using the table function for discrete parameters and summary for those which are continuous. This is also helpful for users who are analysing publicly available data and have limited knowledge about the identification search parameters.\n\nExperimental quality control of TMT-labelled quantitive proteomics data takes place in two steps: (1) assessment of the raw mass spectrometry data, and (2) evaluation of TMT labelling efficiency.\n\nHaving taken an initial look at the output of the identification search, it is possible to create some simple plots to inspect the raw mass spectrometry data. Such plots are useful in revealing problems that may have occurred during the mass spectrometry run but are far from extensive. Users who wish to carry out a more in-depth evaluation of the raw mass spectrometry data may benefit from use of the Spectra Bioconductor package which allows for visualisation and exploration of raw chromatograms and spectra, among other features.19\n\nThe first plot we generate looks at the delta precursor mass, that is the difference between observed and estimated precursor mass, across retention time. Importantly, exploration of this raw data feature can only be done when using the raw data prior to recalibration. For users of Proteome Discoverer, this means using the spectral files node rather than the spectral files recalibration node.\n\nSince we applied a precursor mass tolerance of 10 ppm during the identification search, all of the PSMs are within ±10 ppm. Ideally, however, we want the majority of the data to be within ±5 ppm since smaller delta masses correspond to a greater rate of correct peptide identifications. From the graph we have plotted we can see that indeed the majority of PSMs are within ±5 ppm. If users find that too many PSMs are outside of the desired ±5 ppm, it is advisable to check the calibration of the mass spectrometer.\n\nThe second quality control plot of raw data is that of MS2 ion inject time across the retention time gradient. Here, it is desirable to achieve an average MS2 injection time of 50 ms or less, although the exact target threshold will depend upon the sample load. If the average ion inject time is longer than desired, then the ion transfer tube and/or front end optics of the instrument may require cleaning.\n\nFrom this plot we can see that whilst there is a high density of PSMs at low inject times, there are also many data points found at the 50 ms threshold. This indicates that by increasing the time allowed for ions to accumulate in the ion trap, the number of PSMs could also have been increased. Finally, we inspect the distribution of PSMs across both the ion injection time and retention time by plotting histograms.\n\nThe four plots that we have generated look relatively standard with no obvious problems indicated. Therefore, we continue by evaluating the quality of the processed data.\n\nThe most fundamental data quality control step in a TMT experiment is to check the TMT labelling efficiency. TMT labels react with amine groups present at the peptide N-terminus as well as the side chain of lysine (K) residues. Of note, lysine residues can be TMT modified regardless of whether they are present at the C-terminus of a trypic peptide or internally following miscleavage.\n\nTo evaluate the TMT labelling efficiency, a separate identification search of the raw data was completed with lysine (K) and peptide N-termini TMT labels considered as dynamic modifications rather than static. No additional residues (S or T) were evaluated for labelling in the search. This allows the search engine to assess the presence of both the modified (TMT labelled) and unmodified (original) forms of each peptide. The relative proportions of modified and unmodified peptides can then be used to calculate the TMT labelling efficiency. To demonstrate how to check for TMT labelling efficiency, only two of the eight fractions were utilised for this search.\n\nAs we will only look at TMT efficiency at the PSM-level, here we upload the .txt file directly as a SummarizedExperiment rather than a QFeatures object. This is done using the readSummarizedExperiment function and the same arguments as those in readQFeatures.\n\nInformation about the presence of labels is stored within the ‘Modifications’ feature of the rowData. Using this information, the TMT labelling efficiency of the experiment is calculated using the code chunks below. Users should alter this code if TMTpro reagents are being used such that “TMT6plex” is replaced by “TMTpro”.\n\nFirst we consider the efficiency of peptide N-termini TMT labelling. We use the grep function to identify PSMs which are annotated as having an N-Term TMT6plex modification. We then calculate the number of PSMs with this annotation as a proportion of the total number of PSMs.\n\nSecondly, we consider the TMT labelling efficiency of lysine (K) residues. As mentioned above, lysine residues can be TMT labelled regardless of their position within a peptide. Hence, we here calculate lysine labelling efficiency on a per lysine residue basis.\n\nUsers should aim for an overall TMT labelling efficiency >90% in order to achieve reliable quantitation. In cases where labelling efficiency is towards the lower end of the acceptable range, TMT labels should be set as dynamic modifications during the final identification search, although this will increase the search space and time as well as influencing false discovery rate (FDR) calculations. A summary of the current advice from Thermo Fisher is provided in Table 2. Where labelling efficiency is calculated as being between categories, how to progress is ultimately decided by the user.\n\nSince the use-case data has a sufficiently high TMT labelling efficiency, we can continue to use the output of the identification search. This search considered TMT labelling of lysines as a static modification whilst N-terminal labelling was kept as dynamic, to investigate the presence of protein N-terminal modifications.\n\nBeing confident that the experiment and identification search were successful, we can now begin with some basic data cleaning. However, we also want to keep a copy of the raw PSM data. Therefore, we first create a second copy of the PSM SummarizedExperiment, called “psms_filtered”, and add it to the QFeatures object. This is done using the addAssay function. All changes made at the PSM-level will then only be applied to this second copy, so that we can refer back to the original data if needed.\n\nOf note, manually adding an assay (or SummarizedExperiment) to the QFeatures object does not automatically generate links between these assays. We will manually add the explicit links later, after we complete data cleaning and filtering.\n\nThe cleaning steps included in this section are non-specific and should be applied to all quantitative proteomics datasets. The names of key parameters will vary in data outputs from alternative third party software, however, and users should remain aware of both terminology changes over time as well as the introduction of new filters. All data cleaning steps are completed in the same way. We first determine how many rows, here PSMs, meet the conditions for removal. This is achieved by using the dplyr::count function. The unwanted rows are removed using the filterFeatures function. Since we only wish to apply the filters to the “psms_filtered” level, we specify this by using the i = argument. If this argument is not used, filterFeatures will remove features from all assays within a QFeatures object.\n\nThe first common cleaning step we carry out is the removal of PSMs that have not been assigned to a master protein during the identification search. This can happen when the search software is unable to resolve conflicts caused by the presence of the isobaric amino acids leucine and isoleucine. Before implementing the filter, it is useful to find out how many PSMs we expect to remove. This is easily done by using the dplyr::count on the master protein column. Any master proteins that return TRUE will be removed by filtering. If this returns no TRUE values, users should move on to the next filtering step without removing rows as this will introduce an error.\n\nFor users who wish to explicitly track the process of data cleaning, the code chunk below demonstrates how to print a message containing the number of features removed.\n\nThis code could be adapted to each cleaning and filtering step. To maintain simplicity of this workflow, we will not print explicit messages at each step. Instead, the decision to do so is left to the user.\n\nNext we remove PSMs corresponding to contaminant proteins. Such proteins can be introduced intentionally as reagents during sample preparation, as is the case for digestive enzymes, or accidentally, as seen with human keratins derived from skin and hair. Since these proteins do not contribute to the biological question being asked and it is standard practice to remove them from the data. This is done by using a carefully curated, sample-specific contaminant database. Critically, the database used for filtering should be the same one that was used during the identification search. Whilst it is possible to remove contaminants using the filterFeatures function on a contaminants annotation column (as per the QFeatures processing vignette), we demonstrate how to filter using only contaminant protein accessions for users who do not have contaminant annotations within their identification data.\n\nFor this experiment, a contaminant database from Ref. 20 was used. The .fasta file for this database is available at the Hao Group’s Github Repository for Protein Contaminant Libraries for DDA and DIA Proteomics and specifically can be found at https://github.com/HaoGroup-ProtContLib/Protein-Contaminant-Libraries-for-DDA-and-DIA-Proteomics/tree/main/Universal%20protein%20contaminant%20FASTA. Here, we import this file using the fasta.index function from the Biostrings package.21 This function requires a file path to the .fasta file and then asks users to specify the sequence type. In this case we have amino acid sequences so pass seqtype = \"AA\". The function returns a data.frame with one row per FASTA entry. We then can extract the protein accessions from the fasta file. Users will need to alter the below code according to the contaminant file used.\n\nNow we have our contaminant list by accession number, we can identify and remove PSMs with any contaminant protein within their “Protein.Accessions”. Importantly, filtering on “Protein.Accessions” ensures the removal of PSMs which matched to a protein group containing a contaminant protein, even if the contaminant protein is not the group’s master protein.\n\nAt this point, users can also remove any additional proteins which may not have been included in the contaminant database. For example, users may wish to remove human trypsin (accession P35050) should it appear in their data.\n\nSeveral third party softwares also have the option to directly annotate which fasta file (here, the human proteome or contaminant database) a PSM is derived from. In such cases, filtering can be simplified by removing PSMs annotated as contaminants in the output file.\n\nNow that we are left with only PSMs matched to proteins of interest, we filter out PSMs which cannot be used for quantitation. This includes some PSMs which lack quantitative information altogether. In outputs derived from Proteome Discoverer this information is included in the “Quan.Info” column where PSMs are annotated as having “NoQuanLabels”. For users who have considered both lysine and N-terminal TMT labels as static modifications, the data should not contain any PSMs without quantitative information. However, since the use-case data was derived from a search in which N-terminal TMT modifications were dynamic, the data does include this annotation. Users are reminded that column names are typically software-specific as the “Quan.Info” column is found only in outputs derived from Proteome Discoverer. However, the majority of alternative third party softwares will have an equivalent column containing the same information.\n\nThis point in the workflow is a good time to check whether there are any other annotations within the “Quan.Info” column. For example, if there are any PSMs which have been “ExcludedByMethod”, this indicates that a PSM-level filter was applied in Proteome Discoverer during the identification search. If this is the case, users should determine which filter has been applied to the data and decide whether to remove the PSMs which were “ExcludedByMethod” (thereby applying the pre-set threshold) or leave them in (disregard the threshold).\n\nIn the above code chunk we see there are no remaining annotations in the “Quan.Info” column so we can continue.\n\nThe next step is to consider which PSMs are to be used for quantitation. There are two ways in which a PSM can be considered as unique. The first and most pure form of uniqueness comes from a PSM corresponding to a single protein only. This results in the PSM being allocated to one protein and one protein group. However, it is common to expand the definition of unique to include PSMs that map to multiple proteins within a single protein group. That is PSMs which are allocated to more than one protein but only one protein group. This distinction is ultimately up to the user. By contrast, PSMs corresponding to razor and shared peptides are linked to multiple proteins across multiple protein groups. In this workflow, the final grouping of peptides to proteins will be done based on master protein accession. Therefore, differential expression analysis will be based on protein groups, and we here consider unique as any PSM linked to only one protein group. This means removing PSMs where “Number.of.Protein.Groups” is not equal to 1.\n\nIn the below code chunk we count the number of PSMs linked to more than 1 protein group.\n\nWe again use the filterFeatures function to retain PSMs linked to only 1 protein group and discard any PSMs linked to more 1 group.\n\nAdditional considerations regarding protein isoforms\n\nUsers searching against a database that includes protein isoforms must take extra caution when defining ‘unique’ PSMs. A PSM that corresponds to a single protein when data is searched against the proteome without isoforms may correspond to multiple proteins once additional isoforms are included. As a result, PSMs or peptides that were previously mapped to one protein and one protein group could instead be mapped to multiple proteins and one protein group. These PSMs would be filtered out by defining ‘unique’ as corresponding to only one protein and one protein group, but would be retained if the definition was expanded to multiple proteins and one protein group. Users should be aware of these possibilities and select their filtering strategy based on the biological question of interest.\n\nAnother filter that is important for quantitation is that of PSM rank. Since individual spectra can have multiple candidate peptide matches, Proteome Discoverer uses a scoring algorithm to determine the probability of a PSM being incorrect. Once each candidate PSM has been given a score, the one with the lowest score (lowest probability of being incorrect) is allocated rank 1. The PSM with the second lowest probability of being incorrect is rank 2, and so on. For the analysis, we only want rank 1 PSMs to be retained.\n\nThe majority of search engines, including SequestHT, also provide their own PSM rank. To be conservative and ensure accurate quantitation, we also only retain PSMs that have a search engine rank of 1.\n\nFinally, we retain only unambiguous PSMs. Since there are several candidate peptides for each spectra, Proteome Discoverer allocates each PSM a level of ambiguity to indicate whether it was possible to determine a definite PSM or whether one had to be selected from a number of candidates. The allocation of PSM ambiguity takes place during the process of protein grouping and the definitions of each ambiguity assignment are given below in Table 3.\n\nImportantly, depending upon the software being used, output files may already have excluded some of these categories. It is still good to check before proceeding with the data.\n\nNow that we have finished the non-specific data cleaning, we can pause and check to see what this has done to the data. We determine the number and proportion of PSMs, peptides, and proteins lost from the original dataset.\n\nThe next step is to take a look at the data and make informed decisions about in-depth filtering. Here, we focus on three key quality control filters for TMT data: 1) average reporter ion signal-to-noise (S/N) ratio, 2) percentage co-isolation interference, and 3) percentage SPS mass match. It is possible to set thresholds for these three parameters during the identification search. However, specifying thresholds prior to exploring the data could lead to unnecessarily excessive data exclusion or the retention of poor quality PSMs. We suggest that users set the thresholds for all three aforementioned filters to 0 during the identification search, thus allowing maximum flexibility during data processing. In all cases, quality control filtering represents a trade-off between ensuring high quality data and losing potentially informative data. This means that the thresholds used for such filtering will likely depend upon the initial quality of the data and the number of PSMs, as well as the experimental goal being stringent or exploratory.\n\nIntensity measurements derived from a small number of ions tend to be more variable and less accurate. Therefore, reporter ion spectra with peaks generated from a small number of ions should be filtered out to ensure accurate quantitation and avoid stochastic ion effects. When using an orbitrap analyser, as was the case in the collection of the use-case data, the number of ions is proportional to the S/N value of a peak. Hence, the average reporter ion S/N ratio can be used to filter out quantification based on too few ions.\n\nTo determine an appropriate reporter ion S/N threshold we need to understand the original, unfiltered data. Here, we print a summary of the average reporter S/N before plotting a simple histogram to visualise the data. The default threshold for average reporter ion S/N when filtering within Proteome Discoverer is 10, or 1 on the base-10 logarithmic scale displayed here. We include a line to show where this threshold would be on the data distribution.\n\nFrom the distribution of the data it is clear that applying such a threshold would not result in dramatic data loss. Whilst we could set a higher threshold for more stringent analysis, this would lead to unnecessary data loss. Therefore, we keep PSMs with an average reporter ion S/N threshold of 10 or more. We also remove PSMs that have an NA value for their average reporter ion S/N since their quality cannot be guaranteed. This is done by including na.rm = TRUE.\n\nA second data-dependent quality control parameter which should be considered is the isolation interference. The first type of interference that occurs during a TMT experiment is reporter ion interference, also known as cross-label isotopic impurity. This type of interference arises from manufacturing-level impurities and experimental error. The former should be reduced somewhat by the inclusion of lot-specific correction factors in the search set-up and users should ensure that these corrections are applied. In Proteome Discoverer this means setting “Apply Quan Value Corrections” to “TRUE” within the reporter ions quantifier node. The second form of interference is co-isolation interference which occurs during the MS run when multiple labelled precursor peptides are co-isolated in a single data acquisition window. Following fragmentation of the co-isolated peptides, this results in an MS2 or MS3 reporter ion peak (depending upon the experimental design) derived from multiple precursor peptides. Hence, co-isolation interference leads to inaccurate quantitation of the identified peptide. This problem is reduced by filtering out PSMs with a high percentage isolation interference value. As was the case for reporter ion S/N, Proteome Discoverer has a suggested default threshold for isolation interference - 50% for MS2 experiments and 75% for SPS-MS3 experiments.\n\nAgain, we get a summary and visualise the data using the code chunk below.\n\nLooking at the data, very few PSMs have an isolation interference above the suggested threshold, and hence minimal data will be lost. Again, we choose to apply the standard threshold with the understanding that decreasing the threshold would result in greater data loss. Importantly, we are able to apply relatively standard thresholds here as the preliminary exploration did not expose any problems with the experimental data (in terms of labelling or MS analysis). If users have reason to believe the data is of poorer quality then more stringent thresholding should be considered.\n\nThe final quality control filter that we will apply is a percentage SPS mass match threshold. SPS mass match is a metric which has been introduced by Proteome Discoverer versions 2.3 and above to quantify the percentage of SPS-MS3 fragments that can still be explicitly traced back to the precursor peptide. This parameter is of particular importance given that quantitation is based on the SPS-MS3 spectra. Unfortunately, the SPS Mass Match percentage is currently only a feature of Proteome Discoverer (2.3 and above) and will not be available to users of other third party software.\n\nWe follow the same format as before to investigate the SPS Mass Match (%) distribution of the data. The default threshold within Proteome Discoverer is a SPS Mass Match above 65%. In reality, since SPS Mass Match is only reported to the nearest 10%, removing PSMs annotated with a value below 65% means removing those with 60% or less. Hence, only PSMs with 70% SPS Mass Match or above would be retained. We can see how many PSMs would be lost based on such thresholds using the code chunk below.\n\nFrom the summary and histogram we can see that the distribution of SPS Mass Matches is much less skewed than that of average reporter ion S/N or isolation interference. This means that whilst the application of thresholds on average reporter ion S/N and isolation interference led to minimal data loss, attempting to impose a threshold on SPS Mass Match represents a much greater trade-off between data quality and quantity. For simplicity, here we choose to use the standard threshold of 65%.\n\nAs we did after the non-specific cleaning steps, we check to see how many PSMs, peptides and proteins have been removed throughout the in-depth data-specific filtering.\n\nHaving finished the data cleaning at the PSM-level, the final step is to deal with missing data. Missing values represent a common challenge in quantitative proteomics and there is no consensus within the literature on how this challenge should be addressed. Indeed, missing values fall into different categories based on the reason they were generated, and each category is best dealt with in a different way. There are three main categories of missing data: missing completely at random (MCAR), missing at random (MAR) and missing not at random (MNAR). Within proteomics, values which are MCAR arise due to technical variation or stochastic fluctuations and emerge in a uniform, intensity-independent distribution. Examples include values for peptides which cannot be consistently identified or are unable to be efficiently ionised. By contrast, MNAR values are expected to occur in an intensity-dependent manner due to the presence of peptides at abundances below the limit of detection.17,22,23 In many cases this is due to the biological condition being evaluated, for example the cell type or treatment applied.\n\nTo simplify this process, we consider the management of missing data in three steps. The first step is to determine the presence and pattern of missing values within the data. Next, we filter out data which exceed the desired proportion of missing values. This includes removing PSMs with a greater number of missing values across samples than we deem acceptable, as well as whole samples in cases where the proportion of missing values is substantially higher than the average. Finally, imputation can be used to replace any remaining NA values within the dataset. This final step is optional and can equally be done prior to filtering if the user wishes to impute all missing values without removing any PSMs, although this is not recommended. Further, whilst it is possible to complete such steps at the peptide- or protein-level, we advise management of missing values at the lowest data level to minimise the effect of implicit imputation during aggregation.\n\nFirst, to determine the presence of missing values in the PSM-level data we use the nNA function within the QFeatures infrastructure. This function will return the absolute number and percentage of missing values both per sample and as an average. Importantly, alternative third-party software may output missing values in formats other than NA, such as zero, or infinite. In such cases, missing values can be converted directly into NA values through use of the zeroIsNA or infIsNA functions within the QFeatures infrastructure.\n\nWe can see that the data only contains 0.003% missing values, corresponding to 4 NA values. This low proportion is due to a combination of the TMT labelling strategy and the stringent PSM quality control filtering. In particular, co-isolation interference when using TMT labels often results in very low quantification values for peptides which should actually be missing or ‘NA’. Nevertheless, we continue and check for sample-specific bias in the distribution of NAs by plotting a simple histogram. We also use colour to indicate the condition of each sample as to check for condition-specific bias.\n\nThe percentage of missing values is sufficiently low that none of the samples need be removed. Further, there is no sample- or condition-specific bias in the data. We can get more information about the PSMs with NA values using the code below.\n\nFrom this output we can see that the maximum number of NA values per PSM is one. This information is useful to know as it may inform the filtering strategy in the next step.\n\nFirst we apply some standard filtering. Typically, it is desirable to remove features, here PSMs, with greater than 20% missing values. We can do this using the filterNA function in QFeatures, as outlined below. We pass the function the SummarizedExperiment and use the pNA = argument to specify the maximum proportion of NA values to allow.\n\nAlthough the use-case data does not contain any PSMs with >20% missing values, we demonstrate how to apply the desired filter below.\n\nSince previous exploration of missing data did not reveal any sample with an excessive number of NA values, we do not need to remove any samples from the analysis.\n\nAlthough not covered here, users may wish to carry out condition-specific filtering in cases where the exploration of missing values revealed a condition- specific bias, or where the experimental question requires. This would be the case, for example, if one condition was transfected to express proteins of interest whilst the control condition lacked these proteins. Filtering of both conditions together could, therefore, lead to the removal of proteins of interest.\n\nThe final step is to consider whether to impute the remaining missing values within the data. Imputation refers to the replacement of missing values with probable values. Since imputation requires complex assumptions and can have substantial effects on downstream statistical analysis, we here choose to skip imputation. This is reasonable given that we only have 3 missing values at the PSM-level, and that some of these will likely be removed by aggregation. A more in-depth discussion of imputation will be provided below in the LFQ workflow.\n\nThus far we have checked that the experimental data we are using is of high quality by visualising the raw data and calculating TMT labelling efficiency. We then carried out non-specific data cleaning, data-specific filtering steps and management of missing data. Here, we present a combined summary of these PSM processing steps.\n\nOnce satisfied that the PSM-level data is clean and of high quality, the PSM-level quantitative data is log transformed. log2 transformation is a standard step when dealing with quantitative proteomics data since protein abundances are dramatically skewed towards zero. Such a skewed distribution is to be expected given that the majority of cellular proteins present at any one time are of relatively low abundance, whilst only a few highly abundant proteins exist. To perform the logarithmic transformation and generate normally distributed data we pass the PSM-level data in the QFeatures object to the logTransform function, as per the below code chunk.\n\nFor the aggregation itself we use the aggregateFeatures function and provide the base level from which we wish to aggregate, the log PSM-level data in this case. We also tell the function which column to aggregate, which is specified by the fcol argument. We will first aggregate from PSM to peptide to create explicit QFeatures links. This means grouping by PSM “Sequence”.\n\nAs well as grouping PSMs according to their peptide sequence, the quantitative values for each PSM must be aggregated into a single peptide-level value. The default aggregation method within aggregateFeatures is the robustSummary function from the MsCoreUtils package.19 This method is a form of robust regression and is described in detail elsewhere.24 Nevertheless, the user must decide which aggregation method is most appropriate for their data and biological question. Further, an understanding of the selected method is critical given that aggregation is a form of implicit imputation and has substantial effects on the downstream data. Indeed, aggregation methods have different ways of dealing with missing data, either by removal or propagation. Options of aggregation methods within the aggregateFeatures function include MsCoreUtils::medianPolish, MsCoreUtils::robustSummary, base::colMeans, base::colSums, and matrixStats::colMedians. Users should also be aware that some methods have specific input requirements. For example, robustSummary assumes that intensities have already been log transformed.\n\nHere, we use robustSummary to aggregate from PSM to peptide-level. This method is currently considered to be state-of-the-art as it is more robust against outliers than other aggregation methods.24,25 We also include na.rm = TRUE to exclude any NA values prior to completing the summarisation.\n\nWe are now left with a QFeatures object holding the PSM and peptide-level data in their own SummarizedExperiments. Importantly, an explicit link has been maintained between the two levels and this makes it possible to gain information about all PSMs that were aggregated into a peptide.\n\nIf users did not impute prior to aggregation, NA values within the PSM-level data may have propagated into NaN values. This is because peptides only supported by PSMs containing missing values would not have any quantitative value to which a sum or median function, for example, can be applied. Therefore, we check for NaN and convert back to NA values to facilitate compatibility with downstream processing.\n\nNext, using the same approach as above, we use the aggregateFeatures function to assemble the peptides into proteins. As before, we must pass several arguments to the function. Namely, the QFeatures object i.e. cp_qf, the data level we wish to aggregation from i.e. log_peptides, the column of the rowData defining how to aggregate the features i.e. by \"Master.Protein.Accessions\" and a name for the new data level e.g. \"log_proteins\". We again choose to use robustSummary as our aggregation method and we pass na.rm = TRUE to ignore NA values. Users can type ?aggregateFeatures to see more information. Users should be aware that peptides are grouped by their master protein accession and, therefore, downstream differential expression analysis will consider protein groups rather than individual proteins.\n\nFollowing aggregation, we have a total of 3289 proteins remaining within the data.\n\nAfter transforming the data, we normalise the protein-level abundances. Normalization is a process of correction whereby quantitative data is returned to its original, or ‘normal’, state. In expression proteomics, the aim of post-acquisition data normalization is to minimise the biases that arises due to experimental error and technological variation. Specifically, the removal of random variation and batch effects will allow samples to be aligned prior to downstream analysis. Importantly, however, users must also be aware of any normalization that has taken place within their sample preparation, as this will ultimately influence the presence of differentially abundant proteins downstream. An extensive review on normalization strategies, both experimental and computational, is provided in Ref. 26.\n\nUnfortunately, there is not currently a single normalization method which performs best for all quantitative proteomics datasets. Within the Bioconductor packages, however, exists NormalyzerDE, a tool for evaluating different normalisation methods.27 By passing a SummarizedExperiment object to the normalyzer function it is possible to generate a report comparing common normalisation strategies, such as total intensity (TI), median intensity (MedI), average intensity (AI), quantile (from the preprocessCore package),28 NormFinder (NM),29 Variance Stabilising Normalization (VSN, from the vsn package),30 Robust Linear Regression (RLR), and LOESS (from the limma package).31 A number of qualitative and quantitative evaluation measures are provided within the report, including total intensity, Pooled intragroup Coefficient of Variation (PCV), Pooled intragroup Median Absolute Deviation (PMDA), CV-intensity plots, MA-plots, Pearson and Spearman correlation.\n\nNormalyzer accepts intensity data in a raw format, prior to log transformation. Therefore, we first generate a protein-level SummarizedExperiment from our PSM-level data prior to transformation.\n\nHence, we will use the “proteins_direct” SummarizedExperiment here and the function will do the log2 transformation for us. A second important consideration is that missing values must be denoted ‘NA’, not zero, NaN or infinite. We can pass the SummarizedExperiment containing the protein data to the normalyzer function. With this, we provide a name for the report and the directory in which to save the report. The normalyzer function also expects two pieces of information, the sample name and corresponding experimental group. We previously annotated the data with this information through the sample and condition columns of the colData, so we tell the normalyzer function to look here.\n\nThe function will take a few minutes to run, particularly if there are many samples. Once complete, the report can be accessed as a .pdf file containing plots such as those displayed in Figure 4.\n\nBoxplots (top) and scatterplots (bottom) are two of the evaluation measures within the normalyzer report. Samples are grouped based on their condition to provide users with an easy way to evaluate the suitability of different normalization methods for their data. The log2 data can be used as a reference to compare the data pre- and post-normalization.\n\nSince the normalyzer report did not indicate any superior normalisation method in this case, we will apply a center median approach here. To do this, we pass the log transformed protein-level data to the normalize function in QFeatures. We specify the method of normalisation that we wish to apply i.e. method = \"center.median\" and name the new data level e.g. name = \"log_norm_proteins\". Of note, for users who wish to apply VSN normalisation the raw protein data must be passed (prior to any log transformation) as the log transformation is done internally when specify method = \"vsn\". All other methods require users to explicitly perform log transformation on their data before use. More details can be found in the QFeatures documentation, please type help(\"normalize,QFeatures-method\").\n\nTo evaluate the effect of normalisation we plot a simple boxplot.\n\nWe can now generate a density plot to help us visualise what the process of log transformation and normalisation has done to the data. This is done using the plotDensities function from the limma package.\n\nAfter completing all data pre-processing, we now add explicit links between our final protein-level data and the raw PSM-level data which we created as an untouched copy. This allows us to investigate all data corresponding to the final proteins, including the data that has since been removed. To do this, we use the addAssayLinks function, demonstrated below. We can check that the assay links have been generated correctly by passing our QFeatures object to the AssayLink function along with the assay of interest (i =).\n\nOne of the characteristic attributes of the QFeatures infrastructure is that explicit links have been maintained throughout the aggregation process. This means that we can now access all data corresponding to a protein, its component peptides and PSMs. One way to do this is through the use of the subsetByFeature function which will return a new QFeatures object containing data for the desired feature across all levels. For example, if we wish to subset information about the protein “Q01581”, that is hydroxymethylglutaryl-CoA synthase, we could use the following code:\n\nWe find that in this data the protein Q01581 has 15 peptides and 27 supporting its identification and quantitation. We also see that the original data prior to processing contained 42 PSMs in support of this protein.\n\nFurther, we can visualise the process of aggregation that has led to the protein-level abundance data for Q01581, as demonstrated below. Of note, this plot shows the protein data prior to normalisation.\n\nAnother benefit of the explicit links maintained within a QFeatures object is the ease at which we can determine PSM and peptide support per protein. When applying the aggregateFeatures function a column, termed \".n\", is created within the rowData of the new SummarizedExperiment. This column indicates how many lower-level features were aggregated into each new higher-level feature. Hence, \".n\" in the peptide-level data represents how many PSMs were aggregated into a peptide, whilst in the protein-level data it tells us how many peptides were grouped into a master protein. For ease of plotting, we will use the \"proteins_direct\" data generated above. Since this data was generated via direct aggregation of PSM to protein, \".n\" this will tell us PSM support per protein. We plot these data as simple histograms.\n\n\n\nAt this point, users may wish to include additional quality control filtering based on PSM and/or peptide support per protein. Given the extensive quality control filtering already applied in this workflow, we decide not to remove additional proteins based on PSM or peptide support.\n\nFinally, we save the protein-level data and export the QFeatures object into an .rda file so that we can re-load it later at convenience.\n\n\nLabel-free data processing workflow\n\nHaving discussed the processing of quantitative TMT-labelled data, we now move on to consider that of label-free quantitative (LFQ) data. As described previously, the cell culture supernatant fractions of triplicate control and treated HEK293 cells were kept label-free. As such, each sample was analysed using an independent mass spectrometry run without pre-fractionation. Again, a two-hour gradient in an Orbitrap Lumos Tribrid mass spectrometer coupled to an UltiMate 3000 HPLC system was applied. Given that much of the TMT pre-processing workflow also applies to label-free data, we only discuss steps which are different to those previously described. Readers are advised to refer to the TMT processing workflow for a more in-depth explanation of any shared steps.\n\nAs was the case for TMT labelled cell pellets, raw LFQ data from supernatant samples was searched using Proteome Discoverer 2.5. The GitHub repository associated with this manuscript can be found at https://github.com/CambridgeCentreForProteomics/f1000_expression_proteomics which contains the identification search along with an additional explanation of key parameters in an appendix. To begin processing LFQ data, users should export a peptide-level .txt file from the results of their identification search.\n\nUnlike the TMT-labelled use-case data which was processed from the PSM-level, the label-free use-case data can only be considered from the peptide-level up. This is because a retention time alignment algorithm (equivalent to match between runs) was applied to the PSM-level data. This means that peptides can be identified in samples even without a corresponding PSM, simply by sharing feature information across runs.\n\nWe locate the PeptideGroups .txt file and upload this into a QFeatures data container in the same way as before. Since the samples are already stored in the correct order, we simply identify the quantitative columns by their indices.\n\nIn the code chunk below, we again use the readQFeatures function to import our data into R and create a QFeatures object. We find the abundance data is located in columns 21 to 26 and thus pass this to ecol. After import we annotate the colData.\n\nNext, we check the names of the features within the peptide-level rowData. These features differ from those found at the PSM-level and users should be aware that they have reduced post-search control over the quality of PSMs included in the peptide quantitation, and which method of aggregation is used to define these. Proteome Discoverer uses the sum of PSM quantitative values to calculate peptide-level values. Other third-party softwares may use different methods.\n\nWe also determine the number of PSMs, peptides and proteins represented within the initial data. Since identical peptide sequences with different modifications are stored as separate entities, the output of dim will not tell us the number of peptides. Instead, we need to consider only unique peptide sequence entries, as demonstrated in the code chunk below.\n\nThus, the search identified 144302 PSMs corresponding to 20312 peptides and 3941 proteins. Finally, we take a look at some of the key parameters applied during the identification search. This is an important verification step, particularly for those using publicly available data with limited access to parameter settings.\n\nThe preliminary data is as expected so we continue on to evaluate the quality of the raw data.\n\nTo briefly assess the quality of the raw mass spectrometry data from which the search results were derived, we create simple plots. In contrast to the previous PSM processing workflow, we do not have access to information about ion injection times from the peptide-level file. However, we can still look at the peptide delta mass across retention time, as well as the frequency of peptides across the retention time gradient.\n\nFor a more in-depth discussion of these plots users should refer back to the TMT processing workflow. Since neither plot indicates any major problems with the MS runs, we continue on to basic data cleaning.\n\nAs discussed in detail above, there are several basic data cleaning steps which are non-specific and should be applied to all quantitative datasets, regardless of the quantitation method or data level (PSM, peptide or protein). These steps are as follows:\n\n1. Removal of features without a master protein accession\n\n2. Removal of features corresponding to protein groups which contain a contaminant\n\n3. Removal of features without quantitative data\n\n4. (Optional) Removal of features which are not unique to a protein group\n\n5. Removal of features not allocated rank 1 during the identification search\n\n6. Removal of features not annotated as unambiguous\n\nIn addition to these standard steps, LFQ data should be filtered to remove peptides that were not quantified based on a monoisotopic peak. The monoisotopic peak is that which comprises the most abundant natural isotope of each constituent element. For bottom-up proteomics, this typically translates to the peptides containing carbon-12 and nitrogen-14. When the different isotopes are well resolved, the monoisotopic peak usually provides the most accurate measurement.\n\nBefore we remove any data, we first create a second copy of the original SummarizedExperiment, as to retain a copy of the raw data for reference. As before we use the addAssay function.\n\nHere, cleaning is done is two steps. The first is the removal of contaminant proteins using the self-defined find_cont function. Refer back to the TMT processing workflow for more details.\n\nSecond, we carry out all remaining cleaning using the filterFeatures function as before.\n\nAs before, we check to see whether additional annotations remain within the “Quan.Info” column.\n\nAs in the previous example, we assess the impact that cleaning has had on the data. Specifically, we determine the number and proportion of PSMs, peptides and proteins lost. Again, when we refer to the number of peptides we only consider unique peptide sequences, not those that differ in their modifications.\n\nWhen extracting data from the peptide-level .txt file rather than aggregating up from a PSM file, additional parameters exist within the peptide rowData. Such parameters include Quality PEP, Quality q-value, and SVM score, as well as similar scoring parameters provided by the search engine. Although we will not complete additional filtering based on these parameters in this workflow, users may wish to explore this option.\n\nHaving cleaned the peptide-level data we now move onto the management of missing data. This is of particular importance for LFQ workflows where the missing value challenge is amplified by intrinsic variability between independent MS runs. As before, the management of missing data can be divided into three steps: 1) exploring the presence and distribution of missing values, (2) filtering out missing values, and (3) optional imputation.\n\nThe aim of the first step is to determine how many missing values are present within the data, and how they are distributed between samples and/or conditions.\n\nAs expected, the LFQ data contains a higher proportion of missing values as compared to the TMT-labelled data. There are 15863 missing (NA) values within the data, which corresponds to 15%. We check for sample- and condition-specific biases in the distribution of these NA values.\n\nWhilst S1 and S4 have a slightly higher proportion of missing values, all of the samples are within an acceptable range to continue. Again, there is no evidence of a condition-specific bias in the data.\n\nWe next filter out features, here peptides, which comprise 20% or more missing values.\n\nFinally, we check how many missing values remain in the data before making a decision as to whether imputation is required.\n\nThere are 2452 missing values remaining. The presence of proteins with single or low peptide support means that some of these NA values will likely be propagated upward during aggregation. Whilst NA values were traditionally problematic during the application of downstream statistical methods, there are now a number of algorithms that allow statistics to be completed on data containing missing values. For example, the MSqRob224,25,32 package facilitates statistical differential expression analysis on datasets without the need for imputation and functions within the QFeatures infrastructure. Nevertheless, for the purpose of demonstration, we here choose to impute the raw intensity data.\n\nAs eluded to above, the most appropriate method to determine such probable values is dependent upon why the value is missing, that is whether it is MCAR or MNAR. Although the optimal imputation method is specific to each dataset, left-censored methods (e.g. minimal value approaches, limit of detection) have proven favorable for data with a high proportion of MNAR values whilst hot deck methods (e.g. k-nearest neighbours, random forest, maximum likelihood methods) are more appropriate when the majority of missing data is MCAR [e.g. Refs. 23, 33]. Within the QFeatures infrastructure imputation is carried out by passing the data to the impute function, please see ?impute for more information. To see which imputation methods are supported by this function we use the following code:\n\nUnfortunately, it is very challenging to determine the reason(s) behind missing data, and in most cases experiments contain a mixture of MCAR and MNAR. For LFQ data where little is know about the cause of missing values it is advisable to use methods optimised for MCAR. Here we will use the baseline k-nearest neighbours (k-NN) imputation on the raw peptide intensities. Of note, users who wish to utilise an alternative imputation method should check whether their selected method has a requirement for normality. If the method requires data to display a normal distribution, users must log2 transform the data prior to imputation.\n\nFollowing imputation we check to ensure that the distribution of the data has not dramatically changed. To do so we create a density plot of the data pre- and post-imputation.\n\nFrom this plot the change in the data appears to be minimal. We can further validate this by comparing the summary statistics of the data pre- and post-imputation.\n\nComparison of the two tables reveals minimal change within the data. However, we find that S1 and S4 display greater differences between pre- and post-imputation statistics because of the higher number of missing values which required imputation.\n\nIn the following code chunk we log2 transform the peptide-level data to generate a near-normal distribution within the quantitative data. This is necessary prior to the use of robustSummary aggregation.\n\nNow that we are happy with the peptide-level data, we aggregate upward to proteins using the aggregateFeatures function.\n\nFinally, we complete the data processing by normalising quantitation between samples. This is done using the \"center.median\" method via the normalize function.\n\nThe final dataset is comprised of 2837 proteins. We will save the protein-level SummarizedExperiment file as well as exporting the final QFeatures object.\n\n\nExploration of protein data\n\nHaving described the processing steps for quantitative proteomics data, we next demonstrate how to explore the protein-level data prior to statistical analysis. For this we will utilise the TMT-labelled cell pellet dataset since it contains a greater number of proteins.\n\nWe will first generate correlation plots between pairs of samples. To do this we use the corrplot package to calculate and plot the Pearson’s correlation coefficient between each sample pair. The cor function within the corrplot package will create a correlation matrix but requires a data.frame, matrix or a vector of class numeric as input. To convert the QFeatures assay data into a data.frame we use the as.data.frame function.\n\nNow we can visualise the correlation data using pairwise scatter plots and a correlation heat map.\n\nFrom these plots we can see that all replicate pairs have a Pearson’s correlation coefficient >0.98 whilst the correlation between pairs of control and treated samples is somewhat lower. Users may interpret this information as an early indication that some proteins may be differentially abundant between the two groups.\n\nOf note, whilst correlation is widely applied as a measure of reproducibility, users are reminded that correlation coefficients alone are not informative of reproducibility.34,35 This is especially true for expression proteomics data in which high correlation values are likely due to the majority of proteins remaining at similar levels regardless of cellular perturbation. Users are directed to Ref. 36 for additional information regarding how to determine the calculation of experimental reproducibility.\n\nPrincipal Component Analysis (PCA) is a dimensionality reduction method which aims to simplify complex datasets and facilitate the visualisation of multi-dimensional data. Here we use the prcomp function from the stats package to perform the PCA. Since PCA does not accept missing values and we did not impute the TMT data, the filterNA function can be used to remove any missing values that may be present in the protein-level data. We then extract and transpose the assay data before passing it to the prcomp function to carry out PCA.\n\nWe can get an idea of the outcome of the PCA by running the summary function on the results of the PCA.\n\nFinally, we create a PCA plot. For additional PCA exploration and visualization tools users are directed to the factoextra package.\n\nBefore carrying out differential expression analysis, it is first necessary to explore the presence of batch effects within the data. Batch effects are derived from non-biological factors which impact the experimental data. These include reagents, instrumentation, personnel and laboratory conditions. In most cases the increased variation caused by batch effects will lead to reduced downstream statistical power. On the other hand, if correlated with the experimental sub- groups, batch effects can also lead to confounded results and the incorrect biological interpretation of differential expression.37\n\nGiven that the use-case data was derived from a small experiment with only six samples and a single TMTplex, there are minimal batch effects to explore here. For users analysing larger experiments completed over long period of time, across several laboratories/individuals, or using multiple TMTplex reagents, it is advisable to annotate the PCA plot with all potential batch factors. If data is found to cluster based on any of these factors, batch effects should be incorporated into downstream analyses. For example, users can apply the removeBatchEffect function from the limma package.\n\nThe last section of this workflow demonstrates how to gain biological insights from the resulting list of proteins. Again we will utilise the TMT-labelled cell pellet data, although the process would be exactly the same for the LFQ supernatant protein list. Users are reminded that although referred to as differential ‘expression’ analysis, abundance is determined by both protein synthesis and degradation.\n\nWe first extract the protein-level SummarizedExperiment from the cell pellet TMT QFeatures object and specify the study factors. Here we are interested in discovering differences between conditions, control and treated. As well as assigning these conditions to each sample, we can define the control group as the reference level such that differential abundance is reported relative to the control. This means that when we get the results of the statistical analysis, ‘upregulated’ will refer to increased abundance in treated cells relative to control controls.\n\nBioconductor contains several packages dedicated to the statistical analysis of proteomics data. For example, MSstats and MSstatsTMT can be used to determine differential protein expression within both DDA and DIA datasets for LFQ and TMT, respectively.38,39 Of note, MSstatsTMT includes additional functionality for dealing with larger, multi-plexed TMT experiments. For LFQ experiments, proDA, prolfqua and MSqRob2 can be utilised, among others.32,40 Here, we will use the limma package.41 limma is widely used for the analysis of large omics datasets and has several models that allow differential abundance to be assessed in multifactorial experiments. This is useful because it allows multiple factors, including TMTplex, to be integrated into the model itself, thus minimising the effects of confounding factors. In this example we will apply limma’s empirical Bayes moderated t-test, a method that is appropriate for small sample sizes.31\n\nWe first use the model.matrix function to create a matrix in which each of the samples are annotated based on the factors we wish to model, here the condition group. This ultimately defines the ‘design’ of the model, that is how the samples are distributed between the groups of interest. We then fit a linear model to the abundance data of each protein by passing the data and model design matrix to the lmFit function. Finally, we update the estimated standard error for each model coefficient using the eBayes function. This function borrows information across features, here proteins, to shift the per-protein variance estimates towards an expected value based on the variance estimates of other proteins with similar mean intensity. This empirical Bayes technique has been shown to reduce the number of false positives for proteins with small variances as well as increase the power of detection for differentially abundant proteins with larger variances.42 Further, we use the trend = TRUE argument when passing the eBayes function so that an intensity-dependent trend can be fitted to the prior variances. For more information about the limma trend method users are directed to Ref. 43.\n\nHaving applied the model to the data, we need to verify that this model was appropriate and that the statistical assumptions were met. To do this we first generate an SA plot using the plotSA function within limma. An SA plot shows the log2 residual standard deviation (sigma) against log average abundance and is a simple way to visualise the trend that has been fitted to the data.\n\nThe residual standard deviation is a measure of model accuracy and is most easily conceptualised as a measurement of how far from the model prediction each data point lies. The smaller the residual standard deviation, the closer the fit between the model and observed data.\n\nNext we will plot a p-value histogram. Importantly, this histogram shows the distribution of p-values prior to any multiple hypothesis test correction or FDR control. This means plotting the P.value variable, not the adj.P.Val.\n\nThe figure displayed shows an anti-conservative p-value distribution. The flat distribution across the base of the graph represents the non-significant p-values spread uniformly between 0 and 1, whilst the peak close to 0 contains significant p-values, along with some false positives. For a more thorough explanation of interpreting p-value distributions, including why your data may not produce an anti-conservative distribution if your statistical model is inappropriate, please see Ref. 44. Now, having applied the statistical model and verified it’s suitability, we take an initial look at the outputs.\n\nThe results table contains several important pieces of information. Each master protein is represented by its accession number and has an associated log2 fold change, that is the log2 difference in mean abundance between conditions, as well as a log2 mean expression across all six samples, termed AveExpr. Since we carried out an empirical Bayes moderated t-test, each protein also has a moderated t-statistic and associated p-value. The moderated t-statistic can be interpreted in the same way as a standard t-statistic. Each protein also has an adjusted p-value which accounts for multiple hypothesis testing to control the overall FDR. The default method for multiple hypothesis corrections within the topTable function that we applied is the Benjamini and Hochberg (BH) adjustment,45 although we could have specified an alternative. Finally, the B-statistic represents the log-odds that a protein is differentially abundant between the two conditions, and the data is presented in descending order with those with the highest log-odds of differential abundance at the top.\n\nWe can add annotations to this results table based on the user-defined significance thresholds. In the literature, for stringent analyses an FDR-adjusted p-value threshold of 0.01 is most frequently used, or 0.05 for exploratory analyses. Ultimately these thresholds are arbitrary and set by the user. The addition of a log-fold change (logFC) threshold is at the users discretion and can be useful to determine significant results of biological relevance. When using a TMT labelling strategy the co-isolation interference can lead to substantial and uneven ratio compression, thus it is not recommended to apply a fold change threshold here.\n\nIn the next code chunk, we use the decideTests function to determine how many proteins are significantly up- and down- regulated in the treated compared to control HEK293 cells. We tell this function to classify the significance of each t-statistic based on a BH-adjusted p-value of 0.01. If we had not used TMT labels and wished to include a logFC threshold, we could have included lfc = as an argument. The function will then output a numerical matrix containing either -1, 0, or 1 for each protein in each condition, where a value of -1 indicates significant downregulation, 0 not significant and 1 significant upregulation. To simplify interpretation, we print a summary of this matrix.\n\nFrom this table we can see that 395 proteins were downregulated in treated HEK293 cells compared to the control group whilst 325 were upregulated. Given that no logFC threshold was applied some of the significant differences in abundance may be small. Further, these results mean little without any information about which proteins these were and what roles they play within the cell. We subset the significant proteins so that we can investigate them further.\n\nBefore looking deeper into which proteins have differential abundance, we first create some simple plots to visualise the results. Volcano plots and MA plots are two of the common visualisations used in this instance. When plotting the former, users are advised to plot raw p-values rather than their derivative BH-adjusted p-values. Point colours can be used to indicate significance based on BH-adjusted p-values, as is shown in the code chunk below.\n\nThe final step in the processing workflow is to apply Gene Ontology (GO) enrichment analyses to gain a biological understanding of the proteins which were either up or downregulated in HEK293 cells upon treatment. GO terms provide descriptions for genes and their corresponding proteins in the form of Molecular Functions (MF), Biological Processes (BP) and Cellular Components (CC). By carrying out GO enrichment analysis we can determine whether the frequency of any of these terms is higher than expected in the proteins of interest compared to all of the proteins which were detected. Such results can indicate whether proteins that were increased or decreased in abundance in treated HEK293 cells represent particular cellular locations, biological pathways or cellular functions.\n\nAlthough GO enrichment analysis can be carried out online using websites such as GOrilla46 or PantherDB,47,48 we advise against this due to a lack of traceability and reproducibility. Instead, readers are advised to make use of GO enrichment packages within the Bioconductor infrastructure. Many such packages exist, including topGO,49 GOfuncR,50 and clusterProfiler.51 Here we will use enrichGO function in the clusterProfiler package.\n\nFirst, we subset the accessions of proteins that we consider to be significantly up or downregulated. These will be our proteins of interest.\n\nNext, we input the UniProt IDs of up and downregulated proteins into the GO enrichment analyses, as demonstrated below. Importantly, we provide the protein list of interest as the foreground and a list of all proteins identified within the study as the background, or ‘universe’. The keyType argument is used to tell the function that our protein accessions are in UniProt format. This allows mapping from UniProt ID back to a database containing the entire human genome (org.Hs.eg.db). We also inform the function which GO categories we wish to consider, here “ALL”, meaning BP, MF and CC.\n\nAs well as the information outlined above, there is the opportunity for users to specify various thresholds for statistical significance. These include thresholds on original and adjusted p-values (using the pvalueCutoff argument) as well as q-values (via the qvalueCutoff argument). Although many papers often use ‘q- value’ to mean ‘BH-adjusted p-value’, the two are not always the same and users should be explicit about the statistical thresholds that they have applied. For exploratory purposes we will use the standard BH method for FDR control and set p-value, BH-adjusted p-value, and q-value thresholds of 0.05.\n\nWe can see from the results that there are 2 significantly enriched terms associated with the upregulated proteins. Next, we take a look at the downregulated proteins.\n\nThe downregulated proteins contain 69 significantly enriched GO terms. There are many ways in which users can represent these results visually. Here, we create a barplot using the barplot function from the enrichplot package.52 Users are directed to the vignette of the enrichplot package for additional visualisation options and guidance. We plot the first 10 GO terms i.e. the 10 GO terms with the greatest enrichment.\n\n\nWriting and exporting data\n\nFinally, we export the results of our statistical analyses as .csv files.\n\nUsers can also use the ggsave function to export any of the figures generated.\n\n\nDiscussion and conclusion\n\nExpression proteomics is becoming an increasingly important tool in modern molecular biology. As more researchers participate in expression proteomics, either by collecting data or accessing data collected by others, there is a need for clear illustration(s) of how to deal with such complex data.\n\nExisting bottom-up proteomics workflows for differential expression analysis either provide pipelines with limited user control and flexibility (e.g., MSstats and MSstatsTMT38,39), can only be applied to specific data formats (e.g., Proteus which is limited to input from MaxQuant53), or provide very limited commentary. The latter directly contributes to a problematic disconnect between researchers and their data whereby the users do not understand if or why each step is necessary for their given dataset and biological question. This can prevent researchers from refining a workflow to fit their specific needs. Finally, the majority of proteomics workflows utilise data.frame or tibble structures which limits their traceability, as is the case for protti, promor and prolfqua.54–56\n\nThe workflow presented here outlines in completion how to process, analyse and interpret LFQ and TMT expression proteomics data derived from a bottom-up DDA experiment. Critically, we emphasize quality control and data-guided decisions with an extensive explanation of all key steps and how they may differ in various scenarios (e.g., the quantitation method, instrumentation and biological question). Our workflow takes advantage of the relatively recent QFeatures infrastructure to ensure explicit and transparent data pre-processing as well as to provide an easy way for users to trace back through their analyses. These features are particularly important for beginners who wish to gain a better understanding of their data and how it changes throughout this workflow.\n\nNo single workflow can demonstrate the processing, analysis and interpretation of all proteomics data. Our workflow is currently suitable for DDA datasets with label-free or TMT-based quantitation. We do not include examples of experiments that combine data from multiple TMTplexes, although the code provided could easily be expanded to include such a scenario. This workflow provides an in-depth user-friendly pipeline for both new and experienced proteomics data analysts.\n\n\nSession information and getting help\n\nThe workflows provided involve use of functions from many different R/Bioconductor packages. The sessionInfo function provides an easy way to summarize all packages and corresponding their versions used to generate this document. Should software updates lead to the generation of errors or different results to those demonstrated here, such changes should be easily traced.\n\nUsers are advised to update R itself as well as packages as required. Bioconductor packages can be updated using the BiocManager::install() function, as shown below.\n\n\nAuthor contributions\n\nC. H. conceptualisation, investigation, methodology, project administration, software, validation, writing – original draft preparation, review and editing; C. S. D. software and writing - review and editing; T. K. methodology, supervision, software, writing - review and editing; K. S. L. funding acquisition, supervision, writing - review and editing; L. M. B. conceptualisation, methodology, supervision, writing - review and editing.", "appendix": "Data availability\n\nThis workflow is written in the R statistical programming language and uses freely available open-source software packages from CRAN and Bioconductor. Version numbers for all packages are shown in the Session information section.\n\nRaw mass spectrometry data is freely available online through the ProteomeXchange Consortium via the PRIDE repository with identifier PXD041794. All processed data is available at http://doi.org/10.5281/zenodo.7837375, and at GitHub repository https://github.com/CambridgeCentreFor Proteomics/f1000_expression_proteomics .\n\n\nAcknowledgements\n\nThe authors would like to thank Savvas Kourtis from the Centre for Genomic Regulation, Barcelona, and Oliver M. Crook, from the Department of Statistics, Oxford University, UK, for trialing this workflow.\n\n\nReferences\n\nPina-Jiménez E, Calzada F, Bautista E, et al.: Incomptine a induces apoptosis, ROS production and a differential protein expression on non-hodgkin’s lymphoma cells. Int. J. Mol. Sci. September 2021; 22(19): 10516. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmiri-Dashatan N, Ahmadi N, Rezaei-Tavirani M, et al.: Identification of differential protein expression and putative drug target in metacyclic stage of leishmania major and leishmania tropica: A quantitative proteomics and computational view. Comp. Immunol. Microbiol. Infect. Dis. April 2021; 75: 101617. PubMed Abstract \| Publisher Full Text\n\nAnitua E, de la Fuente M , Muruzabal F, et al.: Differential profile of protein expression on human keratocytes treated with autologous serum and plasma rich in growth factors (PRGF). PLoS One. October 2018; 13(10): e0205073. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDupree EJ, Jayathirtha M, Yorkey H, et al.: A critical review of bottom-up proteomics: The good, the bad, and the future of this field. Proteomes. July 2020; 8(3): 14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nObermaier C, Griebel A, Westermeier R: Principles of protein labeling techniques. Methods in Molecular Biology. New York: Springer; 2015; 153–165. Publisher Full Text\n\nFernández-Costa C, Martínez-Bartolomé S, McClatchy DB, et al.: Impact of the identification strategy on the reproducibility of the DDA and DIA results. J. Proteome Res. June 2020; 19(8): 3153–3161. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlex H, Noble WS, Wolf-Yadlin A: Technical advances in proteomics: new developments in data-independent acquisition. F1000Res. March 2016; 5: 419. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nR Development Core Team: R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2011. 3-900051-07-0. Reference Source\n\nHuber W, Carey VJ, Gentleman R, et al.: Orchestrating high-throughput genomic analysis with bioconductor. Nat. Methods. January 2015; 12(2): 115–121. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHutchings C, Dawson C, Krueger T, et al.: A Bioconductor workflow for processing, evaluating and interpreting expression proteomics data.2023. Reference Source\n\nMcAlister GC, Nusinow DP, Jedrychowski MP, et al.: MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal. Chem. July 2014; 86(14): 7150–7158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTing L, Rad R, Gygi SP, et al.: MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods. October 2011; 8(11): 937–940. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlubell DL, Wilmarth PA, Zhao Y, et al.: Extended multiplexing of tandem mass tags (TMT) labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue. Mol. Cell. Proteomics. May 2017; 16(5): 873–890. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrenes A, Hukelmann J, Bensaddek D, et al.: Multibatch TMT reveals false positives, batch effects and missing values. Mol. Cell. Proteomics. October 2019; 18(10): 1967–1980. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPerez-Riverol Y, Bai J, Bandla C, et al.: The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. November 2021; 50(D1): D543–D552. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeutsch EW, Bandeira N, Perez-Riverol Y, et al.: The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res. November 2022; 51(D1): D1539–D1548. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGatto L, Vanderaa C: QFeatures: Quantitative features for mass spectrometry data. R package version 1.9.2. 2023. Reference Source\n\nMorgan M, Obenchain V, Hester J, et al.: SummarizedExperiment: SummarizedExperiment container. R package version 1.29.1. 2022. Reference Source\n\nRainer J, Vicini A, Salzer L, et al.: A modular and expandable ecosystem for metabolomics data annotation in r. Metabolites. February 2022; 12(2): 173. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFrankenfield AM, Ni J, Ahmed M, et al.: Protein contaminants matter: Building universal protein contaminant libraries for DDA and DIA proteomics. J. Proteome Res. July 2022; 21(9): 2104–2113. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPages H, Aboyoun P, Gentleman R, et al.: Biostrings: Efficient Manipulation of Biological Strings. R package version 2.66.0. 2022.\n\nKarpievitch Y, Stanley J, Taverner T, et al.: A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics. June 2009; 25(16): 2028–2034. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLazar C, Gatto L, Ferro M, et al.: Accounting for the multiple natures of missing salues in label-free quantitative proteomics data sets to compare imputation strategies. J. Proteome Res. March 2016; 15(4): 1116–1125. PubMed Abstract \| Publisher Full Text\n\nSticker A, Goeminne L, Martens L, et al.: Robust summarization and inference in proteome-wide label-free quantification. Mol. Cell. Proteomics. July 2020; 19(7): 1209–1219. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoeminne LJE, Gevaert K, Clement L: Peptide-level robust ridge regression improves estimation, sensitivity, and specificity in data-dependent quantitative label-free shotgun proteomics. Mol. Cell. Proteomics. February 2016; 15(2): 657–668. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nO’Rourke MB, Town SEL, Dalla PV, et al.: What is normalization? the strategies employed in top-down and bottom-up proteome analysis workflows. Proteomes. August 2019; 7(3): 29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWillforss J, Chawade A, Levander F: NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis. J. Proteome Res. October 2018; 18(2): 732–740. PubMed Abstract \| Publisher Full Text\n\nBolstad B: preprocessCore: A collection of pre-processing functions. R package version 1.60.2. 2023.\n\nAndersen CL, Jensen JL, Ørntoft TF: Normalization of real-time quantitative reverse transcription-PCR data: A model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. August 2004; 64(15): 5245–5250. PubMed Abstract \| Publisher Full Text\n\nHuber W, von Heydebreck A , Sültmann H, et al.: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. July 2002; 18(suppl_1): S96–S104. Publisher Full Text\n\nSmyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. January 2004; 3(1): 1–25. PubMed Abstract \| Publisher Full Text\n\nGoeminne LJE, Sticker A, Martens L, et al.: MSqRob takes the missing hurdle: Uniting intensity- and count-based proteomics. Anal. Chem. March 2020; 92(9): 6278–6287. PubMed Abstract \| Publisher Full Text\n\nLiu M, Dongre A: Proper imputation of missing values in proteomics datasets for differential expression analysis. Brief. Bioinform. June 2021; 22(3). PubMed Abstract \| Publisher Full Text\n\nIrizarry R: Correlation is not a measure of reproducibility.2015. Reference Source\n\nBunting KV, Steeds RP, Slater LT, et al.: A practical guide to assess the reproducibility of echocardiographic measurements. J. Am. Soc. Echocardiogr. December 2019; 32(12): 1505–1515. PubMed Abstract \| Publisher Full Text\n\nDarbani B, Stewart CN: Reproducibility and reliability assays of the gene expression-measurements. J. Biol. Res (Thessalon). May 2014; 21(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeek JT, Scharpf RB, Bravo HC, et al.: Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. September 2010; 11(10): 733–739. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoi M, Chang C-Y, Clough T, et al.: MSstats: an r package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics. May 2014; 30(17): 2524–2526. PubMed Abstract \| Publisher Full Text\n\nHuang T, Choi M, Tzouros M, et al.: MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures. Mol. Cell. Proteomics. October 2020; 19(10): 1706–1723. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWolski WE, Nanni P, Grossmann J, et al.: prolfqua: A comprehensive R-package for proteomics differential expression analysis. J. Proteome Res. March 2023; 22(4): 1092–1104. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRitchie ME, Phipson B, Di W, et al.: limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. January 2015; 43(7): e47–e47. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPhipson B, Lee S, Majewski IJ, et al.: Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. Ann. Appl. Stat. June 2016; 10(2): 946–963. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLaw CW, Chen Y, Shi W, et al.: voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014; 15(2): R29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobinson D: How to interpret a p-value histogram.2014. Reference Source\n\nBenjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 1995; 57(1): 289–300. Publisher Full Text\n\nEden E, Navon R, Steinfeld I, et al.: GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics. February 2009; 10(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMi H, Muruganujan A, Thomas PD: PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. November 2012; 41(D1): D377–D386. Publisher Full Text\n\nThomas PD, Ebert D, Muruganujan A, et al.: PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. November 2021; 31(1): 8–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlexa A\": topGO: Enrichment Analysis for Gene Ontology. R package version 2.50.0. 2022.\n\nGrote S: GOfuncR: Gene ontology enrichment using FUNC. R package version 1.18.0. 2022.\n\nTianzhi W, Erqiang H, Shuangbin X, et al.: clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation. August 2021; 2(3): 100141. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYu G: enrichplot: Visualization of Functional Enrichment Result. R package version 1.18.3. 2022.\n\nGierlinski M, Gastaldello F, Cole C, et al.: Proteus: an R package for downstream analysis of maxquant output. bioRxiv. 2018. Publisher Full Text\n\nRanathunge C, Patel SS, Pinky L, et al.: promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling. bioRxiv. 2023. Publisher Full Text\n\nQuast J-P, Schuster D, Picotti P: protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data. Bioinform. Adv. December 2021; 2(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWolski WE, Nanni P, Grossmann J, et al.: Ralph Schlapbach, and Christian Panse. prolfqua: A comprehensive r-package for proteomics differential expression analysis. bioRxiv. 2022. Publisher Full Text" }	[ { "id": "221416", "date": "27 Nov 2023", "name": "Diogo Borges Lima", "expertise": [ "Reviewer Expertise I have experience in proteomics analyses (qualitative and quantitative)", "XL-MS analysis. I also develop software for identifying and quantifying proteomics datasets." ], "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 entitled \"A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data\" regards a full and comprehensive workflow for performing not only qualitative but also quantitative proteomics analysis.\nThe manuscript is very well written and describes in detail the whole workflow for quantifying proteomics data. The authors focused on the LFQ analysis and TMT (for labeled datasets). However, this workflow relies on the results from a search engine that will provide the identified peptides. On this manuscript the authors used results from Proteome Discoverer.\nI recommended the publication, but I would like to pinpoint some minor comments:\na) Although the authors mentioned the quantitation analyses by using TMT for labeled datasets, why they didn't show the analysis by using SILAC, once it uses XIC (the same strategy used by LFQ)?\nb) The authors used Proteome Discoverer as search engine, and the provided a template to import the results into the workflow. They could also provide other templates to turn this workflow more versatile, such as FragPipe, Patternlab for Proteomics, etc.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "12036", "date": "25 Sep 2024", "name": "Lisa Breckels", "role": "Author Response", "response": "We thank Dr. Lima for taking the time to review our workflow paper. The main aim of this workflow was to provide an overview of the essential steps required for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. We show two use case examples, one labelled TMT experiment and one label-free experimental design. It would have been nice to also include a SILAC use-case example, among other designs, but in the interest of length of the workflow we chose these two designs as they are typically the most popular in the field. Further, statistical analysis of SILAC experiments often applies a ratiometric approach, which differs from the statistics discussed here. As Dr. Lima states we indeed use Proteome Discoverer to process the data and show how to import a PSM, peptide or protein .txt data table into R and into a QFeatures object. All third-party MS search engines typically output a data table of quantitation data and for flexibility this is where we start our analysis. Header names in the output data will differ between softwares but should be transferable. Another popular third-party software used for quantitation and identification is MaxQuant and we have added a new section in the Appendix of our Github repository to show users how one might use data from MaxQuant in the context of this workflow." } ] }, { "id": "221410", "date": "27 Nov 2023", "name": "Marie Locard-Paulet", "expertise": [ "Reviewer Expertise I work on MS-based proteomics data analysis and computational mass spectrometry." ], "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 provide the full description of a R-based workflow applied to quantitative proteomics data analysis (TMT and label-free data). It makes use of QFeature objects, a structure that is very well suited for bottom-up proteomics data analysis. I think that this is a very nice step-by-step tutorial for MS-based proteomics data analysis with R for people who start in the field and have limited coding skills. Beyond its educational aspect, it provides the backbones of a data analysis pipeline that can be modified and published alongside any manuscript that includes MS-based proteomics data analysis.\nThe manuscript is very well written, and the authors provide very clear and detailed instructions on how to use the workflow. The figures are also very clear and informative. They present the data, detail what quality control to perform to assess if the data are suitable for statistical analysis. This workflow contains a lot of useful QC plots and checks that are often overlooked, including TMT labelling efficiency calculation. It makes it a good step-by-step guide on how to analyze TMT-labelled bottom-up data. I really like the description on how to double check quality metrics such as S/N and isolation interference to adapt them to the data.\nThe raw data is available in PRIDE and all the fasta files and the Proteome Discoverer output files are in Zenodo. The code is in a github repository. I easily found all the data associated with this manuscript.\nMajor comments:\nIt should be made clear that this script is tailored for Proteome Discoverer outputs (and maybe even for a given version of Proteome Discoverer). For most of the plotting/filtering/analysis steps, changing input would only require adapting the column names/headers, and most of the time it is very well discussed by the authors. Nevertheless, right now this script is only adapted to Proteome Discoverer outputs and this should be made clear in the abstract and the introduction, as well as the discussion.\n\nAggregation of PSM quantification values to peptides and proteins:\nHere, the authors choose to aggregate all PSM intensities corresponding to the same sequence (stripped of its modifications). I would aggregate the PSM quantities per peptidoform (sequence + localized modifications) since two ions can have the same sequence but with modifications that are differentially regulated between the conditions compared. This should be mentioned.\n\nFor the GO-term enrichment: only the majority protein accessions are reported in the output of the limma analysis. So there is only one gene per feature. How do you make sure that it is the most representative annotation for a given protein group? I am fully aware that this issue is ignored by the community (for lack of alternative strategy), and that most of the time people just pick one accession per group for GO-term enrichment analysis. So, I am not asking the authors to find a solution. Nevertheless, it would be nice to mention that the output of the enrichment will depend on what accession is picked per group.\nMinor comments:\nI would remove contaminants before estimation of TMT labelling efficiency.\n\nI find the paragraph “Additional considerations regarding protein isoforms” unclear. The authors should rephrase sentences such as this one: “PSMs or peptides that were previously mapped to one protein and one protein group could instead be mapped to multiple proteins and one protein group.” Maybe they should use the term “canonical protein” to be more precise?\nIn any cases, the issue of peptide uniqueness does not depend only on the presence of isoforms in the fasta file but also on the strategy that was chosen for protein inference. I agree with the authors that people should precisely describe what peptides/PSMs were used for quantification, and it is good to mention it. Nevertheless, this level of detail on general MS-based proteomics concept may not be necessary here. (So the entire paragraph on isoforms could maybe be removed, especially since isoforms are not mentioned later).\n\nIn the paragraph “Removing PSMs that are not rank 1”:\nI think that the “PSM category” that is discussed a bit later is specific of Proteome Discoverer. Some search engines report PSMs of equal score (this would correspond to the “pretty rank” in Mascot). I don’t think that all this should necessarily be discussed in this manuscript, but I insist on the fact that the workflow is tuned for Proteome Discoverer output and this should be made clear in the introduction/abstract.\n\nIn the paragraph “Managing missing data” for the TMT:\nthe authors mention MCAR, MAR, and MNAR, but do they all apply here? I would expect TMT-labelled data to mostly have missing values due to ions being under the limit of detection because when an ion is fragmented, the reporter ions used for relative quantification are often all detected. Isn’t it the case? Knowing this should restrict the choice for a more suited strategy of replacement of missing values.\nStill on missing values: page 33, it is stated that “Typically, it is desirable to remove features, here PSMs, with greater than 20% missing values”. Why this number? Is this accepted by the entire community? (this comment also applies to the same step in the LFQ analysis.\nRegarding missing value replacement (discussion on LFQ, page 55): it is really nice to provide references of strategies applied to replacement of missing values. It is indeed a tricky decision to make (how to replace? Should we replace?) and there is no one-size-fits-them-all method. Why do you choose to replace at peptide level and not protein level?\n\nPage 38: what do the authors mean by “report did not indicate any superior normalization method”? How would we know what normalization method works best? This point is because I am curious, not to correct any obvious mistake. It is great to try out different normalization strategies, but I don’t really see how to pick one based on the boxplots of normalized intensities (Figure 4).\n\nThe authors normalize the data after protein aggregation and not at the PSM level. Is this general practice? Wouldn’t it make sense to normalize before aggregation?\n\nPage 44; “Data import, housekeeping and exploration”:\nthe authors mention that LFQ analysis cannot be performed at PSM level but has to be done at peptide level. I think that this is dependent on the software tool that is used, and this may be specific of Proteome Discoverer. Match between run is performed at the ion level, but the intensity retrieved at this step can be reported at PSM level. I think that this is the case in MaxQuant “evidence.txt” tables, if I am not mistaken.\n\nPage 63: DEqMS could be mentioned since it is specifically developed for proteomics statistical analysis. (DOI: 10.1074/mcp.TIR119.001646)\n\nThis is more of a naïve question regarding using Limma in this context: does it make sense to model the variance depending on intensity after missing value replacement? I know that this manuscript may not be the place to discuss this, but I would be interested to know what the authors’ opinion is on this question.\n\nAdditional suggestions (only suggestions that may totally be ignored/dismissed by the authors if they don’t think that they’ll improve their manuscript): The data is available in PRIDE (PXD041794), but the information necessary to match TMT channel/sample to conditions/replicates is only available in the associated paper. It would be great to add the Table 1 of the manuscript and a link to the zenodo repository in PRIDE alongside the data. An even better solution would be to provide the metadata in the SDRF-Proteomics format (https://www.nature.com/articles/s41467-021-26111-3; there is a GUI to generate these files now: https://lessdrf.streamlit.app/). This would facilitate data reuse and transparency.\nSmall comments / typos:\nPage 3, in the code at the bottom of the page: the “,” is missing after “stringr”.\n\nParagraph \"Assessing the impact of non-specific data cleaning”, in the table (and other similar tables or mentions of number of protein groups and peptide stripped sequences): “proteins” should be replaced by “protein groups” since this is what is actually counted. If the authors wanted to be more precise, they could also specify that the “peptides” correspond to peptide sequences stripped of all modifications.\n\nBar plot of missing value proportion page 32: what does the red dashed line correspond to?\n\nPage 37, when running the function `normalizer`, I got an error “No RT column specified (column named 'RT') or option not specified Skipping RT normalization.” And could not get the expected report. I am not familiar with the tool and did not investigate further.\n\nI don’t think that “softwares” can be used. There is no “s” at the end.\n\nPage 51: “cleaning is done is two steps” should be “cleaning is done in two steps”\n\nPage 54: in the bar plot of missing value count, what is the dashed red line?\n\nPage 55: “If the method requires data to display a normal distribution, users must log2 transform the data prior to imputation.” -> is there a reason to perform missing values replacement before log transformation? If not, this step could be moved to after log transform?\n\nPage 66: “If we had not used TMT labels and wished to include a logFC threshold, we could have included lfc = as an argument”. The characters of “lfc = as” are in a different police, I think that this is a bit unclear since the “as” should be regular text. Also, maybe you could explain “have included lfc = followed by the minimum absolute log2-transformed fold change”.\n\nPage 72: “summarize all packages and corresponding their versions used to generate” -> the sentence does not seem correct to me.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "12037", "date": "25 Sep 2024", "name": "Lisa Breckels", "role": "Author Response", "response": "We thank Dr Locard-Paulet for her positive comments and have answered her additional comments below. Reviewer Comments: Major comments: It should be made clear that this script is tailored for Proteome Discoverer outputs (and maybe even for a given version of Proteome Discoverer). For most of the plotting/filtering/analysis steps, changing input would only require adapting the column names/headers, and most of the time it is very well discussed by the authors. Nevertheless, right now this script is only adapted to Proteome Discoverer outputs and this should be made clear in the abstract and the introduction, as well as the discussion. Author Response: We appreciate that both use-case datasets in this workflow were processed using Proteome Discoverer and have added text to emphasise this further in the abstract and introduction. Nevertheless, we feel that the workflow is still useful to users of alternative third-party software as the general data processing steps, and extensive discussion of these, remains relevant. To help users make the most out of this workflow, we have provided information on how to adapt the workflow from Proteome Discoverer files to those generated by MaxQuant, a free and accessible search software. This information is provided in a new section in the Appendix of our Github repository. Reviewer Comments: Aggregation of PSM quantification values to peptides and proteins: Here, the authors choose to aggregate all PSM intensities corresponding to the same sequence (stripped of its modifications). I would aggregate the PSM quantities per peptidoform (sequence + localized modifications) since two ions can have the same sequence but with modifications that are differentially regulated between the conditions compared. This should be mentioned. Author Response: As Dr Locard-Paulet mentions, it is possible for the same peptide sequence with and without modifications to behave differently. We have added the following to the workflow to acknowledge this: “For simplicity, we here aggregate all PSMs corresponding to the same stripped peptide sequence, regardless of whether they contain different modifications. If users are interested in exploring differential expression of protein isoforms or have reason to believe that post-translational modifications may be important in answering their question, PSMs could also be aggregated by \"Annotated.Sequence\" to preserve this information.” We agree that this point is worth drawing attention to. In order to observe any differential abundance of peptides when modified, statistical analysis would need to be carried out at the peptide-level. Since this is outside of the scope of this workflow, we continue to aggregate using the stripped sequence column to facilitate statistical analysis at the protein level. Reviewer Comments: For the GO-term enrichment: only the majority protein accessions are reported in the output of the limma analysis. So there is only one gene per feature. How do you make sure that it is the most representative annotation for a given protein group? I am fully aware that this issue is ignored by the community (for lack of alternative strategy), and that most of the time people just pick one accession per group for GO-term enrichment analysis. So, I am not asking the authors to find a solution. Nevertheless, it would be nice to mention that the output of the enrichment will depend on what accession is picked per group. Author Response: We agree with and acknowledge this point. Indeed, it is a limitation of protein inference that results in statistics and interpretation being done at the level of protein groups rather than individual proteins. As a result, we would always encourage users to explore their statistical hits, particularly those of interest for follow up. This would include tracing the protein group back down all data levels and potentially plotting an aggregation graph, as demonstrated in “Exploration of data using QFeatures links”. With regard to the output of GO enrichment, we do not expect the overall biological interpretation to be dramatically skewed as only protein lists with multiple proteins with the same GO annotation will be considered enriched. Therefore, even if a few of the master proteins are not representative of the protein which is actually changing in abundance, these few cases are unlikely to cause an incorrect enrichment. Nevertheless, it is always worthwhile for the user to examine the results to verify correct interpretation. Reviewer Comments: Minor comments: I would remove contaminants before estimation of TMT labelling efficiency. I find the paragraph “Additional considerations regarding protein isoforms” unclear. The authors should rephrase sentences such as this one: “PSMs or peptides that were previously mapped to one protein and one protein group could instead be mapped to multiple proteins and one protein group.” Maybe they should use the term “canonical protein” to be more precise? In any cases, the issue of peptide uniqueness does not depend only on the presence of isoforms in the fasta file but also on the strategy that was chosen for protein inference. I agree with the authors that people should precisely describe what peptides/PSMs were used for quantification, and it is good to mention it. Nevertheless, this level of detail on general MS-based proteomics concept may not be necessary here. (So the entire paragraph on isoforms could maybe be removed, especially since isoforms are not mentioned later). Author Response: We thank Dr Locard-Paulet for her input on this complex issue. We agree that for a beginner-level workflow, the discussion of isoforms may be confusing. We have removed the paragraph about isoforms, whilst adding some further comment on the importance of defining uniqueness above. Reviewer Comments: In the paragraph “Removing PSMs that are not rank 1”: I think that the “PSM category” that is discussed a bit later is specific of Proteome Discoverer. Some search engines report PSMs of equal score (this would correspond to the “pretty rank” in Mascot). I don’t think that all this should necessarily be discussed in this manuscript, but I insist on the fact that the workflow is tuned for Proteome Discoverer output and this should be made clear in the introduction/abstract. Author Response: We have included additional emphasis on Proteome Discoverer in the introduction to this workflow. That said, users of alternative software will still benefit from being aware of the concept of ‘PSM rank’. Reviewer Comments: In the paragraph “Managing missing data” for the TMT: the authors mention MCAR, MAR, and MNAR, but do they all apply here? I would expect TMT-labelled data to mostly have missing values due to ions being under the limit of detection because when an ion is fragmented, the reporter ions used for relative quantification are often all detected. Isn’t it the case? Knowing this should restrict the choice for a more suited strategy of replacement of missing values. Author Response: Indeed, knowing the reason behind missing values is important in deciding upon an imputation method. We have added an additional few sentences to outline this in the “Imputation” section of the TMT workflow. Nonetheless, we still wish to emphasise that in the use-case, and most datasets with such little missingness, it is not necessary to impute. Additional discussion has also been added under “The importance of knowing what you expect in missing values” to ensure that users consider their experimental design and quantitation strategy when assessing and dealing with missing values. Reviewer Comments: Still on missing values: page 33, it is stated that “Typically, it is desirable to remove features, here PSMs, with greater than 20% missing values”. Why this number? Is this accepted by the entire community? (this comment also applies to the same step in the LFQ analysis. Author Response: The percentage of missing data to allow per dataset will depend on the experimental design and number of samples. There are no strict rules on what one should allow and if imputation is required several groups report that up to 20% missing values in quantitative proteomics is acceptable (please see, for example, https://doi.org/10.1038/s41597-024-02922-z and https://doi.org/10.1186/s12864-022-08723-1) to maintain data structure as close to reality as possible. Reviewer Comments: Regarding missing value replacement (discussion on LFQ, page 55): it is really nice to provide references of strategies applied to replacement of missing values. It is indeed a tricky decision to make (how to replace? Should we replace?) and there is no one-size-fits-them-all method. Why do you choose to replace at peptide level and not protein level? Author Response: The reason that we typically choose to impute at the lowest possible data level is to avoid the implicit imputation that occurs during aggregation. For example, if a protein is supported by two peptides, and one peptide contains missing values whilst the other does not, aggregation would result in a protein level quantitation value without the user explicitly stating how to deal with the missing value. Reviewer Comments: Page 38: what do the authors mean by “report did not indicate any superior normalization method”? How would we know what normalization method works best? This point is because I am curious, not to correct any obvious mistake. It is great to try out different normalization strategies, but I don’t really see how to pick one based on the boxplots of normalized intensities (Figure 4). Author Response: In our experience of sharing and teaching this workflow, we have found that one of the most common questions is in regard to selecting an appropriate normalisation method. Therefore, we decided to include NormalyzerDE as one approach for users to make this decision. However, we appreciate that the results of this comparison are not particularly informative for either of the use-case datasets. As a result, we have decided to remove the NormalyzerDE example from the workflow and instead include further discussion. Reviewer Comments: The authors normalize the data after protein aggregation and not at the PSM level. Is this general practice? Wouldn’t it make sense to normalize before aggregation? Author Response: We acknowledge that this decision is not a simple one, and not one which has a consensus in the literature. For example, some workflows choose to normalise at lower data levels so that normalisation can occur prior to imputation. We typically choose to normalise data at the protein level because this is the level at which statistical analyses are carried out. As the goal of normalisation is to remove non-biological variation to increase statistical power and lead to the discovery of meaningful, biological variation, we feel it makes the most sense to do this step immediately before statistics. Normalising the data at PSM or peptide level would not account for any small variation re-introduced during aggregation (depending upon the selected aggregation method). Reviewer Comments: Page 44; “Data import, housekeeping and exploration”: the authors mention that LFQ analysis cannot be performed at PSM level but has to be done at peptide level. I think that this is dependent on the software tool that is used, and this may be specific of Proteome Discoverer. Match between run is performed at the ion level, but the intensity retrieved at this step can be reported at PSM level. I think that this is the case in MaxQuant “evidence.txt” tables, if I am not mistaken. Author Response: We thank Dr Locard-Paulet for pointing this out and have adjusted the text in the LFQ data import section accordingly. Reviewer Comments: Page 63: DEqMS could be mentioned since it is specifically developed for proteomics statistical analysis. (http://doi.org/10.1074/mcp.TIR119.001646) Author Response: Thank you for this suggestion. We have now mentioned and referenced this package in the appropriate place. Reviewer Comments: This is more of a naïve question regarding using Limma in this context: does it make sense to model the variance depending on intensity after missing value replacement? I know that this manuscript may not be the place to discuss this, but I would be interested to know what the authors’ opinion is on this question. Author Response: We agree with the reviewer that one does need to be cautious, and in the text, we advise users to check their data following imputation and that the distribution has not dramatically changed. As we mention in the manuscript it is now possible to use packages such as msqRob2 to facilitates statistical differential expression analysis on datasets without the need for imputation. With the limma package, for a given protein, the cases with missing values are removed both from the data and design matrix. That is, the linear model is fitted to the non-missing values. If a particular regression co-efficient cannot be estimated from the observed data for a protein of interest, then a NA value will be returned for that coefficient. Reviewer Comments: Additional suggestions (only suggestions that may totally be ignored/dismissed by the authors if they don’t think that they’ll improve their manuscript): The data is available in PRIDE (PXD041794), but the information necessary to match TMT channel/sample to conditions/replicates is only available in the associated paper. It would be great to add the Table 1 of the manuscript and a link to the zenodo repository in PRIDE alongside the data. An even better solution would be to provide the metadata in the SDRF-Proteomics format (https://www.nature.com/articles/s41467-021-26111-3; there is a GUI to generate these files now: https://lessdrf.streamlit.app/). This would facilitate data reuse and transparency. Small comments / typos: Page 3, in the code at the bottom of the page: the “,” is missing after “stringr”. Paragraph \"Assessing the impact of non-specific data cleaning”, in the table (and other similar tables or mentions of number of protein groups and peptide stripped sequences): “proteins” should be replaced by “protein groups” since this is what is actually counted. If the authors wanted to be more precise, they could also specify that the “peptides” correspond to peptide sequences stripped of all modifications. Bar plot of missing value proportion page 32: what does the red dashed line correspond to? Page 37, when running the function `normalizer`, I got an error “No RT column specified (column named 'RT') or option not specified Skipping RT normalization.” And could not get the expected report. I am not familiar with the tool and did not investigate further. I don’t think that “softwares” can be used. There is no “s” at the end. Page 51: “cleaning is done is two steps” should be “cleaning is done in two steps” Page 54: in the bar plot of missing value count, what is the dashed red line? Page 55: “If the method requires data to display a normal distribution, users must log2 transform the data prior to imputation.” -> is there a reason to perform missing values replacement before log transformation? If not, this step could be moved to after log transform? Page 66: “If we had not used TMT labels and wished to include a logFC threshold, we could have included lfc = as an argument”. The characters of “lfc = as” are in a different police, I think that this is a bit unclear since the “as” should be regular text. Also, maybe you could explain “have included lfc = followed by the minimum absolute log2-transformed fold change”. Page 72: “summarize all packages and corresponding their versions used to generate” -> the sentence does not seem correct to me. Author Response: We would like to thank Dr. Locard-Paulet for being so thorough in reviewing the manuscript. We have corrected the highlighted typos." } ] }, { "id": "221408", "date": "18 Dec 2023", "name": "Amit Kumar Yadav", "expertise": [ "Reviewer Expertise quantitative proteomics", "bioinformatics", "computational biology", "proteome informatics" ], "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 by Hutchings et al titled \"A Bioconductor Workflow for Processing, Evaluating, and Interpreting Expression Proteomics Data\" provides a detailed overview tutorial of the interpretation of quantitative proteomics data through R environment using TMT and LFQ workflows as examples.\nMajor comments:\nThe use of open-source tools ensures transparency and reproducibility. The open-source R software packages from the Bioconductor project also add credibility to the workflow. The workflow described is comprehensive and is a good tutorial for analysis. The article describes the comprehensive workflow with R commands, covering data import, quality control, differential expression analysis, and gene ontology enrichment analysis. This approach ensures a holistic understanding of expression proteomics. The described use-case examples from TMT and LFQ provides practical relevance and enhances the applicability of the workflow. The target audience is for beginners who are also familiar with R. It may also be helpful to optionally provide shiny app (for GUI based application) that biologists who are unfamiliar with CLI, can also use.\nMinor Comments:\nThis article deals with Proteome Discoverer output. Maybe inclusion of MaxQuant or other workflows may add to it reach. The difference between razor and shared peptides is not clear. Perhaps rephrasing would help a newcomer to proteomics. Page 40, (Under section Visualising Aggregation) “…15 peptides and 27 supporting…”. Did the author mean 27 PSMs? It is missing in the sentence. Please clarify if these were peptides or PSMs? PCA is not considered fit when there are lot of missing values as in LFQ analysis. Should these be removed before PCA? Authors have conflated modified and non-modified forms of the same peptides during analysis. This may not be able to detect modified changes if differential in nature. Perhaps “quantitative proteomics” is a more appropriate term than “Expression proteomics”.\nThe article appears to be a valuable contribution to the field of quantitative proteomics, especially for R users, providing a comprehensive and user-friendly workflow.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "12038", "date": "25 Sep 2024", "name": "Lisa Breckels", "role": "Author Response", "response": "We would like to thank Dr. Yadav for reviewing our workflow paper and providing positive feedback. In response to Dr. Yadav’s minor comments, we have provided additional information on how to use this workflow with output from MaxQuant. This information can be found in a new section in the Appendix of our Github repository and is mentioned explicitly in the workflow. The sentence regarding shared and unique peptides has been changed slightly and additional discussion added to emphasise how protein inference and presence of isoforms can alter the definition of ‘unique’ peptides. We agree that missing values need to be addressed before performing PCA and as such in the workflow we use the function filterNA in QFeatures to remove missing data prior to any PCA performed. We have also explicitly stated that we conflate modified and non-modified forms of each peptides, and that users could aggregate by “Annotated. Sequence” if they wish to retain this information. However, the discovery of differences in the behaviour of these peptides would require peptide-level statistical analyses, which is outside of the scope of this workflow." } ] } ]	1	https://f1000research.com/articles/12-1402
https://f1000research.com/articles/13-978/v1	29 Aug 24	{ "type": "Research Article", "title": "Neutrophil-to-lymphocyte and platelet-to-lymphocyte ratios in bacterial infections: contributions to diagnostic strategies in a tertiary care hospital in Tunisia", "authors": [ "Jihed Anoun", "Mariem Ajmi", "Salma Riahi", "Yosra Dhaha", "Donia Mbarki", "Imen ben Hassine", "Wiem Romdhane", "Wafa Baya", "Najah Adaily", "Anis Mzabi", "Fatma Ben Fredj", "Amina Bouattay", "Jihed Anoun", "Mariem Ajmi", "Yosra Dhaha", "Donia Mbarki", "Imen ben Hassine", "Wiem Romdhane", "Wafa Baya", "Najah Adaily", "Anis Mzabi", "Fatma Ben Fredj", "Amina Bouattay" ], "abstract": "Background Bacterial infections continue to pose a global health challenge, driven by antibiotic resistance and septicemia. This study aimed to assess the diagnostic utility of neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) in bacterial infections versus non-infectious causes of inflammation.\n\nMethods A prospective study included 164 adult patients who were divided into two groups: a group of patients with confirmed bacterial infections and a second group of patients with other diagnoses (inflammatory pathologies, neoplasms, venous thromboembolic diseases, etc.). NLR and PLR values were compared between the bacterial infection group and the non-infectious causes group and the diagnostic performances of NLR and PLR for detecting bacterial infections were evaluated in comparison with other infection markers.\n\nResults NLR and PLR were significantly higher in bacterial infections (p < 10^-6), and NLR was correlated positively with inflammation markers. NLR and PLR demonstrated significant potential in diagnosing bacterial infections, with an AUC of 0.72 and 0.60, respectively, using the following cutoff values: 4.3 for NLR and 183 for PLR.\n\nConclusion These findings underscore the importance of NLR and PLR as adjunctive tools for bacterial infection diagnosis.", "keywords": [ "Infections", "Neutrophil-to-lymphocyte ratio (NLR)", "Platelet-to-lymphocyte ratio (PLR)", "Diagnosis." ], "content": "Introduction\n\nBacterial infections are common conditions affecting millions of people worldwide. Due to the rise in antibiotic resistance and septicemia, bacterial infections remain one of the leading causes of death on a global scale. In 2019, deaths associated with bacterial infections accounted for 13.6% of all deaths.1\n\nSome infections are relatively benign, while others can be much more serious, requiring urgent medical intervention, even hospitalization. This presents a significant challenge for healthcare professionals.\n\nThe “gold standard” for diagnosing a bacterial infection involves isolating the pathogenic microorganism, but this approach is not always straightforward in routine practice. Despite the availability of numerous diagnostic tools, optimizing patient management remains fundamental for effective treatment. Several inflammatory markers have proven their effectiveness in diagnosing, prognosing, and assessing treatment response. These markers include C-reactive protein (CRP), white blood cell count, and procalcitonin (PCT).2\n\nGrowing interest is emerging in new markers such as the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR). Their relevance stems from changes observed in the number of neutrophilic granulocytes, platelets, and lymphocytes during the inflammatory response.3,4\n\nIn response to a bacterial infection, the number of neutrophilic granulocytes and platelets increases, while the number of lymphocytes decreases due to redistribution and increased apoptosis.4 NLR and PLR prove to be a rapid, cost-effective, and applicable approach for early diagnosis, treatment, and prognosis of various diseases, such as cancer, community-acquired pneumonia, and sepsis.5–7\n\nThe aim of this study was to investigate the diagnostic utility of NLR and PLR in bacterial infections compared to other non-infectious causes of inflammation.\n\n\nMethods\n\nTo address the research question, a prospective comparative study was conducted within the internal medicine department. The study included a total of 164 patients admitted between January 1st and July 31st, 2023.\n\nInclusion criteria\n\n• Adults aged 18 and older admitted to the internal medicine department between January 1st and July 31st, 2023.\n\nExclusion criteria\n\n• Previous antibiotic treatment before admission (one week before admission).\n\n• Patients taking immunosuppressive treatments.\n\nFor each patient, the following parameters were recorded upon admission:\n\n• Demographic data, medical history, and clinical symptoms.\n\n• Results of laboratory analyses, including complete blood count (absolute neutrophil, platelet, and lymphocyte counts), and other inflammatory markers such as CRP and PCT (CRP with normal range < 5mg/L and PCT with normal range < 0.1 ng/ml); We considered PCT positive for infectious diseases when it was > 0.25 ng/ml).\n\nNLR and PLR were calculated by dividing the number of neutrophils by the number of lymphocytes and the number of platelets by the number of lymphocytes, respectively. The normal range of neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) varies from 1 to 3 and 90 to 210, accordingly.8 NLR and PLR values were compared between the bacterial infection group and the non-infectious causes group.\n\nWhite blood cell (WBC) and differential cell counts were obtained using the DxH 900 hematology system by Beckman Coulter, California, USA.\n\nStatistical analysis was carried out using the software packages SPSS 21 (IBM SPSS Statistics for Windows, Version 21.0. Armonk, NY: IBM Corp) and MedCalc Statistical Software version 19.2.6 (MedCalc Software bv, Ostend, Belgium; https://www.medcalc.org; 2020) and appropriate statistical tests, such as the Mann-Whitney test and Kruskal-Wallis test, were applied as dictated by the data characteristics and study requirements.\n\nThe significance level for statistical analysis was set at p < 0.05, denoting that differences between groups and the strength of parameter correlations were assessed against this predetermined threshold.\n\nThe correlation coefficient (r) was employed to measure the strength and direction of linear relationships between parameters. An r-value close to 1 indicated a strong positive correlation, while an r-value close to -1 indicated a strong negative correlation. An r-value close to 0 suggested a weak or non-existent correlation between parameters.\n\nThe significance levels were indicated as follows:\n\na p < 0.05\n\nb p < 0.01\n\nc p < 0.001\n\nROC curves were plotted to compare the diagnostic accuracy of NLR, PLR, CRP, and PCT in the context of bacterial infections versus non-infectious causes. The diagnostic performances of NLR, CRP, and PCT for detecting bacterial infections were evaluated by calculating sensitivity and specificity.\n\n\n\n- The prior agreement of the departments’ chiefs concerned with the study (the internal medicine department and the hematology laboratory) was obtained, as well as the initial approval from the ethics committee of Sahloul University Hospital of Sousse on May 11, 2022, under the number HS 22-2022, this approval confirms that there are no ethical issues concerning the work.\n\n- Written and verbal consent were obtained from all participants before their involvement in the study, ensuring that their rights, privacy, and confidentiality were rigorously upheld throughout the research process.\n\n\nResults\n\nA total of 164 patients were included in the study. The study population was divided into two groups: a group of patients with confirmed bacterial infections and a second group of patients with other diagnoses (inflammatory pathologies, neoplasms, venous thromboembolic diseases, etc.). The median age within this study population was 50 years (ranging from 37 to 66 years), with a male-to-female ratio of 0.76. The epidemiological characteristics and the mean rates of NLR, PLR, PCT and CRP are described in Table 1.\n\nOur findings revealed that bacterial infections are linked to a notable increase in the NLR to 9.7 (normal range from 1 to 3) and the PLR to 218.14 (normal range from 90 to 210). Additionally, patients with neoplasms also demonstrate elevated PLR and NLR.\n\nOur results revealed significant variations in NLR based on gender. Indeed, men generally had slightly higher NLR values than women, with means of 7.2 in men and 4.7 in women (p<10-6). In addition to gender-based variations, we also observed significant differences in NLR based on age. Specifically, older subjects had higher NLR values, with a mean of 8.8 compared to 4.3 in younger individuals (p=0.001).\n\nIn the group of patients with bacterial infections, there were significantly higher levels of NLR, PLR, PCT, CRP, and absolute neutrophil count (ANC) compared to those with non-infectious diseases (p<10-6) (see Table 2).\n\n* The significance levels were indicated as follows: a: p<0.05; b: p<0.01; c: p<0.001.\n\nSimilarly, there was a significant difference between groups with inflammatory diseases, venous thromboembolic diseases, and neoplasms (Table 3).\n\n** The compared non-infectious disease groups were as follows: Group 1: Inflammatory Diseases; Group 2: Venous Thromboembolic Diseases; Group 3: Neoplasms.\n\nA significant positive correlation was found between NLR and PLR and inflammation markers (CRP and PCT) (see Table 4).\n\nThe analysis of ROC curves showed that the NLR had a sensitivity of 65.38% and a specificity of 76.47% in predicting bacterial infections in patients with clinical symptoms, with an optimal threshold value of 4.3 and an area under the curve (AUC) of 0.72 (95% CI, [0.65-0.8]. The PLR also showed prediction performance with a sensitivity of 55.3%, a specificity of 70.5%, an optimal threshold value of 183, and an AUC of 0.6 (95% CI, [0.52-0.68]).\n\nThe diagnostic performance evaluation of the four markers, namely CRP, PCT, NLR, and PLR, was conducted to predict bacterial infections in patients with clinical symptoms. CRP had the highest sensitivity and specificity with 69.23% and 88.35% respectively. The results are summarized in Table 5.\n\nThe area under the ROC curve for NLR was 0.72 (95% CI, [0.65-0.8]), indicating a good diagnostic performance. Similarly, PCT had an AUC of 0.72 (95% CI, [0.62-0.82]), while PLR demonstrated an AUC of 0.6 (95% CI, [0.52-0.68]). Finally, CRP exhibited the highest AUC at 0.82 (95% CI, [0.75-0.9]) (see Figure 1).\n\n\nDiscussion\n\nBacterial infections are a significant public health problem due to their severity and associated complications. Healthcare professionals are turning more frequently to markers of inflammation to quickly assess these infections and guide diagnostic strategies, regardless of the initial symptoms. Bacterial infections are often accompanied by a systemic inflammatory response, leading to changes in the levels of certain blood cells, including neutrophils, lymphocytes, and platelets. The increase in NLR and PLR during bacterial infections is mainly explained by the body’s inflammatory response to the infection. Neutrophils are the major immune cells involved in the defense against bacterial infections. When a bacterial infection occurs, the number of neutrophils in the blood increases rapidly in response to the bacterial invasion. Lymphocytes, on the other hand, are immune cells that play an essential role in regulating the immune response. During a bacterial infection, the number of lymphocytes may temporarily fall as some of them are mobilized to the site of infection to help fight the bacteria. The NLR therefore increases as a result of the increase in neutrophils and the temporary decrease in lymphocytes. Similarly, the PLR ratio increases because platelets, although initially designed for blood coagulation, can also be mobilized in response to inflammation. This increase in platelets can be observed during bacterial infections as a result of the body’s general inflammatory response.4\n\nOur study analyzed a group of 164 participants aged 19 to 92 years, with a male-to-female ratio of 0.76. The study population was divided into two groups: a group with confirmed bacterial infections and a group with other diagnoses. The primary objective of this study was to describe the diagnostic utility of NLR and PLR ratios in bacterial infections compared to other non-infectious causes of inflammation.\n\nAnalyses revealed that patients with bacterial infections had significantly higher levels of NLR (9.7), PLR (218.14), PCT (3.3 ng/mL), CRP (138.14mg/L), and ANC (9015.66 WBCs/μL) compared to those with non-infectious diseases. In addition, significant positive correlations were observed between NLR, PLR, and markers of inflammation.\n\nROC curves confirmed that NLR and PLR were good diagnostic indicators of bacterial infections, with AUC values of 0.72 and 0.6, respectively. These results highlight the importance of these ratios in the management of patients with bacterial infections.\n\nClinical studies, such as the one conducted by Zahorec and al. on patients with confirmed bacterial infections, have demonstrated a significant increase in the NLR compared to reference values, suggesting its utility as a reliable indicator.9 Similarly, Wang and al. have investigated the potential of the PLR as an indicator of systemic inflammation, with a specific focus on sepsis cases. Their findings suggested that PLR could indeed serve as a valuable prognostic indicator for sepsis and a significant association between elevated PLR values and unfavorable outcomes in sepsis patients was demonstrated.10\n\nThe use of NLR and PLR markers is crucial for a rapid identification of bacterial infections, particularly when initial clinical manifestations are inconspicuous. These markers offer an interesting insight into the patient’s immune and inflammatory status at the beginning of their admission, allowing earlier and more accurate management. Identifying substantial deviations from reference values enables healthcare professionals to promptly suspect an underlying bacterial infection, even with mild symptoms. This proactive approach helps managing ulterior investigations and monitoring the effectiveness of treatments. In consequence, clinicians could predict severe complications and enhance clinical outcomes.11,12\n\nOur results revealed significant variations in NLR based on gender. Indeed, men generally had slightly higher NLR values than women, with means of 7.2 in men and 4.7 in women (p < 10-6), consistent with trends observed in other studies, including the one conducted by Fors and al. In this large-scale study, NLR values were on average higher in men (median of 2.69) than in women (median of 2.35) with a p value < 0.001.13 Additionally, our identification of age-related differences, with older individuals exhibiting elevated NLR levels (mean of 8.8) compared to their younger counterparts, is in agreement with the broader literature on age-related changes in inflammatory markers.14\n\nThis observation of NLR variations by gender underscores the importance of considering this difference when interpreting results and evaluating the diagnosis of bacterial infections.\n\nFurthermore, the results of our study indicate that these markers have an important diagnostic utility in bacterial infections. Indeed, NLR and PLR values, along with levels of PCT, and CRP, were significantly higher in patients with bacterial infections compared to those with other pathologies, which is in line with the literature data.15–18\n\nTo illustrate, in our study, the means values were as follows: PCT, 3.2 ng/mL; CRP, 152 mg/L; NLR, 9.7; PLR, 218. These results are consistent with several other recent studies on bacterial infections. In another study by Li and colleagues, the median PCT in patients with bacterial infections was similar, with a value of 0.67 ng/mL.19 Additionally, Ding and al also found comparable results for NLR, with a median of 8.7 in patients with bacterial infections.2 Similarly, Yang and colleagues reported a mean PLR of 169.5 in patients with bacterial infections, which corroborates our findings.20\n\nHowever, it is important to note that in the non-infectious pathology group, we observed significantly lower levels, with mean values of PCT, NLR, and PLR of 0.21 ng/mL, 3.9, and 174, respectively.\n\nIn the context of our study, we also evaluated the diagnostic performance of NLR, PLR, and CRP in predicting bacterial infections using the Receiver Operating Characteristic (ROC) curve areas (AUC). Our results showed that NLR had an AUC of 0.72, while PLR had an AUC of 0.6. Although these values indicate a reasonable ability of these markers to differentiate bacterial infections from other pathologies, CRP showed the highest AUC of 0.82, highlighting its superior effectiveness in predicting bacterial infections.\n\nThese findings are in line with previous works. For example, Cai and colleagues’ study in 2017 which evaluated NLR in predicting bacterial infections in patients with decompensated cirrhosis, confirmed a significant AUC value of approximately 0.824. In this retrospective study involving 2066 decompensated cirrhotic patients, the incidence of hospital-acquired (HA) bacterial infections was approximately 35.87% in the training cohort and 31.05% in the validation cohort. Multivariate analysis identified total bilirubin, albumin, white blood cell count, and NLR as independent predictors of HA bacterial infections. These results reinforce the importance of NLR as a valuable and noninvasive marker for early detection and prediction of hospital-acquired bacterial infections in individuals with decompensated cirrhosis.21 Similarly, Thill and colleagues’ study (2019) examined the diagnostic value of NLR in the context of fever and inflammatory syndromes in internal medicine, reinforcing our findings regarding NLR.4 In this prospective study of 184 hospitalized patients in internal medicine, the NLR was assessed as a diagnostic marker to differentiate bacterial infections from other causes of fever and inflammation. The study revealed that NLR, with an optimal threshold of seven, showed significance in the presence of 82 bacterial infection cases, and its Area Under the ROC Curve (AUC) was 0.64, comparable to CRP and PCT in this clinical context.\n\nIt is important to note that CRP has consistently demonstrated superior diagnostic performance in the context of bacterial infections. In this regard, Legrain and al. (2017) also contributed to the understanding of CRP’s effectiveness as a distinct indicator of bacterial infections.22\n\nIn contrast, another study conducted by Shanshan Ding et al. yielded contradictory results to ours. This retrospective clinical study aimed to differentiate infectious fever from tumor fever (TF) and assess outcomes in non-neutropenic lung cancer patients (NNLCPs) by evaluating PCT, CRP, and NLR as markers of inflammation.2 The study included 588 febrile NNLCPs, of which 311 had bacterial infections, and 277 had TF. Inflammatory markers (PCT, CRP, white blood cells, neutrophils, and NLR) were significantly higher in bacterial infection cases (p < 0.0001). PCT demonstrated the highest predictive value for bacterial infections (AUC = 0.874), followed by CRP (AUC = 0.855) and NLR (AUC = 0.792) (p < 0.0001). In conclusion, PCT outperformed CRP and NLR in diagnosing bacterial infections in febrile patients and proved useful in assessing clinical outcomes and cancer progression in NNLCPs.\n\nIn summary, our results on the AUCs for NLR, PLR, and CRP align with the conclusions of previous studies, confirming the variable performance of these markers in predicting bacterial infections. CRP remains the most performant marker, while NLR and PLR retain reasonable diagnostic utility. This understanding can guide clinical decision-making for the precise diagnosis of bacterial infections, taking into account the context and individual patient characteristics.\n\nHowever, it is important to note that this study has certain limitations. The relatively small sample size may restrict the generalizability of the results to larger populations. Additionally, it is essential to consider the variability in results based on the nature of bacterial infections and the clinical characteristics of patients.\n\n\nConclusion\n\nIn conclusion, this study has demonstrated that NLR and PLR could have a significant diagnostic role in bacterial infections. These markers could contribute to improving the accuracy of diagnosis, assessing the severity of infection, and guiding therapeutic decisions. However, further research and larger studies are needed to confirm and explore these promising results.\n\nEthical approval was obtained from the ethics committee of Sahloul University Hospital of Sousse on May 11, 2022, under the number HS 22-2022, this approval confirms that there are no ethical issues concerning the work. Written and verbal consent were obtained from all participants before their involvement in the study, ensuring that their rights, privacy, and confidentiality were rigorously upheld throughout the research process.", "appendix": "Data availability\n\nDryad: Data from: The interest of inflammatory biomarkers in the diagnostic approach, https://doi.org/10.5061/dryad.n02v6wx3d. 23\n\nThis project contains following dataset:\n\n1. Data_Inflammatory_Biomarkers_1.sav\n\n2. README\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\nIkuta KS, Swetschinski LR, Robles Aguilar G, et al.: Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. December 2022; 400(10369): 2221–2224.\n\nDing S, Ma J, Song X, et al.: Diagnostic Accuracy of Procalcitonin, Neutrophil-to-Lymphocyte Ratio, and C-Reactive Protein in Detection of Bacterial Infections and Prediction of Outcome in Nonneutropenic Febrile Patients with Lung Malignancy. J. Oncol. 2020; 2020: 2192378.\n\nDjordjevic D, Rondovic G, Surbatovic M, et al.: Neutrophil-to-Lymphocyte Ratio, Monocyte-to-Lymphocyte Ratio, Platelet-to-Lymphocyte Ratio, and Mean Platelet Volume-to-Platelet Count Ratio as Biomarkers in Critically Ill and Injured Patients: Which Ratio to Choose to Predict Outcome and Nature of Bacteremia? Mediat. Inflamm. 2018; 2018: 3758068.\n\nThill P, Legrain A, Salle V, et al.: Valeur diagnostique du rapport neutrophiles/lymphocytes devant une fièvre et/ou un syndrome inflammatoire en médecine interne. Médecine Mal Infect. June 2019; 49(4, Supplement): S67.\n\nHan F, Sheng N, Sheng C, et al.: The diagnostic and prognostic value of haematologic parameters in multiple myeloma patients. Hematol. Amst. Neth. December 2023; 28(1): 2240145.\n\nDafitri IA, Khairsyaf O, Medison I, et al.: Correlation of qSOFA and NLR to Procalcitonin Levels for Predicting Outcome of Pneumonia Sepsis Patients at RSUP dr. M. Djamil Padang. Jurnal Respirologi Indonesia. July 2020; 40(3): 173–181.\n\nBai L, Gong P, Jia X, et al.: Comparison of neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio for the diagnosis of neonatal sepsis: a systematic review and meta-analysis. BMC Pediatr. June 2023; 23(1): 334. PubMed Abstract \| Publisher Full Text\n\nThombare D, Bhalerao A, Dixit P, et al.: Neutrophil-to-Lymphocyte Ratio and Platelet-to-Lymphocyte Ratio in Antenatal Women With Pre-eclampsia: A Case-Control Study. Cureus. June 2023; 15(6).\n\nZáhorec R: Ratio of neutrophil to lymphocyte counts--rapid and simple parameter of systemic inflammation and stress in critically ill. Bratisl. Lek. Listy. 2001; 102: 5–14. PubMed Abstract\n\nWang G, Mivefroshan A, Yaghoobpoor S, et al.: Prognostic Value of Platelet to Lymphocyte Ratio in Sepsis: A Systematic Review and Meta-analysis. Biomed. Res. Int. June 2022; 2022: 9056363.\n\nLi X, Zhu M, Wang J: Clinical application of neutrophil/lymphocyte count ratio in the diagnosis of lung bacterial infections in the elderly. Zhonghua Yi Xue Za Zhi. May 2015; 95(18): 1405–1410. PubMed Abstract\n\nZinellu A, Zinellu E, Mangoni AA, et al.: Clinical significance of the neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio in acute exacerbations of COPD: present and future. Eur. Respir. Rev. December 2022; 31(166).\n\nFors M, Ballaz S, Ramírez H, et al.: Sex-Dependent Performance of the Neutrophil-to-Lymphocyte, Monocyte-to-Lymphocyte, Platelet-to-Lymphocyte and Mean Platelet Volume-to-Platelet Ratios in Discriminating COVID-19 Severity. Front. Cardiovasc. Med. April 2022; 9: 822556.\n\nLin BD, Hottenga JJ, Abdellaoui A, et al.: Causes of variation in the neutrophil–lymphocyte and platelet–lymphocyte ratios: a twin-family study. Biomark. Med. October 2016; 10(10): 1061–1072. PubMed Abstract \| Publisher Full Text\n\nKazimoglu H, Uysal E, Dokur M, et al.: Evaluation of the relationship between neutrophil lymphocyte ratio and the most common bacterial urinary tract infections after transplantation. Bratisl. Lek. Listy. 2019; 120(2): 161–165. PubMed Abstract \| Publisher Full Text\n\nVélez-Páez JL, Tercero-Martínez W, Jiménez-Alulima G, et al.: Neutrophil-to-lymphocyte ratio and mean platelet volume in the diagnosis of bacterial infections in COVID-19 patients. A preliminary analysis from Ecuador. Infez. Med. 2021; 29(4): 530–537. PubMed Abstract \| Publisher Full Text\n\nSchuetz P, Wirz Y, Sager R, et al.: Procalcitonin to initiate or discontinue antibiotics in acute respiratory tract infections. Cochrane Database Syst. Rev. October 2017; 2017(10): CD007498.\n\nMemar MY, Varshochi M, Shokouhi B, et al.: Procalcitonin: The marker of pediatric bacterial infection. Biomed. Pharmacother. Biomed. Pharmacother. December 2017; 96: 936–943.\n\nLi F, Zhang W, Hu H, et al.: Diagnostic value of procalcitonin, C-reactive protein and lactate dehydrogenase in paediatric malignant solid tumour concurrent with infection and tumour progression. Sci. Rep. April 2019; 9: 5903.\n\nYang J, Wang H, Hua Q, et al.: Diagnostic Value of Systemic Inflammatory Response Index for Catheter-Related Bloodstream Infection in Patients Undergoing Haemodialysis. J. Immunol. Res. 2022; 2022: 7453354.\n\nCai YJ, Dong JJ, Dong JZ, et al.: Neutrophil-lymphocyte ratio predicts hospital-acquired bacterial infections in decompensated cirrhosis. Clin. Chim. Acta Int. J. Clin. Chem. June 2017; 469: 201–207.\n\nLegrain A, Thill P, Schmit JL, et al.: Valeur du rapport neutrophiles/lymphocytes pour le diagnostic des infections bactériennes. Rev Médecine Interne. June 2017; 38: A58.\n\nAnoun J, et al.: Data from: The interest of inflammatory biomarkers in the diagnostic approach. [Dataset]. Dryad. 2023. Publisher Full Text" }	[ { "id": "318819", "date": "13 Sep 2024", "name": "Saoussen Chouchene", "expertise": [ "Reviewer Expertise Hematology and immunogenetics" ], "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 examines the utility of two hematological markers, the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR), in diagnosing bacterial infections. Below is a detailed summary and suggestions for improvement.\nArticle Summary Introduction: Bacterial infections are a significant global health challenge, contributing to mortality through antibiotic resistance and complications such as septicemia. While traditional diagnostic methods like pathogen isolation are reliable, they may be impractical or slow. Biomarkers like C-reactive protein (CRP), procalcitonin (PCT), NLR, and PLR offer a simpler, cost-effective means of identifying infections early. NLR and PLR are particularly attractive due to their accessibility. Methods: This prospective study included 164 adult patients admitted to the internal medicine department from January 1st to July 31st, 2023, all of whom had not received prior antibiotics or immunosuppressive therapy. Lab values, including neutrophil, platelet, lymphocyte counts, CRP, and PCT levels, were recorded. NLR and PLR ratios were calculated and compared between patients with bacterial infections and those with non-infectious inflammatory conditions. Diagnostic performance was evaluated using ROC curves through SPSS and MedCalc. Results: Patients with bacterial infections had elevated NLR and PLR. Differences were observed across age and gender, with higher NLR levels in men and older patients. ROC analysis demonstrated moderate diagnostic accuracy for NLR and PLR, with CRP showing the highest accuracy in this population. Discussion: The study confirms that NLR and PLR are useful diagnostic tools for bacterial infections, especially when combined with CRP and PCT. These markers are particularly valuable in settings with limited access to advanced diagnostic technologies. However, CRP remains the most reliable marker. Additionally, patient characteristics like age and gender should be considered when interpreting these values. Conclusion: NLR and PLR hold potential as diagnostic tools for bacterial infections, but further large-scale studies are required to validate these findings. CRP continues to be the most effective biomarker.\nSuggestions for Improvement Introduction:\nStrengths: The rationale for studying NLR and PLR alongside traditional markers is clear. Suggestions: Further elaborate on the limitations of existing diagnostic methods and explain why NLR and PLR may be particularly useful in certain clinical contexts.\nMethods:\nStrengths: Clear methodology and well-defined inclusion/exclusion criteria. Suggestions:\nProvide more details on how bacterial infections were confirmed. The small sample size limits generalizability—address this limitation. Consider the impact of confounding factors such as chronic inflammatory diseases and immune disorders that may affect NLR and PLR.\n\nResults:\nStrengths: Clearly presented results with appropriate statistical analysis. Suggestions: Comparing ROC curve findings with similar studies would strengthen the discussion.\nDiscussion:\nStrengths: Comprehensive discussion linking findings with existing literature. Suggestions:\nCritically evaluate the limitations of NLR and PLR, including potential situations where these markers may be less effective. Explore the clinical relevance of these findings in resource-constrained settings. Offer practical advice for interpreting NLR and PLR in light of patient age and gender differences.\n\nLimitations:\nExpand the limitations section, addressing possible alternative explanations for elevated NLR and PLR and the potential for other inflammatory conditions to mimic these findings.\nEthical Considerations:\nAdequately addressed; no further comments needed.\n\nConclusion This study provides valuable insights into the diagnostic utility of NLR and PLR in bacterial infections. Expanding on confounding factors, refining the clinical implications, and addressing study limitations will improve its scientific rigor. This research significantly contributes to understanding the diagnostic potential of hematological markers, though further studies are encouraged.\nAcceptance Statement: After thorough analysis, I recommend this article for publication, with minor revisions. Its findings are compelling and make a valuable contribution to the field. Expanding the discussion and addressing confounding factors will enhance its overall impact.\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": "12458", "date": "19 Sep 2024", "name": "Salma Riahi", "role": "Author Response", "response": "We express our sincere gratitude for your comprehensive review and approval of our article. Your discerning recommendations have provided us with a clear roadmap for enhancement, and we deeply value the commitment and diligence you have shown in furnishing such meticulous feedback. We are committed to effecting all requisite revisions to elevate the caliber of the composition and enhance the lucidity of our discourse. Your guidance has been instrumental and we are eager to integrate these modifications in accordance with your suggestions." } ] }, { "id": "318817", "date": "17 Sep 2024", "name": "Aya Chakroun", "expertise": [ "Reviewer Expertise areas of expertise: benign and malignant hematologyHematology analyzer technologiesmedical educationStatistical analyses and biomedical 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\nI congratulate you on the choice of subject and the quality of the manuscript. However, there are a few improvements that should be made:\nIn the ”methods” section:\n-Please remove ‘’ To address the research question’’ - Please remove the expression “The study included a total of 164 patients “ . - Please add to the section “Laboratory values and clinical assessment”, an indication of good control of the analytical process through the daily passage of internal quality controls.\nIn the “results” section:\n-please add “footnotes” to the tables, explaining abbreviations and add confidence intervals of r.\nI congratulate you for your scientific rigour and the quality of the discussion of the relevant scientific literature.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12459", "date": "19 Sep 2024", "name": "Salma Riahi", "role": "Author Response", "response": "We greatly appreciate your time and effort in reviewing and approving our article. Your insightful suggestions and feedback are incredibly valuable to us, and we are fully dedicated to implementing the necessary changes to enhance the quality of the writing in accordance with your recommendations. Your input is instrumental in helping us refine and improve our work, and we are truly grateful for your support." } ] }, { "id": "318818", "date": "24 Sep 2024", "name": "Wissal Ben Yahia", "expertise": [ "Reviewer Expertise Systemic diseases as vasculitis and connectivitis", "treatment and etiologic exploration of thrombosis", "and exploration of general signs as fever", "weight loss", "nodes.. medical education", "Simulation", "Statistical analyses" ], "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 congratulate all authors for their strong choice of subject and the quality of the manuscript. I have just some remarks to make better your work : 1. I suggest to add \"Bacteria\" or \"bacterial infection\" as a keyword. 2. There are 2 abbreviations that were explained for the first time in the discussion but were present in the abstract (AUC) and in results for (ROC) so put the explanations on their first appearance. 3. You should add in excluded criteria the exclusion of viral infections and parasitic. 4. exclude the number of the population from the methodology because its a result \" a prospective comparative study was conducted within the internal medicine department on patients admitted between January 1st and July 31st, 2023.\"\n\nThese remarks will just improve your work and do not decrease in any way its rigour and quality.\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/13-978
https://f1000research.com/articles/13-1093/v1	25 Sep 24	{ "type": "Research Article", "title": "The effect of chiropractic spinal manipulation on the H-reflex and muscle strength in children with cerebral palsy: A feasibility study", "authors": [ "Jenna Duehr", "Imran Khan Niazi", "Rasmus Bach Nedergaard", "Denise Taylor", "Heidi Haavik", "Imran Khan Niazi", "Rasmus Bach Nedergaard", "Denise Taylor", "Heidi Haavik" ], "abstract": "Background Children with cerebral palsy (CP) have deficits in various aspects of motor control, including motor neuron excitability, which can affect muscle strength, gait, and ability to perform activities of daily living. Previous research on chiropractic spinal manipulation in healthy adults, athletes, and a brain-injured population has indicated improvements in motor neuron excitability, muscle strength, and various aspects of motor control. Thus, chiropractic spinal manipulation may improve motor control in children with CP.\n\nMethods Children with spastic diplegic CP, aged 8-13 years, were recruited for a randomized, controlled feasibility study. Feasibility was assessed in terms of recruitment strategy and rate, data collection procedures, equipment, intervention, and compliance.\n\nResults Three children completed the data collection comprising pre- and post-measurements of the H reflex, V-wave, and muscle strength. The recruitment strategy and rate were not feasible. The data collection procedures were appropriate and complied with, except for the V-wave measurements. The H-reflex threshold decreased and s50 and slope increased in the participants who received chiropractic spinal manipulation; the opposite was seen in the control group. The changes in MVC force were inconsistent between subjects.\n\nConclusion This study answered some important feasibility questions regarding conducting a large-scale randomized controlled study with the same design. Some aspects proved feasible, such as H-reflex recordings, and some aspects, such as recruitment methods and V-wave recordings, need to be altered for future research in this area.", "keywords": [ "chiropractic", "cerebral palsy", "spinal manipulation", "muscle strength", "motor neuron excitability", "H reflex", "recruitment methods", "V wave" ], "content": "1. Introduction\n\nCerebral palsy (CP) is an umbrella term used to describe a group of non-progressive motor disorders resulting from injury to the developing brain during pregnancy, birth, or in infants up to the age of 2 years.1 Its prevalence is estimated at 2.1 per 1000 live births and is the most common cause of physical disability in children, which has a significant impact on the function and health-related quality of life of those affected.2\n\nInjury to the brain that occurs in those with CP causes problems with motor control, and the child may develop deficits in movement, posture, balance, coordination, and muscle strength, all of which hinder their ability to perform activities of daily living.3–5 Alongside this, there are considerable social, emotional, and economic costs to the individual and their families as they manage the lifelong consequences of the disorder.\n\nMuscle weakness is one of the most widely recognized clinical manifestations of CP and a significant contributor to deficits in gait and function. Previous studies have noted that children with CP have significantly lower muscle strength than typically developing children of a similar age.1,6–8 In a review of 51 articles concerning CP and muscle strength, all concluded that children with CP are weaker than their typically developed peers.9 The hip extensors, ankle dorsiflexors, and ankle plantar flexors were found to be the weakest, with some studies reporting strength values of 24%, 46%, and 36%, respectively, in typically developed children, while others reported values as low as 18% in dorsiflexors and 23% in plantar flexors.6 Ross and Ensberg10 reported a high correlation between strength and Gross motor function classification system (GMFCS) score (r=.83) and stride length (r=.71) and a moderate correlation with gait speed (r=.61).\n\nNumerous studies have assessed the effectiveness of strength or resistance training in increasing muscle strength in children with CP. Systematic reviews on this subject revealed that the evidence is strong for the efficacy of strength training, with the majority of studies reporting significant increases in strength.9,11 However, its effect on functional outcomes and gait is not clear. Not all studies reviewed assessed the impact on function and/or gait, but those that did report small effect sizes on activity and function levels and variable results on mobility, with some studies reporting significant improvement9 and others reporting no improvement.11 This may be partly due to the variability in the strength training regimes, the samples assessed, and the methods used to assess gait and function. Nevertheless, there are indications that improving muscle strength could help alleviate or reduce some of the impairments seen in CP. Further research is needed to assess the impact of improved muscle strength on functional outcomes.\n\nCurrent treatment of CP is based on the neuroplasticity of motor learning and the maximization of the uninjured parts of the brain.12 Neurorehabilitation treatments aim to use the principles of neuroplasticity in that repetitive movements enhance neuronal connections in the brain. Such treatments include the use of specially designed exercise programs, robotic assisted therapies, treadmill exercises, constraint induced therapy, functional electrical muscle stimulation, spinal cord electrical stimulation and loading suits to enhance proprioceptive feedback.4,13 These therapies have shown benefits in reducing spasticity, increasing muscle strength, and improving postural stability; however, there is limited evidence for improvement in functional outcomes and gait after the use of these therapies.13 One of the therapies that utilizes Lokomat, which combines the use of a treadmill, lower limb unloading, orthoses, and a feedback module, is one of the few that show improvements in gait and gross motor functional measures.13 Evidence suggests that it is likely that a combination of therapies has the best results for children.4,13\n\nOver the past 20 years, a growing body of research has investigated the neuroplastic and neuromodulatory effects of chiropractic adjustments and spinal manipulation.14–24 It is hypothesized that articular dysfunction in the spine causes altered afferent input to the brain, which affects how the CNS processes and integrates all subsequent sensory inputs.18,25 Some studies have shown neural plastic changes such as altered sensorimotor integration and motor control after chiropractic SM.14,15,18,20,21,24,26,27 Other studies have shown improvements in muscle strength and motor neuron excitability in healthy adults and elite athletes, as well as in an adult brain injured population (a chronic stroke population).22,28–31\n\nThere is limited research on the effects of spinal manipulation in children with cerebral palsy. One study assessed the effects of spinal manipulation on muscle spasticity and manual dexterity using a randomized controlled trial (RCT) design.32 They enrolled 78 participants with cerebral palsy (age 7-18 years) and randomized them into two groups: a spinal manipulation intervention group and a control group. The researchers found a statistically significant reduction in wrist spasticity in the group that received spinal manipulation compared to the control group.32 No significant differences were noted in manual dexterity. This is the only RCT conducted in this field to date.\n\nMuscle weakness is correlated with gait problems and poor gross motor function in children with CP. Improving muscle strength in this population group could potentially be beneficial over time in changing gait and increasing functionality, particularly at a time when their nervous system and muscles are still developing.9,11,33,34 The changes in motor control, muscle strength, and motor neuron excitability in both healthy and brain-injured adult populations following chiropractic SM and the previously outlined issues with muscle weakness in children with CP provide grounds for investigating the effects of chiropractic SM on muscle strength and motor neuron excitability in children with CP.\n\nResearch investigating this has not been conducted before; therefore, a feasibility study was proposed to assess aspects of the study design, recruitment, and outcome measures before a full-scale RCT was conducted. This study aimed to assess the feasibility of conducting a large-scale, randomized, controlled trial to test the hypothesis that chiropractic SM results in improvements in motor neuron excitability and muscle strength in children with CP.\n\n\n2. Methods\n\nThis study was conducted as a feasibility study utilizing a single-blinded, parallel group, randomized, controlled design. Participants were recruited through the New Zealand Cerebral Palsy Registry (NZCPR). Participants were identified in the NZCPR database that consented to being contacted for research studies. Those identified were further assessed for eligibility for this study. Potential participants were then posted a letter of invitation to participate and a flyer with information about the study. Parents were asked to contact the lead researcher with any questions and/or if they wished to participate in the study. Prior to participation in the study, written informed consent was obtained from the parents of the participants and the participants provided written informed assent. Consent was not obtained from the participants themselves as they were under the age of 16 years, which is the legal age of consent in New Zealand. Written informed assent was obtained from participants instead, as required by the Health and Disability Ethics Committee in New Zealand.\n\nThe chiropractor, who was not involved in data collection or analysis, randomized the participants into one of two groups, SM intervention or passive movement control intervention, through a coin toss in a separate room. A more rigorous randomization procedure, such as computer-generated randomization, was not used because of the small sample size, but would be used in a larger scale study to reduce group differences and potential bias.\n\nFollowing pre-intervention recordings, the chiropractor then took the participant and caregiver to a separate room to perform the spinal examination and provide the SM or control intervention. Participants or caregivers were not informed of the group they were in. Following the intervention, the chiropractor brought the participant and caregiver back to the data collection room for post recordings and then left. Documentation regarding the intervention was maintained by the chiropractor until the data analysis was complete. At no time before this, the researchers involved in data collection and analysis were made aware of the group allocation.\n\nInclusion criteria for this study were children diagnosed with spastic diplegic CP, aged 8-13 years and classified as Level I-II on the Gross Motor Function Classification System (GMFCS). Participants were required to be proficient in English and have been able and willing to sign written informed assent. Exclusion criteria were any known contraindications to chiropractic SM (previous reaction to spinal manipulation, fracture, cancer, recent trauma, ligamentous instability, and known inflammatory or infectious arthritis). Participants who had undergone surgery, inhibiting casts, or botulinum toxin treatment in the last 6 months were also excluded from this study.\n\nAfter the pre-recording session was completed, participants and caregivers were collected by the chiropractor and placed in a separate room. If allocated to the intervention group, participants received chiropractic SM by a registered chiropractor. A full spine check was conducted, and SM was performed on specific segments exhibiting evidence of joint dysfunction, such as restricted intersegmental range of motion, tenderness on palpation, and intervertebral muscle tension. These are all indicators commonly used in chiropractic practice and have been shown to be reliable indicators of spinal dysfunction.35–38 Chiropractors have specific training in pediatric care, and participants were thoroughly assessed and technique adapted to lower force applications when necessary. All SM’s performed, and on which vertebral segments, were recorded by the chiropractor.\n\nIf allocated to the control group, the participants received a control intervention that involved non-specific movements of their head, spine, and body, but did not include the thrust that was given with SM. This was done to control for proprioceptive input that could have neurological consequences that occur during the procedure of checking for spinal dysfunction and placing a person into positions for SM. Following the intervention, the participants were returned to the data collection room, and post-recordings were conducted in the same manner as the pre-recordings.\n\nParticipants and their caregivers attended one data collection session at the Health and Rehabilitation Research Institute of the Auckland University of Technology (AUT). Prior to the recording of outcome measures, the primary researcher discussed the procedures for the study, answered any questions, and obtained informed consent from the participant and caregiver. Following this, a structured interview was conducted to gather information on patients’ age, sex, ethnicity, and health history. Muscle strength, H-reflex, and V-wave recordings were conducted by the primary researcher and a biomedical engineer. To assess compliance and tolerance to the data collection protocol, notes were taken on any observations or comments the participant made about tolerance of the procedures, such as discomfort, boredom, and wanting to stop. At the end of the data collection session, the participants and their families were also asked if they were okay and how they felt about it.\n\nThe muscle strength was recorded by measuring the isometric force of the plantar flexors using a custom-made force transducer. The foot of the affected leg was placed in the force transducer and strapped using Velcro fasteners. The distal thigh was also fixed in place using Velcro fasteners to reduce leg movements during plantar flexion. Once the leg was fixed, the knee angle was measured again post intervention/control to maintain the same conditions. The participant was instructed to push down with their foot as hard as possible for 5 s, which was repeated a total of three times. The participants were verbally encouraged during each MVC to aid in the highest possible contraction. The force was recorded with a CED Power 1401 MK 2 Data Acquisition Board at a sample rate of 1 kHz and an isometric strain gauge (Model MLP100 transducer Techniques Tennecula, California, USA). The corresponding computation was performed using Spike software (https://ced.co.uk/products/spkovin). The strongest MVC of the three measurements was used to compute the 10% amount required as a background plantar flexion contraction during the H- and V-wave recordings.\n\nSurface electromyography (sEMG) measures the electrical activity of a muscle by placing electrodes on the skin over the belly of the muscle.39 The sEMG was used to record the motor response of the soleus muscle for the H, M, and V wave recordings during this experiment. The soleus muscle was identified by asking the patient to stand on the tip of their toes to produce plantar flexion and then palpate the location just lateral to the gastrocnemius muscle. To produce a clear signal and reduce skin impedance, the skin was first prepared by shaving the area, gently abrading the skin with sandpaper, wiping the skin with Nuprep gel, and cleaning the area with alcohol wipes. Subsequently, two bipolar surface electrodes were placed two cm apart along the belly of the soleus muscle, perpendicular to the muscle fibers, to record the innervation zone.40 A ground electrode was placed on the bony prominence of the medial malleolus. The electrodes were then connected via cables to a custom-built amplifier with a built-in stimulus artifact suppressor and a high-pass filter (20 Hz), and the signals were recorded using the SIGNAL software (https://ced.co.uk/products/sigovin).\n\nThe H reflex and Mmax and V waves of the soleus muscle were elicited via electrical stimulation of the tibial nerve. After explaining the procedure to the participant and caregiver, a stimulating electrode (cathode) was placed in the popliteal fossa and the anode electrode was placed just proximal to the patella. This positioning ensures that the H-reflex can be elicited at the lowest possible threshold as the current passes transversely through the tibial nerve. The knee was then bandaged to apply pressure on the cathode for ease of stimulation. Electrical stimulation was delivered by using a Digitimer-isolated stimulator (Digitimer DS7AH, Digitimer Ltd, Hertfordshire, UK). The position of the electrodes was altered accordingly to provide the lowest stimulation intensity while ensuring the activation of the entire soleus muscle.\n\nThe M wave recording was elicited by electrical stimulation of the tibial nerve starting at 5mA and was progressively increased in 5mA increments until the M wave appeared in the sEMG. M-max, which represents the recruitment of all motor axons, is reached when the motor response does not increase with further increases in electrical stimulation, and the H reflex response has disappeared. This value was then recorded as M-max, 10% of which was calculated and used in the H-reflex recording.\n\nFor the H-reflex recording, the participant was asked to push down their foot gently to maintain a contraction at 10% of M-max (as determined above in section 3.2.4.1). This was displayed on a computer screen directly in front of the patient, as a line for visual feedback. The purpose of this low-level constant contraction is to allow for some stable background electrical activity throughout the stimulation protocol so that any changes in the H-reflex can be determined to be due to other test conditions.40 The H-reflex is then elicited via electrical stimulation of the tibial nerve. The participants received 48 stimulations at different intensities, and each stimulation was given at 0.5 ms intervals. Equally dividing the M-max into 16 determined the intensity levels, and then three stimulations per level were applied. The levels were randomly stimulated to reduce the predictability of the participants’ responses.\n\nThe V-wave was then recorded using sEMG and force measurements. Participants were asked to perform three separate MVC’s by pushing down their feet as hard as possible while being verbally encouraged by the researcher. During each of these MVC’s they were given three electrical stimulations at a supra-maximal intensity (110%) of M-max.\n\nVariations can be seen in the H reflex due to changes in subject position during recording, alterations in electrode positioning or contact, and/or alterations in the muscle itself, which can affect study results if adequate H-reflex curve analysis is not performed.40,41 Furthermore, thresholds to elicit the H reflex and M wave can differ not only between subjects but also within subjects, even if tested on the same day.41 In order to account for these changes, to obtain results that reflect genuine H reflex changes from the intervention and to determine the H reflex and V wave at different intensities along the recruitment curve, it is necessary to perform curve fitting and normalization on the raw H reflex data.41 This was performed using the procedure described by Brinkworth41 and used in previous H-reflex studies with chiropractic SM as the intervention.22,28\n\nFirst, the peak-to-peak amplitudes of the H, M, and V waves were obtained from the EMG signals. Normalization was then performed to compare the results between subjects, with M-Max recorded in the pre-assessment used as a normalization factor in that particular session. For each participant in both the pre- and post-sessions, M-max was used for the corresponding H-reflex, M-wave, and V-waves to provide H/Mmax and V/Mmax ratios for each participant. Having this normalized to the specific H-reflex or V-wave stimuli, for each subject and each session allows for a more accurate assessment of the changes in the H-reflex and V-wave represent.22,41 Once normalization was performed, these values were modeled for curve fit analysis with a hyperbolic function for the M wave and a Gaussian equation for the H and V waves.41\n\nAfter curve fitting and normalization were performed, the H-reflex was analyzed for threshold levels by identifying the intensity when the H-reflex curve started to rise. MATLAB code was used as an automatized procedure; however, the time windows for each data set were also manually inspected to ensure the accuracy of this level. The results of each session were then superimposed and post intervention/control results were compared with the intervention/control results. Parameters extracted from the curve-fitted H reflex data were the H reflex threshold, s50, and slope.\n\nAfter curve fitting and normalization, the V wave was analyzed using peak-to-peak amplitudes, which were then superimposed and averaged to produce a mean value difference between the pre- and post sessions.\n\nTo determine the difference in force measurements of maximum voluntary contractions, the EMG signal was manually inspected and analyzed using peak-to-peak amplitude calculations. This was done by placing one cursor at the baseline immediately before the contraction started and placing a second cursor at the end of the contraction immediately before the return to baseline, and then calculating the difference. These values were then compared pre- and post-intervention/control.\n\n\n3. Results\n\n3.1.1 Recruitment\n\nThe participants in this study were recruited through NZCPR. At the time of this study, NZCPR was newly established, and this was the first study to use it for recruitment. Consequently, it took considerable time to set up the process to recruit through them, from the first contact in May 2016 until the first flyers were sent out in July 2017. In addition, because they were a new organization, they were still in the process of approving the registrations that they had on their system, which meant that only the approved registrations could be contacted for this study.\n\nIn total, 50 families that were registered in the Auckland region with a GMFCS of I-II and aged between 8-13 years old were sent the study information over a six-week recruitment period. From this 50, five parents (10%) made contact via email inquiring about participating in the study. Of these, three met the inclusion criteria and were included in the study. The two participants that were not included were excluded because one had athetoid dyskinetic CP and the other was only going to turn eight years old in December, after the study period had finished. This resulted in a recruitment rate of only 6%.\n\nThere was a 100% retention rate for every participant who completed the session. The characteristics of the sample are listed in Table 1. Due to the small and unequal sample sizes, the intervention and control groups were inevitably not equally distributed. Interestingly, although this was not an inclusion criterion, all the participants had previous experience with chiropractic SM.\n\nThe recruitment period was set at 6 weeks, both for timely purposes of completing the study and to have a set limit in place in order to assess the recruitment rate. With three people successfully recruited into the study over a 6-week period, this gives an average of one participant every two weeks.\n\nFor a large scale RCT, an estimated sample size of 128 participants is predicted based on a calculation with a given effect size (d) of 0.5, type 1 error probability (α) of 0.05 and a power of 0.8 (minimally acceptable). Based on this recruitment strategy and a rate of one participant every two weeks, it would take 256 weeks or almost five years to recruit enough people. With a recruitment rate of 6 %, more than 2000 families/potential participants would need to be contacted.\n\n3.1.2 Data collection procedure\n\nAll data collection took place at the Health Research and Rehabilitation Institute of the AUT. This was well received by all participants and had ease of access to disability carparks; families were also familiar with the location due to the gait analysis clinic for children being in the same area. All consent and child assent forms were received and reported to the researcher to be understood by the parent and child. Participants were advised that the sessions would take approximately two hours for the pre- and post-combined. This was fairly accurate for sessions between 90 minutes and two hours.\n\nIn general, the data collection procedure was well tolerated. Owing to the nature of the measurement protocol using electrical stimulation, participants were advised at the beginning of the session that if they did not want to continue, they could ask us to stop at any time. One participant reported feeling bored, had difficulty concentrating, and sat in a chair for the required amount of time, and the parent had to give her a smartphone to play a game to distract her. This participant did not want to do the final part of the pre-session recording, which was the V-wave recording, so this was omitted from the post-session data collection. This was the only indication of poor compliance with the recording protocol. The other two participants had no issues, fully accepted the protocol, and did not complain.\n\n3.1.3 Equipment\n\nThere were some issues with the custom-made force transducers. The one that was initially planned to be used was in use in another study at the time of the first data-collection session and could not be moved. Therefore, the older version that used the same measurement was used for the first participant. The participant reported this as being uncomfortable, which was the same participant who had difficulty accepting the full H, M, and V wave protocols, and it is possible that this was partly due to the discomfort from the force transducer. The second and third participants used the new version, originally planned for use in this study. There have been no reports of discomfort or problems associated with this condition.\n\nAll other equipment worked well and had no issues.\n\n3.1.4 Intervention\n\nThe chiropractic SM and passive control interventions were well tolerated by all participants. No issues were reported by the chiropractor or participants, and all movements were well tolerated. No serious or minor adverse events were reported due to intervention or passive control. All participants had previously received chiropractic care more than one year prior to this study, which may have alleviated any potential concerns.\n\nDue to the small sample size of the three participants and group variation, statistical analysis was not performed on the data obtained for the H reflex, V wave, and force. Therefore, no conclusions will be drawn regarding the efficacy of the intervention versus passive control. The following section will present the results and trends identified, with the aim of determining whether changes can be detected using this protocol and intervention in children with CP in future research studies.\n\n3.2.1 H-reflex\n\nResults from the H-reflex recording showed that both participants in the intervention group had a shift in the H-reflex threshold towards the left, or a lowered threshold, post intervention. This contrasts with the control participant, which had a shift in the H-reflex threshold towards the right, or a higher threshold, post-passive control intervention. Results of the s50 parameter showed that participants in the intervention group both had an increase in s50, suggesting a trend towards a greater number of motor neurons being recruited after chiropractic SM intervention at 50% stimulus compared to pre-intervention. Control participants showed a decrease in s50. Changes in slope showed similar trends with a slope gradient increase after chiropractic SM intervention, suggesting the ability to recruit motor neurons faster. This is in contrast to the passive control intervention, which resulted in a decreased slope gradient. The numerical data for these results are listed in Table 1.\n\n3.2.2 V wave\n\nAs mentioned above, the first participant did not wish to continue with the protocol at that time; therefore, the V wave was only recorded in two participants, one control, and one intervention. The participant who received the passive control intervention showed a mean reduction in the V-wave amplitude post intervention of 0.39%, so there was no real change. The participants who received chiropractic SM intervention showed a mean reduction in V-wave amplitude post intervention of 62.6%. The results are presented in Table 2.\n\n3.2.3 Force\n\nChanges in MVC force were variable between participants.\n\nThe passive control participants had a 19.5% reduction in MVC force post intervention. In the chiropractic SM intervention group, one participant had a 14.3% increase in MVC force, and the other participant had a 48.9% decrease in MVC force. The results are presented in Table 3.\n\n\n4. Discussion\n\nThis study aimed to answer specific feasibility questions to determine whether a full-scale RCT using the same design would be appropriate. Feasibility was assessed in the following areas: recruitment rate and method, equipment, tolerance, and compliance with the intervention and data collection protocol, and to determine whether it is possible to obtain changes in outcome measures. This feasibility study suggests that a full-scale RCT assessing the effects of chiropractic SM on motor neuron excitability and muscle strength in children with CP using the same recruitment methods would not be feasible because of a low recruitment rate that would make recruitment in a timely manner for a larger-scale RCT difficult. However, the results of other aspects of the study indicate positive feasibility, and thus, with alterations to the recruitment methodology, a full-scale RCT could be conducted.\n\nAll recruitment for this study was conducted using NZCPR. The NZCPR is a new organization that was still in its operational stage when this study was conducted; this was not known by the researcher until well into the recruitment setup. Consequently, all recruitment procedures were new and the registry had a limited number of registered and approved families. Contact was made by mailing out study flyers and information sheets to all eligible and registered families, and then parents/caregivers were required to contact the researcher to be involved. This is an example of convenience or availability sampling, and has potential issues.42 First, any results only represent a small sample population; second, it is possible that there are a large number of children with CP in the Auckland region that were not yet on the registry and so were not made aware of the study, both of which introduce sampling bias.42 To alleviate this potential bias and increase recruitment numbers, other sources of potential participants could be used, such as recruiting through CP associations or schools that have specialty programs for CP or high numbers of students with CP. These are potential methods for future research.\n\nIt is also possible that the age range was too small and could have affected the recruitment rate. All participants were aged 12 years; the higher limit of the range was 13, and perhaps having a higher limit may improve recruitment. One parent contacted the researcher about participating, but their child was only turning 8 in December, two months after completion, so perhaps also having a lower limit may have been beneficial. Previous studies assessing the H reflex in children with CP have used age ranges of 5-15 years,43 5-12 years44 and 4-6 years.45 However, as only children aged 12 years were assessed for tolerance and compliance with the data collection protocol and intervention, decreasing the age limit is not recommended, as it is not tested in the younger age group. The possible amended age range could be 8-14 years.\n\nA GMFCS of I-II was set as an inclusion criterion, and participants were only contacted for participation that met this criterion for the NZCPR. This was chosen because GMFCS levels III-V have significantly more mobility impairments and it was thought, as others have suggested, that this would introduce too much variability into the sample set.46 However, it was noted by the NZCPR that there was a low number of children meeting this criterion in the lower socioeconomic regions of Auckland, which had predominately GMFCS levels of III-IV, which may have affected adequate population representation and recruitment rate.\n\nBased on the calculations, a sample size of 128 participants (64 in each group) was estimated for a large-scale study. Based on the recruitment rate found in this feasibility study, this would mean the need to contact more than 2000 families. Exact epidemiological data on the number of children with CP living in Auckland are not available; however, estimates can be made based on population statistics and CP birth rates. In the greater Auckland region (including Counties Manukau and Waitemata), there are an estimated 440,000 people living under the age of 19 with diagnosed CP.47 Based on the birth rate for CP being 2.5 in 1000 live births, this gives an estimated 1100 people living with CP in the greater Auckland region under the age of 19 years. As this does not consider the age range, GMFCS, and other inclusion/exclusion criteria for this study, it may not be possible to contact enough families based on this recruitment strategy.\n\nAs mentioned previously, the results of this study are not intended to be used to make any claims regarding intervention effects. However, it is noted that both participants in the intervention group demonstrated changes in the H-reflex recordings consistent with those observed in previous studies assessing the effects of chiropractic SM on motor neuron excitability.22,28,29 Interestingly, the results of the V wave are not consistent with previous studies that have found an increase in the V wave and force post-chiropractic SM.22,28,29 The V-wave represents volitional drive, which is the amount of voluntary drive during muscle contraction.48 The V-wave amplitude depends on the density of action potentials sent down from the supraspinal centers, which block the antidromic action potentials caused by supramaximal stimulation of the tibial nerve. Thus, if maximal effort is not made during the data collection of the V-waves, their amplitude will be smaller, and the maximum force will be smaller. Therefore, in light of the changes in the H-reflex that are consistent with increased corticospinal excitability after chiropractic SM intervention, and considering that the H-reflex recording protocol did not require any voluntary effort on the child’s behalf, the V-wave and strength results of the one-child post-chiropractic SM showing a 62% decrease in the V-wave and 48.9% decrease in MVC force, is likely due to the child simply not trying to maximally contract their muscle after the chiropractic SM intervention. The V-wave measure and the maximum force output rely on the child trying to contract their muscle as much as they can, and with an almost 50% decrease in force produced after the chiropractic SM intervention, it is unlikely that this child made a maximum effort, especially considering that their H-reflex results indicate an increased corticospinal excitability with a lower H-reflex threshold, increased s50, and increased H-reflex slope. The idea that this child most likely did not try during the V wave and strength data collection post chiropractic SM is also further supported by the fact that one of the other participants would not do the V wave part of the protocol due to fatigue and discomfort. This suggests that if further studies are to be conducted on this population group, the V-wave part of the protocol may need to be omitted or performed earlier in the post-intervention data-recording session.\n\nA lower H-reflex threshold, as has been seen previously in post-chiropractic SM22 would suggest that spinal manipulation lowers the recruitment threshold of motoneurons to Ia afferent input. In other words, the low threshold motoneurons have become more excitable, or the synapses of the Ia primary afferents have become more efficient, since a lower stimulus intensity can now recruit the same motoneurons compared to baseline recordings. The increase in the s50 parameter suggests that a greater number of motor neurons are recruited after chiropractic SM intervention at 50% stimulus compared with pre-intervention.40 A steeper H-reflex slope post-chiropractic SM suggests that motor neurons can be recruited at a faster rate.40 Thus, these three measures that did not require voluntary participation or maximum effort suggest that chiropractic SM intervention resulted in increased corticospinal excitability. These findings could have important implications, as it is thought that those with CP have problems activating available motor units and increasing motor unit firing rates.7 Again, it is important to note that this study was not designed to test efficacy, nor did we have sufficient subjects to make any such claims. Larger-scale studies are needed to further investigate this.\n\nThe feasibility of the data collection protocol is questionable. The acceptability of the protocol was not measured formally; for example, with a post-study questionnaire, tolerance and compliance were assessed as an informal discussion with the participants and parents/caregivers and through observations of the researchers. Consequently, tolerance and compliance of the protocol needs to be viewed with the potential for bias from the researchers in mind, and results interpreted with caution. Of note, one participant was unable to complete the full protocol and did not want to do the V-wave part, which was at the end of each data recording session. This child reported feeling tired and did not want to stay sitting or strapped into the force transducer any longer. This participant had apparent attention deficits and needed to play games on the phone to keep her distracted. There were no exclusion criteria set for comorbid conditions, such as attention-deficit-hyperactivity disorder or autism spectrum disorders, which could potentially be added in future studies, although this would further reduce the potential sample population. Environmental distractors and changes during H-reflex recordings are thought to have an impact on the H-reflex results, so these need to be minimized in future studies.41\n\nNo adverse events due to the intervention were reported by the participants or their families. The chiropractor informed the researcher that all the intervention procedures were well tolerated. Again, this was not formally assessed and poses the potential for bias from the chiropractor.\n\nThis study was conducted using a single-blind approach, in which the researchers were blinded to the group allocation during data collection and analysis. The chiropractor could not be blinded because they had to provide the intervention. Participants were also not told which group they were in, and the control involved the same physical examination, interaction, movement, time, and setup as the SM intervention (but no thrust). This helps to reduce some of the bias that can occur from doctor-patient interaction, proprioceptive input from cutaneous receptors, vestibular input, and mechanoreceptors, and time between pre- and post-data collection sessions, which are arguable issues with manual therapy studies.49 However, it must be noted that in this study, all three participants had chiropractic SM before; thus, participants may have been able to guess which group they were in. However, this was not a variable assessed in the present study.\n\nNo study has assessed changes in muscle strength and motor neuron excitability in children with CP following chiropractic SM; therefore, the role of prior chiropractic care is poorly understood. It is possible that previous chiropractic care could have altered the baseline recordings; however, as none of the participants were new to chiropractic care, this is difficult to assess. However, for all the participants, it had been a minimum of one year since they last had chiropractic SM, so it is unlikely that any effects significantly altered baseline measurements.\n\nThis study has provided valuable insight and knowledge on issues pertaining to conducting research in a population group of children with CP and a chiropractic intervention. Learning from this study can help guide future research, not only using these specific outcome measures but also on recruitment ability for any study involving children with CP. It is evident that there is a strong basis for further assessment of the effects of chiropractic SM on children with CP. Future trials may consider including more ‘low-effort’ functional outcomes, such as gait, quality of life and ability to perform activities of daily living. Recommendations for any future research include recruiting from more sources, such as CP associations or schools, using a multi-tiered recruitment strategy with follow-up phone calls and emails, changing inclusion criteria by extending the age range to 8-14 years, using only the new model force transducer for data collection, and omitting V wave recordings or conducting them earlier in the protocol.\n\nThis study was designed to answer specific feasibility questions, which it has done so adequately. The small sample size (n=3), change in equipment between participants, sampling bias, and uneven sample characteristics are factors that limit any further interpretation of results, efficacy of intervention, and generalizability.\n\nThere was also no formal assessment of tolerance of the data collection protocol or intervention, such as a post-study questionnaire assessing acceptability. This is a limitation of this feasibility study as it introduces bias from the researchers in their observations and questioning of the participants and from the chiropractor in assessing the tolerance of the intervention. The researcher also provided consent and asked if the participant and caregiver understood the consent and assent forms. This could have influenced the responses and introduced bias.\n\nAnother limitation of this study is that all participants had received chiropractic SM before, which means that there is a chance that they were able to guess which intervention they received, and conclusions cannot be made about the tolerance of chiropractic SM intervention in those who had not had SM before.\n\n\n5. Conclusions\n\nIn conclusion, the results of this study provide valuable knowledge on the feasibility of a protocol to measure changes in H, V, and MVC forces in children with CP following chiropractic SM intervention. This is the first study of its kind to address gaps in the current literature on the feasibility of assessing changes in muscle strength and motor neuron excitability in children with CP following chiropractic SM. Much has been learned about adequate recruitment methods, changes that need to be made to the protocol, and tolerance of chiropractic SM as an intervention. The idea to undertake research in this population group was first to investigate a treatment modality, chiropractic, which is noninvasive and has a growing body of evidence to suggest improvements in neurological function, and whether this would allow children with CP to have an improved quality of life and function.\n\nThis feasibility study has shown that modifications to the recruitment method would have to be performed to run a full-scale RCT in this population in the future. Such a full-scale RCT appears to be feasible and should adhere to the recommendations of this thesis, such as modifications in recruitment methods, widening the age range, using only the best equipment, and recording V waves earlier in the collection protocol.\n\n\nAuthor contributions\n\nConceptualization, J.D., D.T., I.K.N., and H.H.; methodology, J.D., D.T., H.H., I.K.N., and R.W.N.; software, I.K.N. and R.W.N.; validation, J. D., D. T., and H.H.; formal analysis, I.K.N and R.W.N.; resources, D.T. and H.H.; data curation, J.D., R.W.N.; writing—original draft preparation, J.D.; writing—review and editing, J.D., D.T.,H.H., I.K.N.; visualization, J.D.; supervision, D.T. and H.H.; project administration, J.D.; funding acquisition, J.D., and H.H. All authors have read and agreed to the published version of the manuscript.\n\n\nInstitutional review board statement\n\nThe study was conducted in accordance with the guidelines of the Declaration of Helsinki and approved by the Health and Disability Ethics Committee of New Zealand (16/NTA/158, 16/11/2016). The date of ethical approval is 16th November 2016.\n\n\nInformed consent statement\n\nInformed consent was obtained from all the subjects involved in the study. Prior to participation in the study, written informed consent was obtained from the parents of the participants and the participants provided written informed assent. Consent was not obtained from the participants themselves as they were under the age of 16 years, which is the legal age of consent in New Zealand. Written informed assent was obtained from participants instead as required by the Health and Disability Ethics Committee in New Zealand.", "appendix": "Data availability statement\n\nThe data are not publicly available because of ethics committee restrictions on data related to vulnerable populations. Readers and reviewers can request to view the data by emailing the corresponding author jenna.duehr@nzchiro.co.nz. The data will be released after approval from the Health and Disability Ethics Committee of New Zealand.\n\n\nReferences\n\nBax M, et al.: Proposed definition and classification of cerebral palsy, April 2005. Dev. Med. Child Neurol. 2005; 47(8): 571–576. PubMed Abstract \| Publisher Full Text\n\nOskoui M, et al.: An update on the prevalence of cerebral palsy: a systematic review and meta-analysis. Dev. Med. Child Neurol. 2013; 55(6): 509–519. PubMed Abstract \| Publisher Full Text\n\nØstensjø S, Carlberg EB, Vøllestad NK: Motor impairments in young children with cerebral palsy: relationship to gross motor function and everyday activities. Dev. Med. Child Neurol. 2004; 46(09): 580–589. PubMed Abstract \| Publisher Full Text\n\nPapavasiliou AS: Management of motor problems in cerebral palsy: A critical update for the clinician. Eur. J. Paediatr. Neurol. 2009; 13: 387–396. PubMed Abstract \| Publisher Full Text\n\nReddihough DS, Collins KJ: The epidemiology and causes of cerebral palsy. Aust. J. Physiother. 2003; 49(1): 7–12. Publisher Full Text\n\nPoon DMY, Hui-Chan CWY: Hyperactive stretch reflexes, co-contraction, and muscle weakness in children with cerebral palsy. Dev. Med. Child Neurol. 2009; 51(2): 128–135.\n\nRose J, McGill KC: Neuromuscular activation and motor-unit firing characteristics in cerebral palsy. Dev. Med. Child Neurol. 2005; 47(5): 329–336. PubMed Abstract \| Publisher Full Text\n\nRose J, McGill KC: The motor unit in cerebral palsy. Dev. Med. Child Neurol. 1998; 40(4): 270–277. Publisher Full Text\n\nMockford M, Caulton JM: Systematic review of progressive strength training in children and adolescents with cerebral palsy who are ambulatory. Pediatr. Phys. Ther. 2008; 20(4): 318–333. PubMed Abstract \| Publisher Full Text\n\nRoss SA, Engsberg JR: Relationships between spasticity, strength, gait, and the GMFM-66 in persons with spastic diplegia cerebral palsy. Arch. Phys. Med. Rehabil. 2007; 88(9): 1114–1120. PubMed Abstract \| Publisher Full Text\n\nDodd KJ, Taylor NF, Damiano DL: A systematic review of the effectiveness of strength-training programs for people with cerebral palsy. Arch. Phys. Med. Rehabil. 2002; 83(8): 1157–1164. Publisher Full Text\n\nDiaz Heijtz R, Forssberg H: Translational studies exploring neuroplasticity associated with motor skill learning and the regulatory role of the dopamine system. Dev. Med. Child Neurol. 2015; 57: 10–14. PubMed Abstract \| Publisher Full Text\n\nSolopova I, et al.: Neurorehabilitation of patients with cerebral palsy. Hum. Physiol. 2015; 41(4): 448–454. Publisher Full Text\n\nHaavik H, Murphy B: Subclinical neck pain and the effects of cervical manipulation on elbow joint position sense. J. Manipulative Physiol. Ther. 2011; 34: 88–97. PubMed Abstract \| Publisher Full Text\n\nHaavik H, Murphy B: The role of spinal manipulation in addressing disordered sensorimotor integration and altered motor control. J. Electromyogr. Kinesiol. 2012; 22(5): 768–776. PubMed Abstract \| Publisher Full Text\n\nHaavik H, et al.: Impact of Spinal Manipulation on Cortical Drive to Upper and Lower Limb Muscles. Brain Sci. 2017; 7(1): 2. Publisher Full Text\n\nHaavik H, et al.: Effects of 12 Weeks of Chiropractic Care on Central Integration of Dual Somatosensory Input in Chronic Pain Patients: A Preliminary Study. J. Manip. Physiol. Ther. 2017; 40(3): 127–138. PubMed Abstract \| Publisher Full Text\n\nHaavik Taylor H, Murphy B: Cervical spine manipulation alters sensorimotor integration: A somatosensory evoked potential study. Clin. Neurophysiol. 2007; 118(2): 391–402. PubMed Abstract \| Publisher Full Text\n\nHaavik Taylor H, Murphy B: Altered sensorimotor integration with cervical spine manipulation. J. Manip. Physiol. Ther. 2008; 31(2): 115–126. PubMed Abstract \| Publisher Full Text\n\nHaavik Taylor H, Murphy B: Altered Central Integration of Dual Somatosensory Input Following Cervical Spine Manipulation. J. Manipulative Physiol. Ther. 2010; 33(3): 178–188. PubMed Abstract \| Publisher Full Text\n\nHaavik Taylor H, Murphy B: The effects of spinal manipulation on central integration of dual somatosensory input observed following motor training: A crossover study. Journal of Manipulative & Physiological Therapeutics. 2010; 33(4): 261–272. PubMed Abstract \| Publisher Full Text\n\nNiazi I, et al.: Changes in H-reflex and V waves following spinal manipulation. Exp. Brain Res. 2015; 233: 1165–1173. PubMed Abstract \| Publisher Full Text\n\nLelic D, et al.: Manipulation of Dysfunctional Spinal Joints Affects Sensorimotor Integration in the Prefrontal Cortex: A Brain Source Localization Study. Neural Plast. 2016; 2016: 3704964.\n\nHolt KR, et al.: Effectiveness of Chiropractic Care to Improve Sensorimotor Function Associated With Falls Risk in Older People: A Randomized Controlled Trial. J. Manip. Physiol. Ther. 2016; 39: 267–278. PubMed Abstract \| Publisher Full Text\n\nTaylor HH, Holt K, Murphy B: Exploring the neuromodulatory effects of the vertebral subluxation and chiropractic care. Chiropractic Journal of Australia. 2010; 40(1): 37.\n\nTaylor HH, Murphy B: Altered sensorimotor integration with cervical spine manipulation. J. Manip. Physiol. Ther. 2008; 31(2): 115–126. PubMed Abstract \| Publisher Full Text\n\nHaavik H, et al.: The contemporary model of vertebral column joint dysfunction and impact of high-velocity, low-amplitude controlled vertebral thrusts on neuromuscular function. Eur. J. Appl. Physiol. 2021; 121(10): 2675–2720. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChristiansen TL, et al.: The effects of a single session of spinal manipulation on strength and cortical drive in athletes. Eur. J. Appl. Physiol. 2018; 118(4): 737–749. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHolt K, et al.: The effects of a single session of chiropractic care on strength, cortical drive, and spinal excitability in stroke patients. Sci. Rep. 2019; 9(1): 2673. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNiazi IK, et al.: The effect of spinal manipulation on the electrophysiological and metabolic properties of the tibialis anterior muscle. Healthcare. MDPI; 2020; 8. . Publisher Full Text\n\nRobinault L, et al.: The effects of spinal manipulation on motor unit behavior. Brain Sci. 2021; 11(1): 105. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKachmar O, et al.: Influence of Spinal Manipulation on Muscle Spasticity and Manual Dexterity in Participants With Cerebral Palsy: Randomized Controlled Trial. J. Chiropr. Med. 2018; 17(3): 141–150. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEek MN, Beckung E: Walking ability is related to muscle strength in children with cerebral palsy. Gait Posture. 2008; 28(3): 366–371. PubMed Abstract \| Publisher Full Text\n\nGeertsen SS, et al.: Impaired gait function in adults with cerebral palsy is associated with reduced rapid force generation and increased passive stiffness. Clin. Neurophysiol. 2015; 126(12): 2320–2329. PubMed Abstract \| Publisher Full Text\n\nHolt K, et al.: INTEREXAMINER RELIABILITY OF A MULTIDIMENSIONAL BATTERY OF TESTS USED TO ASSESS FOR VERTEBRAL SUBLUXATIONS. Chiropr. J. Aust. 2018; 46(1): 100–117.\n\nTriano JJ, et al.: Review of methods used by chiropractors to determine the site for applying manipulation. Chiropr. Man. Therap. 2013; 21(1): 36. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCooperstein R, Young M: The reliability of spinal motion palpation determination of the location of the stiffest spinal site is influenced by confidence ratings: a secondary analysis of three studies. Chiropr. Man. Therap. 2016; 24(1): 1–13. Publisher Full Text\n\nFryer G, Morris T, Gibbons P: Paraspinal muscles and intervertebral dysfunction: part two. J. Manip. Physiol. Ther. 2004; 27(5): 348–357. PubMed Abstract \| Publisher Full Text\n\nCram JR, Kasman GS, Holtz J: Introduction to surface electromyography. Aspen Publishers; 1998.\n\nTucker KJ, Tuncer M, Türker KS: A review of the H-reflex and M-wave in the human triceps surae. Hum. Mov. Sci. 2005; 24(5-6): 667–688. PubMed Abstract \| Publisher Full Text\n\nBrinkworth RSA, et al.: Standardization of H-reflex analyses. J. Neurosci. Methods. 2007; 162(1-2): 1–7. PubMed Abstract \| Publisher Full Text\n\nAcharya A, Prakash AS, Nigam A: Sampling: Why and How of It? Indian J. Med. Special. 2013; 4(2): 330–333.\n\nHodapp M, et al.: Changes in soleus H-reflex modulation after treadmill training in children with cerebral palsy. Brain. 2009; 132(1): 37–44. PubMed Abstract \| Publisher Full Text\n\nFrascarelli F, et al.: Neurophysiological changes induced by the botulinum toxin type A injection in children with cerebral palsy. Eur. J. Paediatr. Neurol. 2011; 15(1): 59–64. PubMed Abstract \| Publisher Full Text\n\nSoriano SG, et al.: Nitrous oxide depresses the H-reflex in children with cerebral palsy. Anesth. Analg. 1995; 80(2): 239–241. PubMed Abstract\n\nPalisano RJ: GMFCS-E & R gross motor function classification system: expanded and revised. Canchild centre for childhood disability research. 2007.\n\nMOH, M.o.H: Population statistics. Ministry of Health; 2016.\n\nAagaard P, et al.: Neural adaptation to resistance training: changes in evoked V-wave and H-reflex responses. J. Appl. Physiol. 2002; 92(6): 2309–2318. PubMed Abstract \| Publisher Full Text\n\nVernon HT, et al.: Validation of a novel sham cervical manipulation procedure. Spine J. 2012; 12(11): 1021–1028. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "342255", "date": "29 Nov 2024", "name": "Qamar Mahmood", "expertise": [ "Reviewer Expertise I have PhD Rehabilitation sciences at my credit. Moreover", "I have more than 34 years of academic and clinical experience in the management of children with Cerebral Palsy." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 explores the feasibility of studying the effects of chiropractic spinal manipulation (SM) on CP-related motor neuron excitability and muscle strength. While it provides valuable insights into logistical challenges and methodological considerations, its small sample size, limited data accessibility due to ethical concerns have reduced its interpretation and generalizability.\nBelow are the serial-wise answers of questions being asked in the report. 2. The study employs a randomized controlled design, which is appropriate for a feasibility study. However, the small sample size (n=3) limits the strengths of the findings and raises concerns about generalizability. 3. The rationale for using specific parameters (e.g., s50, slope) is not fully explained for this population, leaving room for interpretation errors in replication attempts. 4. Due to the very small sample size, statistical analysis was not performed, and thus, there are no interpretations of statistical significance. While this is acceptable in such a small scale feasibility study, it limits the depth of interpretation and validation of trends observed in the results. 5. The data are not publicly available due to ethical restrictions related to vulnerable populations. However, the authors indicate that data can be requested under certain conditions. 6. The conclusions regarding feasibility are supported by the results, particularly concerning recruitment challenges and data collection procedures. However, claims about the effects of chiropractic spinal manipulation on muscle strength and motor neuron excitability are not sufficiently substantiated due to the small sample size and lack of statistical analysis.\nAdditionally, there are minor grammatical issues which have been advised corrections via reviewing suggestions, comments have been embedded within the manuscript so that author can answer and adjust those changes within the manuscript. Few of those suggestions are reproduced here for ease of reference. a. Table of demographic and baseline characteristics of the study population is missing. This table can be added in the manuscript before Table-1. b. It is better to use the key words in alphabetic order, so alphabetize these words. c. In some paragraphs, author has used abbreviation for spinal manipulation as SM, while in others, this abbreviation was not used. Therefore, it is better to have uniform approach of using abbreviation of any word in whole of the manuscript. Principle is that when any word comes first time, write full word along its abbreviation in the bracket. Later only abbreviation can be used. d. Instead of using “non-specific movements of their head, spine, and body”, use proper and specific term as passive range of motion. e. Author has mentioned contact with families in May 2016 and sending flyer in 2017, but when actually this study was conducted. This is missing. Actual dates when the intervention applied and data collected should be mentioned. f. Author stated that for a large scale RCT with sample size of 128, it may take 256 weeks and 2000 families to be contacted in future which seems overestimation due to a specific time and location situation. Participation depends upon many known and un-known factors. Even in one geographical location, responses of same participants may differ at two different timepoints. Moreover, as the sample size is to small, so predication based on it, does not seem justified. Author should be cautious in such interpretations as it may promote de-motivation among future researchers. g. Author reported about a participant which did not complete the assigned task that perhaps that child had apparent attention deficiency issue. But this attention deficiency might be temporary response in some un-wanted scenario. Have the author checked with medical record that whether the child was a diagnosed case of such disorder. If this was just clinical observation, then such claim is not justified. Many children want to move and play instead of being tied to one place. This is normal and natural behavior. Author may amend the sentence.\nAdditional comments mentioned in this attached file link: https://f1000research.s3.amazonaws.com/linked/691601.ID_155618-Reviewer_comment_file-FRES.docx\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1093
https://f1000research.com/articles/13-644/v1	17 Jun 24	{ "type": "Case Report", "title": "Case Report: Giant lung hamartoma : An usual cause of lobectomy in a five-year child", "authors": [ "Sabrine Louhaichi", "Besma Hamdi", "Imen Bouacida", "Yessmine Haddar", "Sarra Trimech", "Jamel Ammar", "Aida Ayadi", "Agnès Hamzaoui", "Baccouche Ines", "Adel Marghli", "Besma Hamdi", "Imen Bouacida", "Yessmine Haddar", "Sarra Trimech", "Jamel Ammar", "Aida Ayadi", "Agnès Hamzaoui", "Baccouche Ines", "Adel Marghli" ], "abstract": "Pulmonary hamartomas are the most common benign tumors of the lung in adults. They are usually asymptomatic because of their small size and their slow-growing character. We report the case of a 5-year-old child presenting with a giant lung mass causing recurrent right pneumonia. Surgical resection with middle lobectomy was performed. Final histology revealed pulmonary hamartoma with predominant adenofibromatous and lipomatous differentiation.", "keywords": [ "lung tumor", "case report", "children", "surgical intervention", "hamartoma" ], "content": "Introduction\n\nLung hamartomas are benign pulmonary tumors characterized by an incidental finding in most cases.1 Compocased of a mixture of variant mesenchymal elements, it is more frequently seen in male adults. Pediatric cases are extremely rare.2–3 Herein we report the case of a pulmonary hamartoma revealed by persistent pneumonia in a five-year-old child.\n\n\nCase report\n\nA five-year-old child was referred to our department in September 2023 because an abnormal pulmonary density of the lower right hemithorax. His past medical history revealed recurrent admissions for right pneumonia during the last two years. The patient complained of chronic productive cough without chest pain or hemoptysis. Physical examination did not reveal abnormalities apart from a decrease in breath sounds in the right lung. Chest radiography revealed a heterogeneous right opacity above the diaphragm as showed in Figure 1.\n\nChest computed tomography revealed a giant cystic and solid mass measuring 122 × 80 × 102 mm compressing the right middle and lower lobes. This mass contained tissular, fatty, and calcified elements, along with multiple airy cysts, suggesting a giant pulmonary hamartoma (Figure 2).\n\nThe patient underwent flexible bronchoscopy, which ruled out endobronchial development of the mass. Cytological examination of the bronchial aspiration fluid revealed negative results for malignancy. Common bacterial and acid-fast bacilli cultures were also negative, and surgery was performed. The patient underwent a right lateral thoracotomy. During exploration, the mass occupied two-thirds of the right thorax and compressed the upper and lower lobes (Figure 3). It depended on the middle lobe, which appeared as a small strip of destroyed lung parenchyma, and atypical resection of the mass followed by a complete right middle lobectomy was performed. The postoperative course was uneventful, and the patient was discharged seven days later.\n\nThe final histology of the tumor showed a well-circumscribed mass measuring 14 × 10 × 5 cm, with predominantly adenofibromatous and lipomatous differentiation, calcifications, and ossified lesions (Figure 4). There was no evidence of cartilage or muscle tissue. The tumor was covered by a thin fibrous capsule. Additionally, diffuse alveolar hemorrhage lesions were observed in the middle lobe. Follow-up at three weeks post-surgery indicated no adverse outcomes.\n\n\nDiscussion\n\nPulmonary hamartomas are benign tumors that often occur in middle-aged adults with male predominance.4 Within the pediatric population, pulmonary hamartomas are significantly rarer.5 It is an incidental finding in most cases, with a diameter ranging from 1 to 8 cm.6 This type of tumor has never been reported as a congenital lesion. Cytogenetic analysis showed abnormalities in chromosomal bands 6p21, 12q14–15, or other regions corresponding to mutations in high-mobility group (HMG) proteins. This group of proteins plays an important role in regulating chromatin architecture and gene expression.7\n\nThe pathological pattern of the tumor usually shows predominant chondroid differentiation with a mixture of adipose tissue, fibrous tissue, smooth muscle, and bone, along with entrapped respiratory epithelium. Immunohistochemical staining is not necessary for the diagnosis.8 In other cases, the major component can define various subtypes of the tumor: lipomatous, adenoleiomyomatous, and fibrous hamartomas.7,9 In the current case, the tumor consisted histologically of glandular lumens and fibrous tissue with some calcifications. No evidence of cartilage or muscle tissue damage was observed.\n\nPulmonary hamartomas are typically asymptomatic. The patient had a medical history of recurrent pneumonia before being referred to our department. Respiratory infections may occur because of mechanical obstruction of the bronchus.\n\nOn tomodensitometry, lung hamartoma usually appears as a lobulated nodule with a heterogeneous density and no pleural traction. Characteristic imaging manifestations include the presence of fat (60% of the cases) and a popcorn appearance of calcifications observed in 5-50% of the cases.10 Malignant transformation is exceedingly rare.11\n\nSurgery is indicated for symptomatic masses or those in which malignancy cannot be excluded.12,13 Enucleation and wedge resection are the most common surgical choices for preserving functional lung tissue.14 However, in our case, tumor resection and middle lobectomy were mandatory because of the large size of the tumor and compression of the surrounding parenchyma.\n\n\nConclusions\n\nLung hamartomas typically occur in adults and are asymptomatic in most cases; parenchymal resection is rarely required when surgery is indicated. Our case is unusual because of its many peculiarities. A 5-year-old child presented with recurrent pneumonia. Moreover, owing to its large size, the tumor caused parenchymal damage, leading to middle lobectomy during surgery. Finally, the tumor was characterized by predominant adenofibromatous differentiation, with no cartilage. Knowledge of atypical presentations of this neoplasm is crucial to avoid misdiagnosis and to guide appropriate surgical treatment, especially in pediatric patients.\n\n\nConsent\n\nWritten informed consent was obtained from the patient’s parents for the publication of this case report and accompanying images.", "appendix": "Data availability\n\nNo data are associated with this article\n\n\nReferences\n\nShukla I, Stead TS, Aleksandrovskiy I, et al.: Symptomatic Pulmonary Hamartoma. Cureus. 2021; 13(9): e18230. PubMed Abstract \| Publisher Full Text\n\nPouessel G, Thumerelle C, Santos C, et al.: Pulmonary hamartochondroma: a rare cause of solitary pulmonary nodule in children. J. Radiol. 2005; 86: 79–82. PubMed Abstract \| Publisher Full Text\n\nZapala MA, Ho-Fung VM, Lee EY: Thoracic Neoplasms in Children: Contemporary Perspectives and Imaging Assessment. Radiol. Clin. North Am. 2017; 55(4): 657–676. Publisher Full Text\n\nGrigoraş A, Amălinei C, Lovin CS, et al.: The clinicopathological challenges of symptomatic and incidental pulmonary hamartomas diagnosis. Romanian J. Morphol. Embryol. 2022; 63(4): 607–613. PubMed Abstract \| Publisher Full Text\n\nSaadi MM, Barakeh DH, Husain S, et al.: Large multicystic pulmonary chondroid hamartoma in a child presenting as pneumothorax. Saudi Med. J. 2015; 36(4): 487–489. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGanti S, Milton R, Davidson L, et al.: Giant pulmonary hamartoma. J. Cardiothorac. Surg. 2006; 1: 19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWick MR: Hamartomas and other tumor-like malformations of the lungs and heart. Semin. Diagn. Pathol. 2019; 36(1): 2–10. PubMed Abstract \| Publisher Full Text\n\nHashimoto H, Tsugeno Y, Sugita K, et al.: Mesenchymal tumors of the lung: diagnostic pathology, molecular pathogenesis, and identified biomarkers. J. Thorac. Dis. 2019; 11(Suppl 1): S9–S24. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang S, Wei J, Yang K, et al.: Mesenchymal cystic hamartoma of the lung: a case report. Medicine. 2022; 101(1): e28242–e28242. Publisher Full Text\n\nLeiter Herrán F, Restrepo CS, Alvarez Gómez DI, et al.: Hamartomas from head to toe: an imaging overview. Br. J. Radiol. Mar 2017; 90(1071): 20160607. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChenkel R, Altfillisch C, Chung J, et al.: Malignant Degeneration of Biopsy-Proven Hamartoma to Chondrosarcoma. Cureus. 2020; 12(12): e12150. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElsayed H, Abdel Hady SM, Elbastawisy SE: Is resection necessary in biopsy-proven asymptomatic pulmonary hamartomas?. Interact. Cardiovasc. Thorac. Surg. 2015; 21: 773–776. PubMed Abstract \| Publisher Full Text\n\nErdogu V, Emetli EY, Kutluk AC, et al.: Does pulmonary hamartoma increase the risk of lung cancer? Outcomes of 38 pulmonary hamartoma cases. Sisli Etfal Hastan Tip Bul. 2021; 55(3): 344–348–344–348. Publisher Full Text\n\nUlas AB, Aydin Y, Eroglu A: Pulmonary Hamartomas: A Single-Center Analysis of 59 Cases. Eur. J. Med. 2022; 54(3): 270–273. Publisher Full Text" }	[ { "id": "294003", "date": "25 Jun 2024", "name": "Hüseyin Fatih Sezer", "expertise": [ "Reviewer Expertise The article is a repetition of what is generally known and has no additional features", "except for some surgical difficulty." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Authors First of all, I would like to thank you for the work you have done to prepare the article. My criticisms and suggestions about the article are as follows. - The purpose of the article should be written more clearly in the introduction, and some more literature information should be added. - The words 'case report, children, surgery' should be removed from keywords and more effective words should be added. - In the discussion section, pathology is included too much, is the article a surgery article or a pathology article? In addition, information about surgery should be added to the discussion (e.g. post-operative complications, postoperative results, etc.) and why anatomical resection is performed or in which cases it can be performed should be explained more clearly and comprehensively. -The conclusion section should be rewritten and unnecessary information should be removed. In addition, the discussion section should include the reasons why the case is considered unusual.\n\nUnfortunately, the article is a repetition of what is generally known and has no additional features, except for some surgical difficulty.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] }, { "id": "317823", "date": "14 Sep 2024", "name": "Duc T Nguyen", "expertise": [ "Reviewer Expertise Pediatrics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 presenting this rare pulmonary hamartoma in children. Please find below a couple of comments you may want to consider for improving the manuscript: - More details regarding the surgery (pre-, intra-, and post-op) would be needed. - As the patient has got recurrent admission for right pneumonia for the past two years, serial results on chest radiography would be helpful.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-644
https://f1000research.com/articles/13-1092/v1	24 Sep 24	{ "type": "Research Article", "title": "Comparison GDP and conventional CPB impact on metabolism in cardiac center Sardjito general hospital", "authors": [ "Bhirowo Yudo Pratomo", "Sudadi Sudadi", "Budi Yuli Setianto", "Tandean Tommy Novenanto", "Fiandila Elvana", "Amar Rayhan", "Juni Kurniawaty", "Sudadi Sudadi", "Budi Yuli Setianto", "Tandean Tommy Novenanto", "Fiandila Elvana", "Amar Rayhan", "Juni Kurniawaty" ], "abstract": "Abstract\nBackground Goal-directed perfusion (GDP) aims to balance oxygen delivery (DO2) and consumption (VO2) in cardiac surgery. Elevated lactate during CPB is common and linked to higher morbidity and mortality. Evaluating lactate with base excess (BE) is vital due to their relationship. Reducing severe BE and lactate predicts cardiac surgery outcomes better.\n\nMethods Fifty adult patients undergoing cardiac surgery with CPB were randomly assigned to either the GDP group or the conventional group. In the GDP group, the priming solution was adjusted to target a hematocrit (HCT) level of 24 to 27% with a pump flow of 1.8 to 2.2 L/min/m2 to maintain mean arterial pressure (MAP) between 60 and 65 mmHg. The primary outcomes was oxygen delivery index (DO2i).\n\nResults There were increasing trends in lactate levels and decreasing trends in BE levels at all timeframes. The GDP mean difference of lactate [1.504 (1.52); p < 0.001] and BE [-0.87 (2.93); p = 0.22] levels showed better value in the GDP group, with statistically significant increased values in the control group for BE [-1.667 (2.93); p = 0.017] and lactate levels [2.215 (2.919); p < 0.001]. The postoperative outcome showed a significant difference in AKI and ventilator time.\n\nConclusions The GDP low flow CPB compared with conventional flow CPB maintained DO2 matched with VO2 with a better clinical values in the lactate and BE levels and significantly lowered AKI and ventilator duration in cardiac surgery.", "keywords": [ "cardiopulmonary bypass", "goal directed perfusion", "lactate", "base excess", "metabolic acidosis" ], "content": "Introduction\n\nThe utilization of cardiopulmonary bypass (CPB), which has been developed and evolving since the 19th century to the present day, has made cardiac surgery more comfortable and feasible.1 However, due to the contact between blood with non physiologist extracorporeal circuit CPB, non-pulsatile blood flow, hemodilution, hypothermia, ischemia-reperfusion injury, and the use of anticoagulants. These can have systemic impacts on hemolysis, inflammation and organ demage.2 The most common complications arise from inflammation and hemolysis, due to shear stress, which can occur from during the operation to post-operation, especially in prolonged CPB.1–3 In addition to those, hyperlactatemia, caused by inadequate delivery of oxygen (DO2) to meet tissue oxygen consumption (VO2), is also a main concern in CPB. When cells are unable to produce aerobic energy, they undergo anaerobic metabolism and produce lactic acid in oxygen deficit condition.4 Hyperlactatemia during CPB is frequent directly linked to higher rates of morbidity and mortality.3 This condition have a corelation with base excess (BE) concentration, which represents the deviation of actual bicarbonate concentration in the blood from a standard reference value. The accumulation of lactate, being a potent anion, disrupts ion balances, resulting in a reduction of BE.5\n\nThe principle of maintaining a balance between DO2 and VO2 is termed goal-directed perfusion (GDP). The normal of VO2 is 260-270 ml/min/m2 deterioration in outcomes due to anaerobic metabolism, maintaining a minimum DO2 requirement above 260-270 ml/min/m2 is essential for perfusionist to ensure DO2 match with the VO2.3,6 GDP is an implementation of goal-directed therapy, a strategy aimed at improving patient outcomes by employing aggressive and intensive treatment with optimized hematocrit (HCT), cardiac output maintenance, fluid, inotropic and vasopressor ussage with advanced monitoring to control normal tissue perfusion.7 GDP linked to the best long-term patient outcomes, including increased rates of survival and improved performance in all major organ systems. This strategy reduces morbidity and speeds up the healing process after surgery.6,8\n\nPrevious studies noted a limitation that did not reporting lactate levels during CPB.9,10 The strong association between hyperlactatemia and poor outcomes post-cardiac surgery reported in earlier research.11,12 Another study highlighted lactate’s correlation with BE, suggesting the need to interpret both together due to BE being a derived parameter.13 Reducing severe BE has a better predictor for postoperative cardiac surgery outcome.14\n\nDue to the limited number of clinical studies on GDP, the researchers propose that the objective of this study is to evaluate the metabolic outcomes patients undergoing cardiac surgery with CPB. Consent with shear stress in CPB aim this study to compare use of GDP low flow CPB with the conventional protocol CPB to make optimal DO2 match with oxygen metabolism. Lactate and BE will be utilized as targeted monitor of oxygen metabolism cells.\n\n\nMethods\n\nThis study was approved by the Universitas Gadjah Mada Ethics Committee (reference approval number KE/FK/0232/EC/2023) and was registered on the International Traditional Medicine Clinical Trial Registry (ISRCTN 17452821) on April 4, 2023. Informed written consent was obtained from all participants.\n\nThis randomized double-blind controlled trial was conducted at Dr. Sardjito General Hospital, Yogyakarta, from July to October 2023. The study included patients aged 18–65 years, classified as NYHA class 1-2, and weighing between 40 and 100 kg, who were scheduled for cardiac surgery with CPB. Exclusion criteria included patients requiring preoperative extracorporeal circulation, intra-aortic balloon pump (IABP), hemodialysis, renal replacement therapy, or intraventricular assist devices, as well as those undergoing emergency or urgent cardiac surgeries. Cardiac surgeries with a CPB time of less than 60 minutes were also excluded.\n\nFifty patients were randomized using a consecutive double-block randomization method into two groups: GDP and control, with 25 patients in each group. The randomization list was kept in sealed envelopes, ensuring that both patients and outcome assessors were blinded to the group assignments.\n\nCardiac surgeries were performed by two experienced surgeons, anesthesiologists, and perfusionists. All patients underwent open-heart surgery with CPB, including coronary artery bypass grafting (CABG), valve repair, and defect closure, following the institutional protocol. Median sternotomy was used as the surgical approach. Continuous arterial line monitors and central venous catheters were installed, with pulmonary artery catheters (PAC) used as needed. All patients received premedication with fentanyl 3-4 μg/kg, followed by induction with propofol 1-2 mg/kg and rocuronium 0.6 mg/kg. Anesthesia was maintained with 50% oxygen in the air, 1-2% sevoflurane, fentanyl 4 μg/kg/hr, and rocuronium 1 mg/kg/hr.\n\nThe CPB protocol was standardized for all patients, using the Livanova Stockert S5 machine (Sorin Group Japan Co., Ltd.) and a CAPIOX FX oxygenator with an integrated arterial filter (Terumo Cardiovascular Group). CPB was initiated after administering heparin at a dose of 3 mg/kg body weight, ensuring an activated clotting time (ACT) exceeding 480 seconds. Both groups received mannitol at 2.5 cc/kg, sodium bicarbonate at 30 mEq, methylprednisolone at 20 mg, 50 cc of 20% albumin, heparin at 5000 IU, and tranexamic acid at 50 mg/kg, according to protocol. Myocardial protection was achieved using 2000 cc of Custodiol Histidine-Tryptophan-Ketoglutarate (HTK) as crystalloid cardioplegia. Protamine was administered post-CPB, along with 50 cc of 20% albumin. Patients were then transferred to the Intensive Care Unit (ICU) for mechanical ventilation and standard postoperative care.\n\nThe GDP protocol focused on dynamically adjusting the CPB pump flow to achieve target DO2 levels. The priming fluid in the GDP group was acetated Ringer’s solution, adjusted based on body weight to maintain a HCT of 24–27% or hemoglobin levels of 7.5–9 g/dl. Body temperature was maintained between 30–33°C. Pump flow rates were adjusted to 1.8–2.2 L/min/m2 to meet target DO2 levels, with mean arterial pressure (MAP) maintained >65 mmHg using norepinephrine (0.1–0.2 μg/kg) as necessary. This approach differs from conventional perfusion, which uses fixed pump flow rates based on body surface area (BSA) without dynamic adjustment according to DO2 targets.\n\nDemographic information, involving age, gender, comorbidities, and relevant patient characteristics, will be systematically collected to offer a comprehensive overview of the study population. This comprehensive data collection approach aims to provide a thorough understanding of the study’s primary and secondary outcomes, allowing for a comprehensive analysis of the impact of the intervention on various physiological parameters and patient recovery. The primary outcome measures were oxygen delivery index (DO2i). Secondary outcome measures include the evaluation of cardiac index (CI), and metabolic parameters such as BE and lactate levels that will be monitored at critical time points, namely pre-CPB (T0), 30-minutes CPB (T1), 60-minutes CPB (T2), 90-minutes CPB (T3), post-CPB (T4), and upon entering the ICU (T5). Trends over time will be assessed to understand variations in metabolic levels during the surgical procedure.\n\nHemoglobin, HCT, CPB time, aortic cross clamp time, blood glucose, and creatinine levels. The study will also assess the duration of ventilator use and the length of stay (LOS) in the ICU. Acute kidney injury (AKI) was diagnosed using Kidney Disease: Improving Global Outcomes (KDIGO) 2012 criteria, which defined as a rising serum creatinine (SCr) levels by ≥0.3 mg/dl within 48 hours.15 We evaluated the SCr levels before and after CPB and determined the AKI status. Hyperlactatemia was defined as a blood lactate level >3 mmol/l. According to this level, hyperlactatemia was correlated with adverse outcomes in cardiac surgery. Lactate acidosis refers to hyperlactatemia patients with a pH lower than 7.35.16,17\n\nData were presented as mean ± standard deviation for normally distributed variables, and median (interquartile range) for non-Gaussian variables. Categorical data were reported as numbers and percentages. Statistical analysis was performed using SPSS version 25 (IBM SPSS Statistics, New York, NY). An independent t-test was used for continuous variables with normal distribution, while the Mann-Whitney test was used for non-parametric data. Categorical data were compared using the chi-squared test. Mean differences between T0 and T2, and T0 and T5, were analyzed using a paired t-test or Wilcoxon test, as appropriate. Statistical significance was set at p < 0.05.\n\n\nResults\n\nFrom July 2023 to November 2023, fifty patients were enrolled in the study, with 25 allocated to the GDP group and 25 to the control group. Patient characteristics and clinical data showed no significant differences between the two groups (p > 0.05) (see Table 1). Intraoperative variables revealed a statistically significant difference in CI, with the control group showing a median of 2.74 (0.73) compared to the GDP group’s median of 2.27 (0.155) (see Table 2). Postoperative outcomes indicated a significant difference in acute kidney injury (AKI) incidence. Six patients in the control group exhibited a serum creatinine increase of 0.3 mg/dL post-CPB, whereas only one patient in the GDP group showed such an increase. Additionally, the median ventilator time was significantly lower in the GDP group (20 hours) compared to the control group (23 hours) (see Table 3).\n\n p-value mark as significant.\n\na p-value was analyzed using Chi Square.\n\nb p-value was analyzed using Mann Whitney.\n\nc p-value was analyzed using Independent T-test.\n\nLactate and BE values across all timeframes (T0–T5) did not differ significantly between the GDP and control groups (p > 0.05) (see Table 4, Figure 1 and Figure 2). However, lactate levels increased over time from the initiation of CPB (T1) to ICU arrival (T5) in both groups. Peak lactate levels during CPB were similar between the groups, with a median of 2.38 (1.555) in the control group and 2.01 (1.985) in the GDP group (see Figure 3). We also compared the change in lactate levels between two specific timeframes, T0 and T4. Both groups showed an improvement in the GDP group correlated to CPB time. The mean difference in lactate levels between T0 and T2 was similar in both groups (0.596 vs. 0.641). However, during 60 minutes of CPB, the post-CPB mean difference in lactate levels was greater in the control group than in the GDP group (1.504 vs. 2.215). Statistically significant differences were observed in BE and lactate levels in the control group (see Table 5 and Figure 4).\n\n* p-value mark as significant.\n\na p-value was analyzed using Independent T-test.\n\nb p-value was analyzed using Mann Whitney.\n\n* p-value mark as significant.\n\na p-value was analyzed using Paired T-Test.\n\nb p-value was analyzed using Wilcoxon.\n\nc p-value was analyzed using Independent T-test.\n\nd p-value was analyzed using Mann Whitney.\n\n\nDiscussion\n\nThis study compared lactate levels at three time points: pre-, during, and post-CPB in cardiac surgery patients. Both groups showed similar results, with no significant differences in baseline characteristics, indicating that they were comparable. Our GDP protocol focused on optimizing DO2 during CPB by adjusting flow rates (1.8–2.2 L/min/m2), hemodilution (HCT 24-27%), mild hypothermia (30–33°C), and maintaining a mean arterial pressure (MAP) >65 mmHg.\n\nDuring CPB, the most fundamental hemodynamic change is the generation of cardiac output by the CPB pump instead of the patient’s heart. Perfusionists typically regulate the pump flow based on patient-specific factors such as height, weight, and core temperature. In this study, the CI and DO2i during CPB significantly aligned with the set flow rates, indicating effective management of DO2. Despite maintaining cardiac output and arterial pressure, CPB often results in decreased VO2, making it crucial to match DO2 with metabolic demands. However, increases in serum lactate levels and evidence of post-CPB organ dysfunction suggest potential impairments in tissue perfusion. Factors contributing to this may include arteriolar constriction, increased edema, loss of pulsatile flow, hypothermia-induced capillary changes, and microemboli formation.\n\nProposed methods to enhance microcirculatory function during CPB include the use of vasopressors or inotropes, hemodilution, mild to moderate hypothermia, maintaining systemic blood pressure, and setting the low flow rate that we applied in this study.18 A recent study reported an association between nadir HCT during CPB and lactate levels, with higher lactate values observed at lower nadir HCT levels. Conversely, the absolute risk of severe hyperlactatemia is 4.3% at a nadir HCT of 25% during CPB, increasing to 8.7% at a nadir HCT of 20% (a relative risk increase of 100%). Hemodilution during CPB is an independent determinant of hyperlactatemia. This association, more evident in cases of severe hyperlactatemia, supports the hypothesis that poor DO2 during CPB, leading to organ ischemia, is the mechanism responsible for hemodilution-associated adverse outcomes.19\n\nThe protective effect of hypothermia is provided mainly by slowing the cellular metabolism and thus decreasing its VO2 and energy demand. Metabolic protection offered by hypothermia enables safe circulatory arrest during cardiac surgical intervention. Blood viscosity increases with hypothermia and allows for the maintenance of a higher perfusion pressure despite hemodilution.12,20 A previous report revealed that patients with mild hypothermia during CPB experienced increased postoperative renal failure and a longer length of stay in the intensive care unit. Although there is no difference in long-term survival, mild hypothermia does not appear to provide significant benefit to patients compared with normothermia. The mild hypothermia was maintained at a temperature of around 32–35°C.21\n\nHyperlactatemia is strongly associated with poor outcomes after cardiac surgery, as reported in previous studies. Blood lactate concentration is one important clinical marker that can reflect the adequacy of systemic perfusion during cardiac surgery. Patients with hyperlactatemia should be treated by normalizing the global delivery of oxygen.11,12 A previous study showed that severely reduced BE was a better predictor of post-cardiac surgery. Lactate levels upon ICU admission (3.9 mmol/l cutoff) and BE (-6.7 cutoff) were predictors of ICU mortality.14 Other studies reported lactate being correlated with BE, suggesting interpreting both together due to BE being a derived parameter.13\n\nIn previous goal-directed randomized controlled trials (RCTs), lactate levels were presented in different results and times, mainly postoperative.22–25 The majority of comparisons of lactate levels were not significant, except one study reported significant differences at four different times, which were immediately after surgery, 6, 12, and 24 hours after ICU admission.25 Even though the research had various lactate levels, the goal-directed group was the group with the lowest mean or median of blood lactate levels compared with the control group, as in the result of this study. A previous goal-directed cohort study reported a decrease in lactate levels after surgery in goal-directed groups.26–28 Blood lactate was significantly lower than the control group but was similar 16 hours after the end of suturing.28 In the early goal-directed therapy showed lactate levels decreased gradually from about 4 mmol/l to below 2 mmol, with a slight spike in 2 days after cardiac surgery.27\n\nGDP strategies were reported to have a better postoperative outcome than the control group. A recent study presented that GDP is not associated with a decrease in AKI. The GDP cohort performed significantly worse than the retrospective control group in terms of acute renal failure (ARF), mortality, intensive care unit readmission, and red blood cells and platelet transfusions.10 Post-CPB lactate in patients with developed AKI and non-AKI was similar.26 Other studies showed different results that GDT strategies reduced AKI incidence and surgery outcome, which were similar to the recent study.29 Perioperative GDP was also shortening the duration of ventilator usage.22,25\n\nWe accepted that the main limitation of this study was the number of patients included. The differences were clear enough to present the GDP strategy of lowering lactate levels, which correlated with several positive outcomes. Nevertheless, this research provides the data that supports the GDP protocols to increase the clinical outcome of cardiac surgery. For further research, it is important to conduct a similar study with a larger-scale study design and add the additional outcome of inflammation and hemolysis to fulfill the development of goal-directed strategies in cardiac surgery.\n\nIn conclusion, Low flow CPB (GDP protocols) maintained DO2 matched with VO2 compared with conventional CPB (lactate and BE levels not significant different). GDP strategy that maintained the hemodynamic parameters with a controlled hemodilution, body temperature, and vasopressor or inotropic administration had a better tendency lactate and BE levels. GDP improved cardiac surgery with CPB patients outcome significantly lowered AKI and ventilator duration compared to conventional flow CPB.\n\nThis study followed the principles of the Declaration of Helsinki and was approved by the Medical and Health Research Ethics Committee at Universitas Gadjah Mada (Approval No. KE/FK/0232/EC/2023; Date of Approval: 14 February 2023). Written informed consent was obtained from all participants or their legal guardians, with assent from minors where applicable. Identifiable data were not published without consent, and anonymized data were used to protect privacy without affecting the scientific validity of the findings.", "appendix": "Data availability\n\nDue to ethical considerations and the need to protect participant privacy, the data from this randomized controlled trial cannot be publicly shared. The data contain sensitive information that cannot be sufficiently de-identified. The Medical and Health Research Ethics Committee at Universitas Gadjah Mada has stipulated that data access may be granted upon reasonable request, subject to ethical approval and participant consent. Interested researchers can contact the authors for details on the application process, including the specific conditions under which access may be granted, such as research use only and compliance with confidentiality agreements.\n\nOpen Science Framework: CONSORT Checklist and Flow Diagram: Comparison GDP and Conventional CPB Impact on Metabolism In Cardiac Center Sardjito General Hospital. https://doi.org/10.17605/OSF.IO/B6359. 30\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nPassaroni AC, Silva MA d M, Yoshida WB: Cardiopulmonary bypass: development of John Gibbon’s heart-lung machine. Rev. Bras. Cir. Cardiovasc. orgao Of da Soc. Bras. Cir. Cardiovasc. 2015; 30(2): 235–245. Publisher Full Text\n\nEvora PRB, Bottura C, Arcêncio L, et al.: Key Points for Curbing Cardiopulmonary Bypass Inflammation. Acta Cir. Bras. 2016; 31 Suppl 1: 45–52. PubMed Abstract \| Publisher Full Text\n\nRanucci M, De Toffol B, Isgrò G, et al.: Hyperlactatemia during cardiopulmonary bypass: determinants and impact on postoperative outcome. Crit. Care. 2006; 10(6): R167. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRanucci M: Perioperative renal failure: hypoperfusion during cardiopulmonary bypass? Semin. Cardiothorac. Vasc. Anesth. 2007 Dec; 11(4): 265–268. PubMed Abstract \| Publisher Full Text\n\nO’Connor E, Fraser JF: The interpretation of perioperative lactate abnormalities in patients undergoing cardiac surgery. Anaesth. Intensive Care. 2012 Jul; 40(4): 598–603. PubMed Abstract \| Publisher Full Text\n\nde Somer F , Mulholland JW, Bryan MR, et al.: O2 delivery and CO2 production during cardiopulmonary bypass as determinants of acute kidney injury: time for a goal-directed perfusion management? Crit. Care. 2011 Aug; 15(4): R192. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDijoy L, Dean JS, Bistrick C, et al.: The History of Goal-Directed Therapy and Relevance to Cardiopulmonary Bypass. J. Extra Corpor. Technol. 2015 Jun; 47(2): 90–94. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurphy GS, Hessel EA 2nd, Groom RC: Optimal perfusion during cardiopulmonary bypass: an evidence-based approach. Anesth. Analg. 2009 May; 108(5): 1394–1417. PubMed Abstract \| Publisher Full Text\n\nRanucci M, Romitti F, Isgrò G, et al.: Oxygen delivery during cardiopulmonary bypass and acute renal failure after coronary operations. Ann. Thorac. Surg. 2005; 80(6): 2213–2220. Publisher Full Text\n\nBroadwin M, Palmeri M, Kelting T, et al.: Goal Directed Perfusion Is Not Associated with a Decrease in Acute Kidney Injury in Patients Predicted to Be at High Risk for Acute Renal Failure after Cardiac Surgery. J. Extra Corpor. Technol. 2022; 54(2): 128–134. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKobayashi Y, Peng YC, Yu E, et al.: Prediction of lactate concentrations after cardiac surgery using machine learning and deep learning approaches. Front. Med. 2023; 10(September): 1–12. Publisher Full Text\n\nAli S, Athar M, Ahmed SM: Basics of CPB. Indian J. Anaesth. 2019; 49(4): 257–262.\n\nYıldırım SA, Canlı MT, Güçyetmez B: Is the Intraoperative Lactate – standard Base Excess Relationship Strong in Cardiac Surgery?2024; 30(1): 9–15.\n\nZante B, Reichenspurner H, Kubik M, et al.: Base excess is superior to lactate-levels in prediction of ICU mortality after cardiac surgery. PLoS One. 2018; 13(10): e0205309. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhwaja A: KDIGO clinical practice guidelines for acute kidney injury. Nephron Clin. Pract. 2012; 120(4): c179–c184. Publisher Full Text\n\nMinton J, Sidebotham DA: Hyperlactatemia and Cardiac Surgery. J. Extra Corpor. Technol. 2017 Mar; 49(1): 7–15. Publisher Full Text\n\nJoudi M, Fathi M, Soltani G, et al.: Factors affecting on serum lactate after cardiac surgery. Anesthesiol. Pain Med. 2014 Oct; 4(4): e18514. Publisher Full Text\n\nEugene A, Hessel I: Cardiopulmonary Bypass: Equipment, Circuits, and Pathophysiology. Hensley’s Practical Approach to Cardiothoracic Anesthesia. 6th Ed.Lippincott Williams & Wilkins (LWW); 2018; p. 848.\n\nRanucci M, Carboni G, Cotza M, et al.: Hemodilution on cardiopulmonary bypass as a determinant of early postoperative hyperlactatemia. PLoS One. 2015; 10(5): 1–10. Publisher Full Text\n\nGocoł R, Hudziak D, Bis J, et al.: The Role of Deep Hypothermia in Cardiac Surgery. Int. J. Environ. Res. Public Health. 2021 Jul; 18(13). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBianco V, Kilic A, Aranda-Michel E, et al.: Mild hypothermia versus normothermia in patients undergoing cardiac surgery. JTCVS Open. 2021; 7(September): 230–242. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTribuddharat S, Sathitkarnmanee T, Ngamsangsirisup K, et al.: Efficacy of intraoperative hemodynamic optimization using flotrac/ev1000 platform for early goal-directed therapy to improve postoperative outcomes in patients undergoing coronary artery bypass graft with cardiopulmonary bypass: A randomized controlled tr. Med. Devices Evid. Res. 2021; 14: 201–209. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMukaida H, Matsushita S, Yamamoto T, et al.: Oxygen delivery-guided perfusion for the prevention of acute kidney injury: A randomized controlled trial. J. Thorac. Cardiovasc. Surg. 2023; 165(2): 750–760.e5. PubMed Abstract \| Publisher Full Text\n\nGoepfert MS, Richter HP, Eulenburg C, et al.: Individually Optimized Hemodynamic Therapy Intensive Care Unit. Anesthesiology. 2015; 119(4): 824–836. Publisher Full Text\n\nKapoor PM, Magoon R, Rawat R, et al.: Perioperative utility of goal-directed therapy in high-risk cardiac patients undergoing coronary artery bypass grafting: A clinical outcome and biomarker-based study. Ann. Card. Anaesth. 2016; 19(4): 638–682. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMukaida H, Matsushita S, Kuwaki K, et al.: Time–dose response of oxygen delivery during cardiopulmonary bypass predicts acute kidney injury. J. Thorac. Cardiovasc. Surg. 2019; 158(2): 492–499. PubMed Abstract \| Publisher Full Text\n\nPatel H, Parikh N, Shah R, et al.: Effect of goal-directed hemodynamic therapy in postcardiac surgery patients. Indian J. Crit. Care Med. 2020; 24(5): 321–326. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoepfert MSG, Reuter DA, Akyol D, et al.: Goal-directed fluid management reduces vasopressor and catecholamine use in cardiac surgery patients. Intensive Care Med. 2007; 33(1): 96–103. PubMed Abstract\n\nThomson R, Meeran H, Valencia O, et al.: Goal-directed therapy after cardiac surgery and the incidence of acute kidney injury. J. Crit. Care. 2014; 29(6): 997–1000. Publisher Full Text\n\nPratomo BY, Sudadi S, Novenanto TT, et al.: CONSORT checklist and flow diagram: Comparison GDP and conventional CPB impact on metabolism in cardiac center sardjito general hospital. OSF. 2024. Publisher Full Text" }	[ { "id": "331069", "date": "31 Oct 2024", "name": "Bingyang Ji", "expertise": [ "Reviewer Expertise The blood conservation and organ protection during cardiopulmonay bypass. Improving the prognosis of extracorporeal life support." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comments: Thanks for giving me the opportunity to review this manuscript. This study describes a randomized controlled trial that aims to compare the clinical outcomes between Goal direct perfusion (GDP) and conventional CPB management. Currently, the topic of GDP application during CPB increased. The scientific problem studied in this manuscript has clinical value. However, this study lacks many important details in the study design description. Additionally, many important results that could influence the study conclusion were not shown. In my opinion, this study required further serious revision. Detailed comments: 1. The definition of GDP management in this study involves many variables, such as HCT, temperature and DO2, but we can't get the details of conventional CPB management, for example, what are the priming conditions for conventional CPB management? Moreover, the author's definition of GDP has changed many times in the article, sometimes claiming according to DO2, and sometimes becoming a comprehensive measure to control several variables, such as priming and body temperature. Please be clear. 2. Secondary outcomes such as the cardiac index cannot be obtained from the study. 3. Key variables such as intraoperative HCT and temperature were not available in the article. The missing of these variables does not prove the effectiveness of GPD management 4. The comparison of DO2 showed that conventional CPB management had a higher DO2i. I question this. This means that conventional CPB management in this study has met the oxygen supply demand. So is it inappropriate to emphasize GDP management of DO2i-target repeatedly in the article? 5. No sample size calculation process. 6. The primary endpoint of this article is DO2i. However, the article is more about comparing the differences between lactate and BE. This does not conform to the logic of clinical trials. 7. GDP management involves many variables. DO2i is the main one. Others such as VO2i should also be collected and displayed.\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?\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": [] }, { "id": "340340", "date": "02 Dec 2024", "name": "Shigeyuki Okahara", "expertise": [ "Reviewer Expertise cardiopulmonary bypass" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript presents the clinical outcomes of a single-center randomized controlled trial comparing two perfusion management strategies, GDP and conventional CPB, with a particular emphasis on oxygen metabolism. The process of determining the optimal pump flow rate remains an unmet clinical need, and this manuscript has the potential to contribute to advancements in this area. However, several unclear points need to be addressed to support the study's conclusions:\nThe objective of this manuscript is to compare GDP low-flow CPB with the conventional CPB protocol. Could the authors clarify whether there are differences between the general concept of GDP and the specific GDP low-flow approach used in this study? Additionally, the rationale for applying this specific approach is not fully explained. What was the target DO2 level in the GDP perfusion protocol? Furthermore, how were the thresholds for hematocrit and body temperature determined? The specific differences in management methods between the two groups are not fully detailed. Could the authors provide a clearer description of the standard perfusion protocol? In the methods section, it is stated that mean differences were analyzed between T0 and T5. However, in the results section, the mean difference is reported between T0 and T4 instead. Additionally, the results section states that \"during 60 minutes of CPB, the post-CPB mean difference in lactate levels was greater in the control group than in the GDP group (1.504 vs. 2.215).\" However, these values (1.504 vs. 2.215) are reported in Table 5 as the mean differences between T0 and T4, not for the 60-minute CPB period. Could the authors clarify these inconsistencies and confirm which timeframes were actually analyzed? Are the 'flow rate' values reported in Table 2 presented as means or medians? In the results section, they are reported as medians. Additionally, Table 2 uses 'flow rate' to refer to cardiac index (CI), which may cause confusion since these terms are distinct. Could the authors clarify and ensure consistent terminology? Regarding pump flow management, Table 2 provides data on flow rate, DO2, and time. Additional intraoperative variables, such as metabolic demand, hemoglobin levels, temperature, fluid balance, and transfusion volumes, should be included to ensure the accuracy of the analysis. In Table 4, lactate values are reported as medians, whereas the corresponding figures present the data as means. Additionally, the results section states that “peak lactate levels during CPB were similar between the groups, with a median of 2.38 (1.555) in the control group and 2.01 (1.985) in the GDP group (see Figure 3).” However, Figure 3 presents these values as means. Could the authors clarify whether the reported lactate levels are medians or means? Furthermore, if the figures represent mean values, standard deviations should also be included in the graphs. In this manuscript, the only perfusion management variables showing significant differences are flow rate and DO2. Based on these results, it seems that low-flow management, independent of DO2, reduced the duration of acute kidney injury and mechanical ventilation while also improving lactate trends between pre- and post-pump measurements. Could the authors comment on the effectiveness of low-flow GDP management based on these findings? The authors state that \"Low flow CPB (GDP protocols) maintained DO2 matched with VO2 compared with conventional CPB.\" However, the data provided does not appear to directly demonstrate DO2-VO2 matching. While the control group achieved higher DO2 levels, to what extent did these fail to meet metabolic demands? I think that presenting only lactate and BE trends is insufficient to address this question.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/13-1092
https://f1000research.com/articles/13-1091/v1	24 Sep 24	{ "type": "Study Protocol", "title": "Effects of pelvic floor muscle training (PFMT) on the sexual function of climacteric women: a systematic review protocol", "authors": [ "Mateus D. A. Lima", "Vanessa Patricia Soares de Sousa", "Rafaela J. S. de Souza", "Maria de F.C. Almeida", "Sarah B. G. de Carvalho", "Saionara M. A. Câmara", "Elizabel de S.R. Viana", "Vanessa Patricia Soares de Sousa", "Rafaela J. S. de Souza", "Maria de F.C. Almeida", "Sarah B. G. de Carvalho", "Saionara M. A. Câmara", "Elizabel de S.R. Viana" ], "abstract": "Introduction Climacteric period signifies a transitional phase characterized by ovarian failure and a decline in estrogen levels, leading to various urogynecological alterations, including potential sexual dysfunctions. Among these, pelvic floor muscle (PFM) function plays a pivotal role in female sexual function. This study aims to evaluate the efficacy of pelvic floor muscle training (PFMT) on the sexual function of climacteric women.\n\nMethods Experimental or quasi-experimental studies published in peer-reviewed journals, assessing the sexual function of perimenopausal women with PFMT as an intervention, will be included. Studies conducted in institutionalized populations or with neurological and cognitive diseases will be excluded. This systematic review protocol follows the recommendations of the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P). The searches will be carried out in the Pubmed, LILACS (Latin American and Caribbean Literature on Health Sciences), Scopus, Web of Science, and PEDro, using the Search equation: climacteric women/menopause and PFMT and (sexual function or sexual dysfunction). The assessment of methodological quality will be carried out using the Pedro and GRADE scale, which will involve two independent researchers to evaluate the criteria. A third researcher will resolve discrepancies.\n\nEthics and disclosure Ethical approval is not required as this is a secondary data study. This systematic review began in April 2024 and all steps are expected to be completed by November 2024.\n\nPROSPERO registration number CRD42024534297", "keywords": [ "Climacteric Women", "Pelvic floor muscle training", "Sexual Function." ], "content": "Introduction\n\nClimeteric period corresponds to the transitional stage from the reproductive phase to the non-reproductive phase in women and is marked by ovarian failure and a consequent abrupt decline in circulating estrogen levels in the female body.1 As a result, there are numerous changes in the urogynecological system during perimenopause, which are a consequence of hypoestrogenism, such as increased risk of vaginal atrophy, reduced libido, and vaginal dryness.2 A greater impairment is observed when there is alteration in the function of the pelvic floor muscles (PFM).3\n\nPFM constitutes a muscle group located in the pelvis, whose main functions include maintaining urinary and fecal continence, supporting pelvic organs, and enabling adequate sexual function.4,5 Female sexual function began to be studied more prominently by Masters and Johnson, who created the female sexual response cycle consisting of the phases of excitement, plateau, orgasm, and resolution.6 Nearly a decade later, Kaplan described a primary phase, which is desire, and suggested that the plateau phase does not exist. Thus, female sexual behavior would correspond to: desire, excitement, orgasm, and resolution.7\n\nBasson (2000) revolutionized the current scenario related to female sexual response. In this proposal, the principle was to make the model nonlinear, bringing the possibility for a woman to initiate the relationship from a state of sexual neutrality. Thus, desire could develop subsequent to sexual activity.8 Female sexual dysfunction (FSD) is described as an alteration in one or more phases of the sexual response cycle.9 One of the risk factors for FSD is alterations in PFM, including muscular hyperactivity, which is related to genitopelvic pain disorder.10 Furthermore, studies show that women with good PFM function have more intense orgasms.11\n\nPelvic floor muscle training (PFMT) is a conservative, accessible, and globally utilized technique in the prevention and treatment of pelvic floor dysfunctions.12 This technique involves voluntary contraction exercises of the PFM, which promote improvement of muscle function.13 When linked to female sexual function, PFMT enhances local sensitivity and contributes to more satisfactory and intense orgasms, which may be reduced in perimenopausal women.14 In other phases of a woman’s life cycle, such as postpartum, there is already evidence showing the effectiveness of PFMT in sexual function.15 However, the literature still lacks data on the perimenopausal population. The aim of this review is to evaluate the effectiveness of pelvic floor muscle training on the sexual function of perimenopausal women.\n\n\nMethods\n\nThe present protocol adheres to the guidelines established by the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P).16 It has been duly registered in the International Prospective Register of Systematic Reviews (PROSPERO) under the title: “Effects of pelvic floor muscle training on the sexual function of climacteric women: a systematic review” (CRD42024534297).\n\nThe PICO acronym was used as a strategy to formulate the following research question: “Is there a superior effect of PFMT over other interventions or placebo in climacteric women with sexual dysfunction?”. This acronym is detailed in Table 1.\n\nTypes of studies\n\nIncluded will be studies published in peer-reviewed journals, of experimental or quasi-experimental nature, whether randomized or non-randomized clinical trials, that have assessed the sexual function of perimenopausal women and have PFMT as an intervention.\n\nTypes of participants\n\nMiddle-aged and elderly women (above 40 years old) in the climacteric period. Excluded from the study will be institutionalized women and those with any condition that could negatively contribute to PFMT, such as neurological or cognitive alterations.17\n\nPFMT will be considered as the intervention and will be compared with other interventions (medicinal and non-medicinal interventions) and health education.\n\nThe primary outcome of this study is sexual function, assessed through the Female Sexual Function Index (FSFI) questionnaire, which identifies possible alterations in sexual function, addressing characteristics involving sexual desire and arousal, as well as lubrication, ability to achieve orgasm, satisfaction, and pain during sexual activity.18\n\nTo achieve the proposed objective, a search will be conducted in the following databases: PubMed, LILACS (Latin American and Caribbean Literature on Health Sciences), Scopus, Web of Science, and PEDro. The search strategy will adopt the following standard formula: “climacteric women/menopause and PFMT and (sexual function or sexual dysfunction)”. No language or publication year limits will be set. Additionally, a manual search will be conducted in the references of included articles. The detailed search strategy by database is described in Table 2.\n\nThe Rayyan platform (Doha, Qatar) will be used for the data collection and analysis process. Initially, duplicate articles will be excluded.19 Subsequently, titles and abstracts will be read, and eligibility criteria will be applied to select only articles relevant to the study. Articles that meet the inclusion criteria will then undergo full-text reading. This process will be carried out by two independent pairs of researchers. In case of discrepancies in the inclusion or exclusion of studies, a third researcher will resolve them.\n\nAfter full-text reading and inclusion of articles, data extraction will be performed for each included article. This procedure will be carried out using an Excel spreadsheet and will be executed independently by the responsible researchers.\n\nThe extracted data from each article will include: primary author, year of publication, country, study design, sample size, mean age of the sample, level of sexual function, intervention and control groups, applied methodology, and main results.\n\nThe methodological quality of the studies will be assessed using the PEDro scale,20 which will be applied by the same researchers from the previous stages. The PEDro scale consists of a set of 11 items, ranging from 0 to 10 points. A score <4 is considered “poor”, 4 to 5 “fair”, 6 to 8 points are considered good, and above 8 are considered excellent. This assessment will be conducted by two independent researchers (M.F.C.A and S.B.G.C). Any discrepancies will be resolved by an independent researcher (M.D.A.L). The GRADE scale will also be used for methodological assessment, adopting the following criteria: risk of bias (PEDro scale), inconsistency, imprecision of results, and publication bias.21 This evaluation format is based on a similar systematic review.22\n\nAll extracted results will be condensed into tables and Figures. A PRISMA flowchart will represent the entire process of study selection.16 If a meta-analysis is feasible, the Jamovi 2.3.28 software (https://www.jamovi.org/) will be used. Heterogeneity will be assessed using the I2 measure and a 95% confidence interval. The following criteria will be used to define heterogeneity cutoff points: ≤25%: low heterogeneity; 25% to 75%: moderate heterogeneity; 75% to 100%: considerable heterogeneity.23,24\n\n\nDiscussion\n\nAlthough pelvic floor muscles play a significant role in the urogenital health of CLIMACTERIC women, the literature still lacks precise information regarding the effectiveness of pelvic floor muscle training (PFMT) on sexual function during this stage of female life. Understanding how an intervention focused on pelvic floor muscles affects sexual function can assist healthcare professionals in making focused and patient-centered decisions regarding patient rehabilitation.\n\nThus, this review will serve as support to guide physiotherapists in prescribing PFMT aiming to improve the sexual function of CLIMACTERIC women.\n\n\nAuthor contributions\n\nMDAL - Conceptualization, Methodology, Project administration, Writing – original draft, Writing – review & editing; VPSS - Conceptualization, Methodology, Visualization, Writing – review & editing; RJSS - Conceptualization, Methodology, Visualization, Writing – review & editing; MFCA - Conceptualization, Methodology, Visualization, Writing – review & editing; SBGC - Conceptualization, Methodology, Visualization, Writing – review & editing; ESRV - Conceptualization, Methodology, Visualization, Writing – review & editing", "appendix": "Data availability\n\nRepository name: OSF, Effects of pelvic floor muscle training (PFMT) on the sexual function of climacteric women: a systematic review protocol; DOI: 10.17605/OSF.IO/WJ5QP 25\n\nThe project contains the following underlying data:\n\n• Data file 1. CHART.tiff\n\n• Data file 2. DATA EXTRACTION\n\n• Data file 3. PRISMA P CHECKLIST.doc\n\n• Data file 4. tiff\n\nPRISMA Checklist for: Effects of pelvic floor muscle training (PFMT) on the sexual function of climacteric women: a systematic review protocol; DOI: 10.17605/OSF.IO/WJ5QP 25\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\nNelson HD: Menopause. Lancet. 2008 Mar; 371(9614): 760–770. Publisher Full Text\n\nLensen S, Bell RJ, Carpenter JS, et al.: A core outcome set for genitourinary symptoms associated with menopause: the COMMA (Core Outcomes in Menopause) global initiative. Menopause. 2021 Aug; 28(8): 859–866. PubMed Abstract \| Publisher Full Text\n\nHillard TC: Pelvic floor function around the menopause and how to improve it. Climacteric. 2019 May 4; 22(3): 213–214. PubMed Abstract \| Publisher Full Text\n\nAshton-Miller JA, DeLancey JOL: Functional anatomy of the female pelvic floor. Ann. N. Y. Acad. Sci. 2007 Apr; 1101: 266–296. Publisher Full Text\n\nEickmeyer SM: Anatomy and Physiology of the Pelvic Floor. Phys. Med. Rehabil. Clin. N. Am. 2017 Aug; 28(3): 455–460. PubMed Abstract \| Publisher Full Text\n\nMasters WH, Johnson VE: The sexual response cycle of the human female. III. The clitoris: anatomic and clinical consideration. West. J. Surg. Obstet. Gynecol. 1962; 70: 248–257. PubMed Abstract\n\nKaplan HS: Hypoactive sexual desire. J. Sex Marital Ther. 1977 Mar; 3(1): 3–9. Publisher Full Text\n\nBasson R: The Female Sexual Response: A Different Model. J. Sex Marital Ther. 2000 Jan; 26(1): 51–65. Publisher Full Text\n\nBasson R, Gilks T: Women’s sexual dysfunction associated with psychiatric disorders and their treatment. Women’s Health (Lond. Engl.). 2018 Jan 1; 14: 174550651876266. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPadoa A, McLean L, Morin M, et al.: “The Overactive Pelvic Floor (OPF) and Sexual Dysfunction” Part 1: Pathophysiology of OPF and Its Impact on the Sexual Response. Sex. Med. Rev. 2021 Jan; 9(1): 64–75. PubMed Abstract \| Publisher Full Text\n\nPasqualotto L, Riccetto C, Biella AF, et al.: Impact of pelvic floor muscle strength on female sexual function: retrospective multicentric cross-sectional study. Int. Urogynecol. J. 2022 Jun; 33(6): 1591–1599. PubMed Abstract \| Publisher Full Text\n\nItkonen Freitas AM, Rahkola-Soisalo P, Mikkola TS, et al.: Current treatments for female primary stress urinary incontinence. Climacteric. 2019 May 4; 22(3): 263–269. Publisher Full Text\n\nOkeahialam NA, Oldfield M, Stewart E, et al.: Pelvic floor muscle training: a practical guide. BMJ. 2022 Sep 5; e070186. Publisher Full Text\n\nFranco MM, Pena CC, de Freitas LM , et al.: Pelvic Floor Muscle Training Effect in Sexual Function in Postmenopausal Women: A Randomized Controlled Trial. J. Sex. Med. 2021 Jul 1; 18(7): 1236–1244. PubMed Abstract \| Publisher Full Text\n\nHadizadeh-Talasaz Z, Sadeghi R, Khadivzadeh T: Effect of pelvic floor muscle training on postpartum sexual function and quality of life: A systematic review and meta-analysis of clinical trials. Taiwan. J. Obstet. Gynecol. 2019 Nov; 58(6): 737–747. PubMed Abstract \| Publisher Full Text\n\nPRISMA-P GroupMoher D, Shamseer L, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst. Rev. 2015 Dec; 4(1): 1. Publisher Full Text\n\nSparaco M, Bonavita S: Pelvic Floor Dysfunctions and Their Rehabilitation in Multiple Sclerosis. JCM. 2022 Mar 31; 11(7): 1941. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWiegel M, Meston C, Rosen R: The Female Sexual Function Index (FSFI): Cross-Validation and Development of Clinical Cutoff Scores. J. Sex Marital Ther. 2005 Jan; 31(1): 1–20. PubMed Abstract \| Publisher Full Text\n\nOuzzani M, Hammady H, Fedorowicz Z, et al.: Rayyan—a web and mobile app for systematic reviews. Syst. Rev. 2016 Dec; 5(1): 210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMacedo LG, Elkins MR, Maher CG, et al.: There was evidence of convergent and construct validity of Physiotherapy Evidence Database quality scale for physiotherapy trials. J. Clin. Epidemiol. 2010 Aug; 63(8): 920–925. PubMed Abstract \| Publisher Full Text\n\nGuyatt G, Oxman AD, Akl EA, et al.: GRADE guidelines: 1. Introduction—GRADE evidence profiles and summary of findings tables. J. Clin. Epidemiol. 2011 Apr; 64(4): 383–394. PubMed Abstract \| Publisher Full Text\n\nJorge CH, Bø K, Chiazuto Catai C, et al.: Pelvic floor muscle training as treatment for female sexual dysfunction: a systematic review and meta-analysis. Am. J. Obstet. Gynecol. 2024 Jul; 231(1): 51–66.e1. PubMed Abstract \| Publisher Full Text\n\njamovi - open statistical software for the desktop and cloud.[cited 2024 Aug 19]. Reference Source\n\nCochrane Handbook for Systematic Reviews of Interventions.[cited 2024 Apr 27]. Reference Source\n\nDe Azevedo Lima MD: Effects of Pelvic Floor Muscle Training (PFMT) on the Sexual Function of Climacteric Women: A Systematic Review Protocol. [Dataset]. OSF. 30 Aug. 2024. Publisher Full Text" }	[ { "id": "335827", "date": "12 Nov 2024", "name": "Maria Letícia A. S. de Carvalho", "expertise": [ "Reviewer Expertise Physical therapist with a focus on women's health. Experienced in clinical trials", "systematic reviews", "and protocol development." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe work is well-developed and clear. However, I would like to highlight some points for improvement:\nIntroduction: Improve the cohesion and flow between paragraphs. For instance, combine the following information, currently presented in separate paragraphs: “A greater impairment is observed when there is alteration in the function of the pelvic floor muscles (PFM).3 PFM constitutes a muscle group located in the pelvis, whose main functions include maintaining urinary and fecal continence, supporting pelvic organs, and enabling adequate sexual function.” Report the experience of the blinded evaluators, specifically if there was any prior training to standardize the evaluation. In the eligibility criteria, the training of pelvic floor muscles mentioned in PICO as the intervention is not included in the search strategy. However, the comparison is described as involving other interventions/placebo. It is stated that studies “that have assessed the sexual function of perimenopausal women and have PFMT as an intervention” will be included. How will this comparison be conducted? How will comparison with other forms and placebo be addressed if only studies involving PFMT are included? In the results section, provide a clearer and more comprehensive description of the expected effects of this study, as well as the limitations encountered thus far.\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": "327041", "date": "19 Nov 2024", "name": "Yasemin Karaaslan", "expertise": [ "Reviewer Expertise Women 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\n- Ensure that the term climacteric is spelled correctly everywhere. - It should be written more clearly and explicitly why PFMT should be used on sexual function in climacteric women. - The discussion section should be written comprehensively. - Other methods used should be clearly written. - How PFMT has been applied in studies. Frankly, I really wanted to see these protocols in this article, but I couldn't find them.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1091
https://f1000research.com/articles/12-376/v1	06 Apr 23	{ "type": "Data Note", "title": "The identification of high-performing antibodies for RNA-binding protein FUS for use in Western Blot, immunoprecipitation, and immunofluorescence", "authors": [ "Walaa Alshalfie", "Maryam Fotouhi", "Riham Ayoubi", "Zhipeng You", "Kathleen Southern", "Peter S. McPherson", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "Walaa Alshalfie", "Maryam Fotouhi", "Riham Ayoubi", "Zhipeng You", "Kathleen Southern", "Peter S. McPherson" ], "abstract": "RNA-binding protein Fused-in Sarcoma (FUS) plays an essential role in various cellular processes. Mutations in the C-terminal domain region, where the nuclear localization signal (NLS) is located, causes the redistribution of FUS from the nucleus to the cytoplasm. In neurons, neurotoxic aggregates are formed as a result, contributing to neurogenerative diseases. Well-characterized anti-FUS antibodies would enable the reproducibility of FUS research, thereby benefiting the scientific community. In this study, we characterized ten FUS 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. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.", "keywords": [ "Uniprot ID P35637", "FUS", "RNA-binding protein FUS", "antibody characterization", "antibody validation", "Western Blot", "immunoprecipitation", "immunofluorescence" ], "content": "Introduction\n\nFused-in Sarcoma (FUS) encodes a DNA/RNA-binding protein involved in numerous cellular processes including transcriptional regulation, RNA splicing, RNA transport and DNA repair.1 Predominantly localized in the nucleus, FUS can shuttle between the nucleus and cytoplasm.2 The FUS transcript is reported to have multiple domains including an N-terminal Gln-Gly-Ser-Tyr -rich region, an RNA-recognition motif, Arg-Gly-Gly repeat regions, a zinc finger motif and a highly conserved C-terminal NLS.3–5\n\nVariants in the FUS gene have been identified as potential causative factors for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD).6–9 FUS related mutations found in familial ALS/FTD patients are clustered in the C-terminal NLS, causing FUS to be mislocalized and accumulate as aggregates in the cytoplasm of neurons, initiating a pathway that contributes to neurodegeneration.6,7 FUS function is reduced when aggregates form, but it is not yet known whether this initiates the pathogenic process or if the aggregates are pathogenic.10 Mechanistic studies would be greatly facilitated with the availability of high-quality antibodies.\n\nHere, we compared the performance of a range of commercially-available antibodies for RNA-binding protein FUS and validated several antibodies for Western Blot, immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of FUS properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type (WT) and knockout (KO) cells.11–15 To identify a cell line that expresses adequate levels of FUS protein to provide sufficient signal to noise, we examined public proteomics databases, namely PaxDB16 and DepMap.17 HeLa was identified as a suitable cell line and thus HeLa was modified with CRISPR/Cas9 to knockout the corresponding FUS gene (Table 1).\n\nFor Western Blot experiments, we resolved proteins from WT and FUS KO cell extracts and probed them side-by-side with all antibodies in parallel12–15 (Figure 1).\n\nLysates of HeLa (WT and FUS KO) were prepared and 30 μg of protein were processed for Western Blot with the indicated FUS 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. An exception was given for antibody GTX101810, which was titrated to 1/3000, as the signal was too weak when following the supplier’s recommendation. Antibody dilution used: NBP2-52874* at 1/1000; GTX101810 at 1/3000; GTX01039* at 1/1000; 60160-1-Ig* at 1/10000; 11570-1-AP at 1/4000; MA3-089* at 1/2000; MA5-32483 at 1/1000, ab124923 at 1/5000; ab154141* at 1/1000; ab243880** at 1/1000. Predicted band size: 53 kDa. Observed specific band size: ~70 kDa. Monoclonal antibody; Recombinant antibody.\n\nFor immunoprecipitation experiments, we used the antibodies to immunopurify FUS from HeLa cell extracts. The performance of each antibody was evaluated by detecting the FUS protein in extracts, in the immunodepleted extracts and in the immunoprecipitates12–15 (Figure 2).\n\nHeLa lysates were prepared, and IP was performed using 1.0 μg of the indicated FUS antibodies pre-coupled to protein G or protein A Sepharose beads. Samples were washed and processed for Western Blot with the indicated FUS antibody. For Western Blot, NBP2-52874 and ab243880** were used at a dilution of 1/2000. The Ponceau stained transfers of each blot are shown for similar reasons as in Figure 1. SM=10% starting material; UB=10% unbound fraction; IP=immunoprecipitated. Monoclonal antibody; Recombinant antibody.\n\nFor immunofluorescence, as described previously, antibodies were screened using a mosaic strategy.18 In brief, we plated WT and KO cells together in the same well and imaged both cell types in the same field of view to reduce staining, imaging and image analysis bias (Figure 3).\n\nHeLa WT and FUS 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 FUS antibodies and with the corresponding Alexa-fluor 555 coupled secondary antibody. Acquisition of the green (identification of WT cells), red (antibody staining) and far-red (identification of KO cells) channels was performed. Representative images of the red (grayscale) channels are shown. WT and KO cells are outlined with yellow and magenta dashed line, respectively. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Exceptions were given for antibodies GTX101810, GTX01039, 60160-1-Ig, 11570-1-AP, MA5-32483* and ab124923*, which were titrated as the signals were too weak when following the supplier’s recommendations. Antibody dilution used: NBP2-52874 at 1/1000; GTX101810 at 1/700; GTX01039* at 1/1000; 60160-1-Ig* at 1/2000; 11570-1-AP at 1/1000; MA3-089* at 1/1000; MA5-32483 at 1/1000; ab124923 at 1/1000; ab154141* at 1/1000; ab243880** at 1/500. Bars=10 μm. Monoclonal antibody; Recombinant antibody.\n\nIn conclusion, we have screened FUS commercial antibodies by Western Blot, immunoprecipitation and immunofluorescence and identified several high-quality antibodies under our standardized experimental conditions. The underlying data can be found on Zenodo.19,20\n\n\nMethods\n\nAll FUS antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers, or RRID, to ensure the antibodies are cited properly.21 Peroxidase-conjugated goat anti-rabbit and anti-mouse antibodies are from Thermo Fisher Scientific (cat. number 65-6120 and 62-6520). Alexa-555-conjugated goat anti-rabbit and anti-mouse secondary antibodies are from Thermo Fisher Scientific (cat. number A21429 and A21424).\n\n Monoclonal antibody.\n\n** Recombinant antibody.\n\nThe HeLa FUS KO clone was generated with low passage cells using an open-access protocol available on Zenodo.org: https://zenodo.org/record/3875777#.ZA-Rxi-96Rv. Two guide RNAs were used to introduce a STOP codon in the FUS gene (sequence guide 1: AGGGAGUCACAAAAGCCACC, sequence guide 2: GGUACGGUGGUGUUGAUGUC).\n\nBoth HeLa WT and FUS KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.22 Cells were cultured in DMEM high-glucose (GE Healthcare cat. number SH30081.01) containing 10% fetal bovine serum (Wisent, cat. number 080450), 2 mM L-glutamate (Wisent cat. number 609065), 100 IU penicillin and 100 μg/mL streptomycin (Wisent cat. number 450201).\n\nWestern Blots were performed as described in our standard operating procedure.23 HeLa WT and FUS KO were collected in RIPA buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1.0 mM EDTA, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS) supplemented with 1× protease inhibitor cocktail mix (MilliporeSigma, cat. number P8340). Lysates were sonicated briefly and incubated for 30 min on ice. Lysates were spun at ~110,000 × g for 15 min at 4°C and equal protein aliquots of the supernatants were analyzed by SDS-PAGE and Western Blot. BLUelf prestained protein ladder from GeneDireX (cat. number PM008-0500) was used.\n\nWestern Blots were performed with large 5-16% polyacrylamide gels 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% bovine serum albumin (BSA) (Wisent, cat. number 800-095) 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) prior to detection with the HyBlot CL autoradiography films (Denville, cat. number 1159T41).\n\nImmunoprecipitation was performed as described in our standard operating procedure.24 Antibody-bead conjugates were prepared by adding 1.0 μg of antibody to 500 μL of phosphate-buffered saline (PBS) (Wisent, cat. number 311-010-CL) with 0,01% triton X-100 (Thermo Fisher Scientific, cat. number BP151-500) in a 1.5 mL microcentrifuge tube, together with 30 μL of protein A- (for rabbit antibodies) or protein G- (for mouse antibodies) Sepharose beads. Tubes were rocked overnight at 4°C followed by two washes to remove unbound antibodies.\n\nHeLa WT were collected in HEPES buffer (20 mM HEPES, 100 mM sodium chloride, 1 mM EDTA, 1% Triton X-100, pH 7.4) supplemented with protease inhibitor. Lysates were rocked 30 min at 4°C and spun at 110,000 × g for 15 min at 4°C. One mL aliquots at 1.0 mg/mL of lysate were incubated with an antibody-bead conjugate for ~2 hours at 4°C. The unbound fractions were collected, and beads were subsequently washed three times with 1.0 mL of HEPES lysis buffer and processed for SDS-PAGE and Western Blot on a 5-16% polyacrylamide gels.\n\nImmunofluorescence was performed as described in our standard operating procedure.12–15,18 HeLa WT and FUS KO were labelled with a green and a far-red fluorescence dye, respectively. The fluorescent dyes used are from Thermo Fisher Scientific (cat. number C2925 and C34565). WT and KO cells were plated on glass coverslips as a mosaic and incubated for 24 hrs in a cell culture incubator at 37oC, 5% CO2. Cells were fixed in 4% paraformaldehyde (PFA) (Beantown chemical, cat. number 140770-10ml) 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 (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 FUS 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. Coverslips were mounted on a microscopic slide using fluorescence mounting media (DAKO).\n\nImaging was performed using a Zeiss LSM 880 laser scanning confocal microscope equipped with a Plan-Apo 40× oil objective (NA = 1.40). Analysis was done using the Zen navigation software (Zeiss). All cell images represent a single focal plane. Figures were assembled with Adobe Photoshop (version 24.1.2) to adjust contrast then assembled with Adobe Illustrator (version 27.3.1).", "appendix": "Data availability\n\nZenodo: Antibody Characterization Report for RNA-binding protein FUS, https://doi.org/10.5281/zenodo.5259944. 19\n\nZenodo: Dataset for the RNA-binding protein FUS antibody screening study, https://doi.org/10.5281/zenodo.7764130. 20\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe would like to thank the NeuroSGC/YCharOS/EDDU collaborative group for their important contribution to the creation of an open scientific ecosystem of antibody manufacturers and knockout cell line suppliers, for the development of community-agreed protocols, and for their shared ideas, resources and collaboration. 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, Kathleen Southern and Zhipeng You.\n\nAn earlier version of this of this article can be found on Zenodo (doi: https://doi.org/10.5281/zenodo.5259945)\n\n\nReferences\n\nYamaguchi A, Takanashi K: FUS interacts with nuclear matrix-associated protein SAFB1 as well as Matrin3 to regulate splicing and ligand-mediated transcription. Sci. Rep. 2016; 6: 35195. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZinszner H, Sok J, Immanuel D, et al.: TLS (FUS) binds RNA in vivo and engages in nucleo-cytoplasmic shuttling. J. Cell Sci. 1997; 110(Pt 15): 1741–1750. PubMed Abstract \| Publisher Full Text\n\nIko Y, Kodama TS, Kasai N, et al.: Domain architectures and characterization of an RNA-binding protein, TLS. J. Biol. Chem. 2004; 279(43): 44834–44840. PubMed Abstract \| Publisher Full Text\n\nDormann D, Rodde R, Edbauer D, et al.: ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import. EMBO J. 2010; 29(16): 2841–2857. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDormann D, Madl T, Valori CF, et al.: Arginine methylation next to the PY-NLS modulates Transportin binding and nuclear import of FUS. EMBO J. 2012; 31(22): 4258–4275. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKwiatkowski TJ Jr, Bosco DA, Leclerc AL, et al.: Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis. Science. 2009; 323(5918): 1205–1208. PubMed Abstract \| Publisher Full Text\n\nVance C, Rogelj B, Hortobágyi T, et al.: Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science. 2009; 323(5918): 1208–1211. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMackenzie IR, Rademakers R, Neumann M: TDP-43 and FUS in amyotrophic lateral sclerosis and frontotemporal dementia. Lancet Neurol. 2010; 9(10): 995–1007. Publisher Full Text\n\nVan Langenhove T, van der Zee J , Sleegers K, et al.: Genetic contribution of FUS to frontotemporal lobar degeneration. Neurology. 2010; 74(5): 366–371. Publisher Full Text\n\nYu Y, Chi B, Xia W, et al.: U1 snRNP is mislocalized in ALS patient fibroblasts bearing NLS mutations in FUS and is required for motor neuron outgrowth in zebrafish. Nucleic Acids Res. 2015; 43(6): 3208–3218. 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\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\nAlshafie W, Ayoubi R, Fotouhi M, et al.: The identification of high-performing antibodies for Moesin for use in Western Blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 172. Publisher Full Text\n\nWorrall D, Ayoubi R, Fotouhi M, et al.: The identification of high-performing antibodies for TDP-43 for use in Western Blot, immunoprecipitation and immunofluorescence [version 1; peer review: 1 approved]. F1000Res. 2023; 12: 277. Publisher Full Text\n\nAyoubi R, Fotouhi M, Southern K, et al.: The identification of high-performing antibodies for transmembrane protein 106B (TMEM106B) for use in Western blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 308. 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\nNusinow DP, Szpyt J, Ghandi M, et al.: Quantitative Proteomics of the Cancer Cell Line Encyclopedia. Cell. 2020; 180(2): 387–402.e16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlshafie W, McPherson P, Laflamme C: Antibody screening by Immunofluorescence.2021.\n\nAlshafie W, Fotouhi M, You Z, et al.: Antibody Characterization Report for RNA-binding protein FUS.2021. Publisher Full Text\n\nLaflamme C: Dataset for RNA-binding protein FUS antibody screening study. [Data set]. Zenodo. 2023. Publisher Full Text\n\nBandrowski A, Pairish M, Eckmann P, et al.: The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res. 2023; 51(D1): D358–D367. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBairoch A: The Cellosaurus, a Cell-Line Knowledge Resource. J. Biomol. Tech. 2018; 29(2): 25–38. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\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": "177190", "date": "15 Jun 2023", "name": "Ryota Hikiami", "expertise": [ "Reviewer Expertise Molecular biology", "neuroscience" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 Laflamme C and co-authors,\nThank you for allowing me to review your manuscript titled \"The identification of high-performing antibodies for RNA binding protein FUS for use in Western Blot, immunoprecipitation, and immunofluorescence.\" Your study investigates the utility of commercially available antibodies targeting FUS, one of the causative genes of ALS, through WB, IP, and IF techniques. The experimental findings presented by the authors are expected to be valuable and beneficial for FUS researchers. While the overall methodology and results are sound, I propose minor revisions.\n1. Introduction (P3, L6-): Unlike ALS, FTD with the FUS gene mutation is rare. Does the attached literature include cases of familial FTLD? If not, I recommend adding relevant references or modifying the text accordingly.\n2. Figure 3 (P5): The mosaic arrangement of WT and KO cells in the image is clear and visually appealing. However, the image coverage appears to be somewhat limited. I suggest expanding the image coverage or adding additional images to enhance the readers' understanding.\n\nI hope these suggestions are helpful in improving the quality and impact of your manuscript. Thank you again for considering my feedback, and I look forward to seeing the revised version.\nBest regards, Ryota Hikiami\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": "9789", "date": "26 Jun 2023", "name": "Kathleen Southern", "role": "Author Response", "response": "Dear Ryota Hikiami, Thank you for your thorough review of this Data Note which analyses the performance of commercial antibodies for RNA binding protein FUS, a potential causative gene in many neurodegenerative diseases. To answer your first point of feedback, literature reference 9, which refers to the publication by Van Langenhove et al., performs a mutational analysis of FUS in patients with cases of FTLD. To further elucidate this fact, we will be submitting a revised version with modified text to include FTLD in the list of neurodegenerative diseases potentially caused by FUS gene variants. As for the second point, we always include a dataset in our reports, which includes all underlying raw data for the experiments performed (reference 20). This increases the transparency and reproducibility of our work. It also allows viewers to have a better understanding of the results and see what wasn’t included in the figures. As for immunofluorescence, the dataset includes czi files of each antibody under the microscope. We hope this provides the additional image coverage you were looking for. Thank you again for your suggestions!" } ] }, { "id": "178227", "date": "23 Jun 2023", "name": "Ralph H. Kehlenbach", "expertise": [], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn their manuscript „The identification of high-performing antibodies for RNA-binding protein FUS for use in Western Blot, immunoprecipitation, and immunofluorescence”, Alshalfie and coauthors perform a thorough comparison of commercial antibodies against FUS, a protein that has gained a lot of interest in the field of neurodegenerative diseases and also in general molecular cell biology. Since many antibodies do not perform as good as they are advertised, such a comparison is highly welcome. The approach (also using knockout cell lines as control) is solid and the results are clear and very well documented. I only have one suggestion: in Table 2, the authors should include one or several column(s) (next to “vendors recommended application”) with comments reflecting the results of the study (e.g. ab243880 seems to work well in WB, in IP and in IF).\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/12-376
https://f1000research.com/articles/9-904/v1	04 Aug 20	{ "type": "Study Protocol", "title": "Protocol for a mixed-methods exploratory investigation into the role of health information technology for the provision of cancer care in Indonesia", "authors": [ "Aufia Espressivo", "Herindita Puspitaningtyas", "Susanna H. Hutajulu", "Anis Fuad", "Matthew J. Allsop", "Aufia Espressivo", "Herindita Puspitaningtyas", "Susanna H. Hutajulu", "Anis Fuad" ], "abstract": "Background: Cancer and its management can incur high costs, high risks and high demand. In Indonesia, there remains gap in the availability of national cancer data despite the establishment of a National Committee for Cancer Control. Multiple pilot projects have been developed by the Ministry of Health to improve the delivery of care, including interventions utilising digital health approaches and integrated referral information systems. However, it is not yet clear to what extent these approaches influence patient management or the experience of cancer patients themselves. This research aims to explore the current role of health information technology (HIT) in the provision of services and treatments for patients with cancer from primary to tertiary healthcare centres in Yogyakarta, Indonesia. Methods: The study will adopt an observational mixed-methods single case study design of health facilities involved in the delivery of cancer services in a sub-national health system. We will collect data through face-to-face interviews with a range of health professionals involved in the delivery of cancer care. Patients will be interviewed to share their views and experiences of the existing cancer referral system and communication with health facilities. Alongside interviews, we will undertake an analysis of routine data from participating health facilities to assess gaps in existing information systems. Data analysis will include framework analysis for qualitative data alongside descriptive analyses of quantitative data. Findings will be used to inform conceptual maps to be presented as part of Theory of Change workshops focused on understanding how the existing cancer referral system works, why and for whom, with a focus on future refinement and intervention development. Conclusion: Our findings will inform critical thinking around the design, implementation, adaptation, and evaluation of existing systems. Through early engagement and participation of key stakeholders and project partners, we intend that findings will have immediate utility.", "keywords": [ "Neoplasms", "Medical Informatics", "Referral and Consultation", "Indonesia" ], "content": "Introduction\n\nIn 2018, there was an estimated 348,809 cases and 207,210 deaths from cancer in Indonesia, projected to increase to 575,814 cases and 366,567 deaths annually by 20401. After stroke, cancer has been reported as a leading cause of death in the country2. A cancer diagnosis can be potentially disastrous, with over 75% of patients with cancer in the Southeast Asia region experiencing death or financial catastrophe within one year3. The limited provision of cancer care in Indonesia was reflected in the Cancer Preparedness Index, an initiative in 20194 to highlight differences in cancer policy and systems between countries and how they relate to outcomes. Indonesia was rated 25th of 28 countries evaluated5, largely influenced by limitations in its service availability, workforce, infrastructure, alongside a lack of cancer research. The consequences of a cancer diagnosis and the limited existing provision provide compelling evidence for the need to develop policies to improve access to and provision of cancer care in the country.\n\nCancer and its management can incur high costs, high risks and high demand6. According to WHO guidelines7, health systems should aim to provide a holistic approach to the management of cancers to prolong lives through early detection, timely diagnosis and adequate treatment, alongside providing palliative care for advanced cancer, carried out within the context of a comprehensive cancer control plan8. For Indonesia, where there is an increasing cancer burden, the Ministry of Health has yet to officially endorse the National Cancer Control Plan9. The current National Cancer Control Plan9 contains 13 strategic goals, including the implementation of national cancer treatment guidelines, development of palliative care provision, and establishment of information and communication technology (ICT) systems to unpin developments in cancer provision10. The last of these is driven in part by the need to enhance data on cancer in the country.\n\nA National Committee for Cancer Control was established in 1989, with one of its programs to develop a cancer registry and provide national cancer data. However, there remain gaps in the availability of national cancer data11. Attempts to develop a national population-based cancer registry have been conducted but stopped due to various reasons12, until it was re-established in 2016. Previously, cancer registries were more often conducted as pathology-based or hospital-based site-specific registries11,12. The more common sources for national cancer data are annual reports from the Ministry of Health, including the Indonesian Health Profile, Indonesian Basic Health Research, and secondary data from Indonesian Universal Health Coverage13–15. Ministry of Health publications provide tabular data from the health system, including cancer, but lack granularity with multiple cancer types grouped under one summary figure.\n\nA further driver for ICT development is to leverage its capabilities to overcome distance-time barriers and facilitate participation in global oncology care, education, and research, alongside opportunities to overcome gaps in patient care and clinical expertise16. Across the spectrum of cancer care, research literature from contexts with differing levels of resource report the role of digital technology is increasing, with their implementation supporting reductions in costs and increases in workflow efficiency, as well as improving overall health care value, patient outcomes, and quality of life7,17–19. The implementation of digital technologies has been shown to enhance the management of cancer care in promoting patient-centeredness frameworks and improving patient care and safety18,19. A major subtype of technology use within cancer care is the health information technology (HIT), which supports the management of health information across computerised systems (e.g. electronic health records, e-prescribing systems) alongside the secure exchange of health information between consumers, providers, payers, and quality monitors20. HIT involves a range of stakeholders to support its coordination and use in providing quality care that can ultimately lead to patient satisfaction21. Its use in the context of cancer care can support improvements in coordination of care, shared care planning, person-centred coordination, and coordination between and within teams22. HIT may be advantageous in the context of health systems in low and middle-income countries (LMICs) due to the extensive coordination of care at and across various levels, including the community level, primary care centres, and secondary and tertiary care levels23.\n\nIn Indonesia, multiple pilot projects have been developed by the Ministry of Health to improve delivery of care, including a mobile phone app to gather data on the health of families and individuals24, integrated referral ICT systems25, integrated telemedicine approaches26 and mobile-phone based data collection approaches for the national health insurance scheme27. Furthermore, various referral applications for use in health care facilities have been developed by the Ministry of Health of the Republic of Indonesia and Badan Penyelenggara Jaminan Sosial (BPJS) Kesehatan (which translates as Social Insurance Administration Organization), a national health insurance provider in Indonesia28,29. More recently, BPJS Kesehatan has required all primary healthcare centres (referred to as Puskesmas in Indonesia) to use P-Care, a cloud-based application aiming to record treatments and services of those covered by BPJS Kesehatan30. Through P-Care, Puskesmas can electronically refer patient information to higher levels of the health system to facilitate and manage bookings and appointments. The Ministry of Health has also developed an Integrated Referral Information System (SISRUTE) that can help health facilities to support similar vertical referrals across different levels of the health system, especially in the case of an emergency and urgent referrals25,31. However, it is not yet clear whether these various technologies improve efficiencies in patient management or improve the experience of patients with certain conditions, such as cancer, that require repeated and frequent visits to health facilities.\n\nDespite being a strategic goal in national planning of cancer control, and its potential value in LMIC settings, such as Indonesia, there has been no research reported that details the existing ICT infrastructure in the delivery of care for patients with cancer. This research seeks to address this gap in knowledge and aims to explore the current role of HIT in the provision of services and treatments for patients with cancer from primary to tertiary healthcare centres. Identifying and mapping existing HIT for cancer care in Indonesia is intended to support critical thinking around the design, implementation, adaptation, and evaluation of existing systems.\n\n\nStudy Protocol\n\n\n\n\nMethods and analysis\n\nIn April 2019, a multi-stakeholder workshop was hosted by the study authors at Universitas Gadjah Mada (UGM), focusing on research priorities for cancer and digital technology research in Indonesia. The study team comprise applied health researchers with cancer and informatics expertise and experienced oncology clinical academics familiar with cancer provision in Yogyakarta. Attendees included representatives from the Ministry of Health (NCD Directorate), Ministry of Research, Technology and Higher Education, Ministry of Finance, Indonesian Cancer Foundation, independent commercial companies working in cancer care, academics from multiple departments in UGM including Internal Medicine, Surgery, Radiology, Public Health, and Nursing, and oncologists from hospitals in Yogyakarta, Indonesia. During discussions, it was highlighted that digital architecture on cancer care is not well understood in Indonesia. Research priorities highlighted during the workshop included determining available technologies used by cancer services, approaches to determining the quality of care delivery, patient-reported outcomes during and after cancer treatments, the development of palliative care approaches, and eliciting patient perspectives on the delivery of care. The proposed work is in response to the first priority, seeking to map the digital architecture of a defined region of Indonesia, to understand how it currently supports cancer care delivery and where there is scope for development.\n\nWe consulted the Indonesian Cancer Foundation (ICF), Yogyakarta branch, on the design of the research study. The ICF is a non-governmental organization that aims to support the Government of Indonesia in its delivery of cancer care, by taking on promotional, preventive, as well as rehabilitative measures and supportive activities. The ICF also advocates on behalf of patients with cancer and their caregivers. We consulted the ICF about the questions for participants to make sure that the topic headings are exhaustive and capture the patient journey from the beginning of care and that the content of topic guides was acceptable to patients. The ICF supported engagement with patient groups and facilitated discussions on the types of study participants that were sought and the representativeness of the target population. We also conducted a preliminary discussion with healthcare professionals to inform the development of the topic guide for the study, ensuring the topic guide captures the flow of patients and the information processes undertaken by health facilities. During the dissemination of findings, we will consult with patient advocacy groups to i) guide key messages from findings of relevance to patients and members of the public; ii) support with developing plain language summaries of study findings for dissemination, and iii) identify which communication channels might be used to disseminate study findings for patient and public audiences.\n\nThe study will adopt an observational mixed-methods single case study design32 of health facilities involved in the delivery of cancer services at the primary, secondary, and tertiary levels in a sub-national health system. For a country implementing decentralization, health politics at a sub-national level is highly influenced by the policy at the national level. An observational mixed-methods single case study design is well-placed to support the development of new theory32. We will use the approach to support the development of underpinning theory that reflects the current structure, content and use of IT infrastructure for referrals within cancer care in Yogyakarta, Indonesia.\n\nMultiple theoretical frameworks have been developed that may have relevance to exploring and understanding HIT adoption and implementation in the health sector33–36. Within this study, we will draw on the socio-technical model37, one of the models used to review HIT comprehensively from various dimensions in the health system. The socio-technical model frames the focus of project activities to focus on multiple, interacting and key components to better understand HIT for cancer care in Yogyakarta. Eight interrelated dimensions of the socio-technical model will be explored: 1) hardware and software computing infrastructure, 2) clinical content, 3) human computer interface, 4) people, 5) workflow and communication, 6) internal organizational policies, procedures, and culture, 7) external rules, regulations, and pressures, and 8) system measurement and monitoring37. While these are presented as single components, the eight specific dimensions are multiple, interacting components with non-linear, emergent, dynamic behaviour (i.e., small changes in one aspect of the system lead to small changes in other parts of the system under some conditions, but large changes at other times). The relationships and dependencies across the dimensions of the HIT for cancer referrals in Yogyakarta will be explored during the intervention development phase of the project. We will develop conceptual maps to depict identified relationships and relay these to system users and policymakers to validate their content and guide discussions around prioritisation of intervention design to refine and develop existing HIT for cancer referrals.\n\nA recent publication of the infrastructure supporting cancer referral systems in Indonesia has been published38. The framework used is based on enterprise architecture (EA) which refers to the Open Group Architecture Framework (TOGAF). This will be used to provide a detailed explanation regarding the structure and key components of the referral system as it relates to cancer, alongside providing insight into the first of the eight dimensions of the socio-technical model to be explored; hardware and software computing. In general, cancer referrals in Indonesia are conducted according to hospital classification type within the national health insurance framework. Although the study will be limited to Yogyakarta, the system observed in this study should also be able to represent the national cancer referral process with slight differences between region caused by availability of services and providers in each area.\n\nThe cancer control program in Indonesia predominantly focuses on promotion and preventative efforts (e.g. increasing knowledge for the public about approaches to cancer prevention and known risk factors) and early detection program at the primary care39. Delivery of care is across general and specialty hospitals which the Indonesian government classifies into several classes (A, B, C, D) based on facilities and the services provided by the hospitals (Table 1)40. Class A hospital is the highest level. This category was established for referral purposes41. For cancer service delivery, management is divided across primary, secondary, and tertiary referral facilities. Cancer services in Indonesia are classified based on the level of service, namely primary care (examination and or basic medical action in the health sector of care/clinic/health centre in the primary health care), secondary care (access to specialist doctors in D type/C type/B type hospitals), tertiary care (medical examination and or treatment performed by oncology subspecialist in A type hospitals)42.\n\nincluding internal medicine, paediatrics, surgery, and obstetrics and gynaecology\n\nincluding anaesthesiology, radiology, clinical pathology, anatomical pathology, and medical rehabilitation\n\nThe provision of services as part of cancer care varies across different levels43. Services at the primary health care level involve education and counselling related to cancer, screening of cancer, providing first aid in cancer emergencies, case finding and passing referrals, and registering cancer data44. Services at the secondary level involves further handling of patient referrals from primary health facilities, managing cancer emergencies, conducting special cancer medical examinations and actions, establishing cancer diagnoses, multidisciplinary teams, providing health lifestyle advice, and conducting cancer data regimens. Services at tertiary level services include conducting primary and secondary checks related to cancer, following up on patient referrals from secondary health facilities and emergency cancer cases, advanced diagnostic investigations, follow-up examinations, integrated management, special medical actions, referrals, and registration of cancer data45.\n\nUsing data from 2015, there were a total of 2,488 hospitals in Indonesia, comprising both general (n = 1,949) and specialty (n = 539) hospitals. As a first step to explore the role of HIT in cancer care, this study focuses on the Special Region of Yogyakarta, a region of Indonesia located on the island of Java. Reflective of population maldistribution in Indonesia, 70% of its inhabitants are condensed on the island of Java, which equals 11.5% of the land area of Indonesia, while the remainder are sparsely distributed across a further 17,000 islands46. The current population of the Special Region of Yogyakarta was 3,656,108 in the most recent 2019 census47.\n\nThe study will be conducted in the Special Region of Yogyakarta, Indonesia, across ten facilities supporting delivery of cancer care. The facilities will be selected through stratified purposeful sampling intended to reflect variation among different levels of the health system (i.e. primary care, D type hospital, C type hospital, B type hospital, and A type hospital). The selected sample will be based on the maturity of the referral system within the healthcare center and whether the health facility is active in the national cancer registry network. A sampling frame will ensure representation of health facilities of each level of care. This includes Primary Health Care Facilities (FKTP) and Advanced Referral Healthcare Facilities (FKRTL). All participating facilities will be based in the Yogyakarta special province, with an overview of facility groupings by health ministerial decree outlined in Table 248.\n\nThe study will recruit staff in healthcare facilities, both those involved in the management of cancer referral systems and those who are providing care to cancer patients (Figure 1). In this study, patients will also be recruited to provide insights into their experience engaging with the referral service system and maintaining communication with the service provider/health facilities.\n\nFollowing the selection of health facilities, interviews with staff and patients will be conducted within each of the participating health center sites. Participants will be purposively sampled to ensure representation of perspectives to inform existing referral processes. This will include both health facility staff who have a direct role in cancer referral management and patients with cancer. Purposive sampling will ensure selection of participants likely to provide richly-textured information relating to referral processes.\n\nInclusion criteria for health facility participants includes working in cancer care at any of the health facilities being recruited from, and having worked in their role for 1 or more years. This will ensure representation of participants across health facilities involved in the referral and management of patients with cancer, alongside the range of staff types working within facilities (i.e. service directors, clinicians, information system managers and cancer program managers). A sampling frame will be developed for selecting patients at each facility, including characteristics of age (adults and children), sex (males and females), cancer type and service currently accessing (including inpatient, outpatient, one day care, and radiotherapy). This will capture variation in the flow and processes of patients across clinical settings. For interviews with child participants, caregivers will be present and accompany them during the interview. Only participants that are able to consent or assent to participation and have no communication impairment will be approached to participate. The criteria and sampling size of the patients are detailed in Table 3.\n\nEach group of patients should represent the distribution of age (adult and children) and sex (male and female)\n\nOnly for A-type and B-type hospitals with one-day care services.\n\n*Only for A-type hospital with radiotherapy services.\n\nThe sample size for health facility and patient participants to be recruited across sites was determined by the exploratory nature of the study and pragmatic considerations (i.e. resource constraints in terms of research budget and research team size). The selection of sites to ensure information-rich data collection was guided through consultation with the District Health Office. The adequacy of data quality and richness being gathered during interviews will be monitored through regular team meetings. A sampling frame for health facility staff is outlined in Table 4 and for patient participants in Table 3. We will consult with the clinical teams in each cancer unit in participation sites to support with patient recruitment.\n\nField observations\n\nWe will carry out participant observation in the field prior to interviews with health professionals to collect information on the routine method and variety of patient data collected in the health facilities. We will explore a range of forms used in the healthcare centers (i.e. patient registration form, referral form, consent form, medical resume). We will also gather data on the availability of radiotherapy and chemotherapy services, including details on the average daily visits, available beds, duration and frequency of the treatments, number of human resources, and the equipment used. The output from the observation will form the basis of interviews with the health personnel.\n\nHealth personnel interviews\n\nSemi-structured face-to-face interviews will be conducted with staff involved in providing care for cancer patients. This includes hospital managers or directors of the patient service, clinicians, and health information system managers. Access to respondents will be through a written letter directed to the management of healthcare facilities. This interview will be conducted with staff from various areas because of the interrelation between units in conducting cancer care, including referral services. Data will be collected from 48 in-depth interviews. Where face-to-face interviews are not possible, interviews will be offered via telephone or video calls in place of meeting face-to-face.\n\nPrior to the interview, written consent will be obtained to record and transcribe the interview. The one-hour semi-structured interviews will be conducted face-to-face by an interviewer; a note-taker will be present for the duration of the interview. Interviewers will record observations about the circumstances of the interview, summarise key opinions and factors that arise, and note considerations for modifying the topic guide for subsequent interviews.\n\nA topic guide and questions have been developed to guide the interview (Table 5). Interviews will focus on the implementation of the existing HITs and cancer registry, the workflow and interoperability, current policies related to HIT, barriers in HIT operation and sharing across different units, and innovation strategies to address the challenges. We will use an interview topic guide to ensure the coverage of our research questions. Evidence from field observations will also be incorporated into interviews as a basis for discussion regarding treatment options and availability. The output of interviews will be centred around the existing and ideal cancer referral pathway, data management, and reporting mechanism to the central government. We anticipate a discussion on the possible gaps in the current pathway, including but not limited to the HIT architecture, digital literacy of the personnel, and human resources constraints.\n\nPatient interviews\n\nFor adult patient participants, in-depth interviews will focus on an exploration of participants’ experiences of using a referral service system and how they maintain communication with the service provider, current use of digital technologies (such as smartphones), and gaps in provision that participants feel would improve or enhance existing service provision for patients with cancer. For child participants, the interview will be conducted with the caregiver to explore their experiences of using the referral systems. The interviews will be conducted following the topic guide detailed in Table 6.\n\nWe will conduct face-to-face interviews with cancer patients. Caregivers, typically family members, often accompany patients to clinical appointments and are involved in the decision making process in Indonesia49. As such we will be flexible about whether interviews are conducted with individual patients or in dyads with their caregivers. All participants will be required to sign an consent form to participate in the study. Prior to the interview, where participant literacy levels are high, written consent will be obtained to record and transcribe the interview. Where literacy is low, verbal consent to record and transcribe the interview will be obtained from the participant. For those providing verbal consent, participants will be asked whether they would like to have a trusted relative or friend as their witness. The 30-minute-interviews will be conducted by an interviewer; As with health professional interviews, interviews will be held by telephone or video calls where face-to-face meetings are not possible.\n\nAudio recording and electronic copies of consent forms will be stored in password-protected files using the Microsoft OneDrive platform. An electronic copy of consent materials will be made as soon as possible following an interview and once an electronic version has been created, paper copies will be destroyed. Only research team members will have access to the OneDrive platform folder set up for the study. On completion of this study, all electronic data on the OneDrive folder, (i.e. electronic copies of consent forms and audio recordings of interviews), will be moved to an electronic archive for 5 years prior to being permanently destroyed. Following completion of the study we will assess the suitability of wider sharing of research data, once deidentified, via a research data repository. All study participants will be assigned an identification code, which will be delinked from their identity across all study documentation.\n\nWe will collect the summary of the distribution and demographic data of cancer patients from hospitals and Puskesmas routine reports, along with data from the district health office; Data will be drawn from the report of the 24-month period prior to the study taking place in May 2020. We will collect the number of admitted and referred cancer patients in the last two years. Variables included will be the type of admission (emergency room, inpatient, outpatient), referral status (referred or not), and the outcome (discharged, died, referred). The data will be used to determine patterns of referral as reflected through routine data and explore whether these data can inform where gaps exist in the existing referral system.\n\nQualitative data. Interviews will be transcribed verbatim before being imported into NVivo 12 software for deductive framework analysis. An initial exploration and charting of pseudonymised transcripts will be undertaken (AE) through a process of line-by-line coding. Initial coding will be conducted using a random set of transcripts (n=3) for each of the three key stakeholder groups (i.e. patients, health professionals involved in the care of patients with cancer, health professionals and administrators involved in the management of cancer referral systems). A final framework will be agreed through discussion with the wider team. Once inconsistencies are resolved, all remaining interview transcripts will be coded within the joint coding frame. In order to explore common themes and divergences across the stakeholder groups, comparative analysis in the framework will be undertaken. A model of the coding frame will be developed, and each theme and subtheme given a definition to ensure internal consistency of each code. Illustrative codes will be reported for each theme, with the study ID code to demonstrate reporting from across the sample breadth. Safeguards for rigour and quality of data analysis will be embedded into the analysis process, including: regular team meetings to discuss transcripts, codes, and development of themes, alongside verification of accuracy of data through listening to audio recordings of interviews and assessing transcripts by team members (AF, MJA). Where possible, respondent validation will be incorporated into the analysis, sharing summaries of preliminary findings with research participants to provide an opportunity for them to engage with, and add to, interview and interpreted data. The final output from the analysis will be used to inform the development of conceptual maps, ensuring representation of data from all participant groups.\n\nQuantitative data. Descriptive statistics will be generated to inform specific themes of interest (as outlined in Table 7). Exploration of routine datasets will provide insights into the current distribution and demographic data of patients accessing cancer services in participating sites. This will also be explored at a regional level, with descriptive analysis of regional data providing insights into the distribution and patterns of cancer prevalence in the Yogyakarta region. Secondary data from routine reports will be analysed using Stata/MP 14.1 (StataCorp LLC, College Station, USA). We will also apply network representation analysis to visualise the data. Pairwise relationships between health facilities across the levels of the health system will be derived from descriptive analysis and will be described as a collection of nodes and edges to depict relationships between the facilities. This is intended to provide visually informative data alongside guiding conceptual model development as part of subsequent Theory of Change workshops.\n\nThis study intends to understand and map existing referral processes as part of cancer service provision in Yogyakarta. However, findings are also intended to be used to guide prioritization of future intervention development to refine existing referral processes. The findings from the quantitative and qualitative components of the study will be fed back to key stakeholders in cancer service delivery within Yogyakarta and national representatives. This will be used to elicit feedback on study findings and derive priorities for future research and intervention development.\n\nA narrative synthesis approach will be used as a framework to guide the describing, comparing and combining of heterogeneous qualitative findings and quantitative results from across the study. The synthesis of findings will be used to generate conceptual maps. We will use elements of Popay et al.’s methodology of narrative synthesis50 which guides the bringing together of disparate literature from multiple sources. We will follow the steps outlined by Popay et al.50, which will include: i) developing a theory of how the referral system currently works, why and for whom; ii) developing a preliminary synthesis of findings from across the study activities; iii) exploring relationships in the data, including exploration of alignment of findings against the TOGAF approach (e.g. components of business, architecture, technology and data) and eight interrelated dimensions of the socio-technical model; and; iv) assessing the robustness of the synthesis. Findings from qualitative and quantitative activities will be synthesised to guide the development of an underpinning theory of how referrals systems currently work within Yogyakarta and generate conceptual maps for refinement through engagement with key stakeholders in the existing cancer referral system, including the Ministry of Health of the Republic of Indonesia, the Ministry of Information and Communication of the Republic of Indonesia, the Yogyakarta Special Region Health Office, the Association of Yogyakarta Special Region Hospitals, and BPJS as the national health coverage agency.\n\nThe use of a conceptual map (also referred to in the literature as logic models, analytical frameworks, concept maps, or influence diagrams) will provide a means of visualising the underlying theory of change beneath the existing referral system as determined through the study. The conceptual map presents a useful framework for describing how the referral system is believed to achieve its effects. By presenting this information graphically, rather than in narrative form, we hope to gain a clearer view of the relationship between constituent parts and how they interact. We will produce different types of conceptual map for engagement with key stakeholders, including both activity maps (focusing on the implementation process and aiming to describe the intention of the referral system and the specific steps needed to achieve this intention) and outcomes maps (focusing on the connections between the resources, activities and the outcomes, which may be subdivided into short-term outcomes, long-term outcomes and impact). Discussions will also incorporate prioritisation of future efforts including around digital health technologies specifically for cancer, regulations that ensure the effectiveness and efficiency of cancer referrals (including financing, infrastructure, human resources, technology regulation, interoperability, and data standards), and potential partnerships between government and private sector (public-private mix).\n\nConceptual maps will be presented, reviewed, discussed and refined during stakeholder meetings and workshops. Two workshops will be conducted. The first will focus on Yogyakarta stakeholders (District Health Office, Provincial Health Office, National Insurance Agencies, Indonesian Cancer Foundation, and health facilities) to determine pathways to impact at the provincial level. The second meeting will focus on the national perspective (with representatives from The Ministry of Health, Yogyakarta Provincial Health Office, National Insurance Agency, and Hospital Organizations) to discuss the recommendations derived from the research and their relevance for national policy. Alongside enhancing and validating findings from the study, conceptual maps will be used formatively as a mechanism for engaging with stakeholders and stimulating debate about future development of the cancer referral system in Yogyakarta. The data collected will be the basis for interventions related to improvement and innovation for cancer referral services in Yogyakarta and may have national relevance.\n\nThe study involves participation of human subjects requiring consideration of ethics issues relating to informed consent of participants, beneficence, ensuring participant confidentiality and protection of study data, and a respect for privacy. This research has received ethical approval from the joint Medical and Health Research Ethics Committee (MHREC) of Universitas Gadjah Mada and Dr. Sardjito Hospital (No. KE/FK/1075/EC/209). The MHREC has the rights to monitor the research activities at any time.\n\nA number of activities will be undertaking to support dissemination of project findings. These will include: (1) developing newsletters and press releases to communicate key project findings to the general public, (2) delivering presentations at local and national conferences in Indonesia, alongside presentation at international conferences, (3) publishing articles in peer-reviewed journals and (4) social media through research team member and institutional accounts. Participants will be anonymised in any dissemination activities. Only pseudonymised, non-identifiable characteristics and quotes will be used in dissemination.\n\nThe study is currently recruiting participants.\n\nThis study has been registered with Research Registry (researchregistry5807) 15/07/2020.\n\n\nConclusion\n\nThis research seeks to determine the current role of HIT in the provision of services and treatments for patients with cancer. Our findings will inform critical thinking around the design, implementation, adaptation, and evaluation of existing systems. Through early engagement and participation of key stakeholders and project partners we intend that findings to have immediate utility. We will disseminate our findings to the Ministry of Health and other key stakeholders, alongside presenting findings at conferences and in peer-reviewed journals. Findings from the study will also be communicated to the government at regional and national levels, hospitals, and primary care centers alongside as part of intervention development and modelling meetings. We will also develop a policy briefing report and an intervention guide related to improving cancer services in Indonesia based on the findings of this study.\n\n\nData availability\n\nNo data are associated with this article\n\nFigshare: SRQR checklist for ‘Protocol for a mixed-methods exploratory investigation of the role of health information technology in the provision of cancer care in Indonesia’ https://doi.org/10.6084/m9.figshare.12656381.v151", "appendix": "References\n\nWHO cancer mortality database (IARC): [cited 28 May 2020]. Reference Source\n\nKimman M, Norman R, Jan S, et al.: The burden of cancer in member countries of the Association of Southeast Asian Nations (ASEAN). Asian Pac J Cancer Prev. 2012; 13(2): 411–420. PubMed Abstract \| Publisher Full Text\n\nACTION Study Group, Kimman M, Jan S, et al.: Catastrophic health expenditure and 12-month mortality associated with cancer in Southeast Asia: results from a longitudinal study in eight countries. BMC Med. 2015; 13: 190. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThe Economist Intelligence Unit: Cancer preparedness around the world: National readiness for a global epidemic. 2019. Reference Source\n\nWorld Cancer Initiative: The Economist Group: [cited 22 May 2020]. Reference Source\n\nPutranto R, Trisnantoro L, Hendra Y: Penghematan Biaya Perawatan Pasien Kanker Terminal Dewasa melalui Konsultasi Tim Paliatif di Rumah Sakit Dr. Cipto Mangunkusumo. Jurnal Penyakit Dalam Indonesia. 2017; 4(1): 35–40. Publisher Full Text\n\nGarg S, Williams NL, Ip A, et al.: Clinical Integration of Digital Solutions in Health Care: An Overview of the Current Landscape of Digital Technologies in Cancer Care. JCO Clin Cancer Inform. 2018; 2: 1–9. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Cancer Control: Knowledge Into Action: WHO Guide for Effective Programmes. World Health Organization; 2007. PubMed Abstract\n\nInternational Atomic Energy Agency: Technical Cooperation Report for 2018. 2019. Reference Source\n\nNational Cancer Committee Regulation: Sect. HK.01.07, 14 2017. Reference Source\n\nTjindarbumi D, Mangunkusumo R: Cancer in Indonesia, Present and Future. Jan J Clin Oncol. 2002; 32(Suppl): S17–S21. PubMed Abstract \| Publisher Full Text\n\nWahidin M, Noviani R, Hermawan S, et al.: Population-Based Cancer Registration in Indonesia. Asian Pac J Cancer Prev. 2012; 13(4): 1709–1710. PubMed Abstract \| Publisher Full Text\n\nPurnamasari D: The Emergence of Non-communicable Disease in Indonesia. Acta Med Indones. 2019; 50(4): 273–274. PubMed Abstract\n\nMinistry of Health Republic of Indonesia: Indonesia Basic Health Research 2018. Jakarta: Ministry of Health Republic of Indonesia; 2018. Reference Source\n\nMinistry of Health Republic of Indonesia Information Center: Indonesia Health Profile 2016. Jakarta: Ministry of Health Republic of Indonesia; 2016. Reference Source\n\nNgwa W, Olver I, Schmeler KM: The Use of Health-Related Technology to Reduce the Gap Between Developed and Undeveloped Regions Around the Globe. Am Soc Clin Oncol Educ Book. 2020; 40: 1–10. PubMed Abstract \| Publisher Full Text\n\nFosdal M: Using Technology to Advance Cancer Survivorship Programs. J Adv Pract Oncol. 2014; 5(5): 340–6. PubMed Abstract \| Free Full Text\n\nDickinson R, Hall S, Sinclair JE, et al.: Using technology to deliver cancer follow-up: a systematic review. BMC Cancer. 2014; 14: 311. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCharalambous A: Utilizing the Advances in Digital Health Solutions to Manage Care in Cancer Patients. Asia Pac J Oncol Nurs. 2019; 6(3): 234–237. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFasola G, Macerelli M, Follador A, et al.: Health Information Technology in Oncology Practice: A Literature Review. Cancer Inform. 2014; 13: 131–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiyanage H, Correa A, Liaw ST, et al.: Does Informatics Enable or Inhibit the Delivery of Patient-centred, Coordinated, and Quality-assured Care: a Delphi Study: A Contribution of the IMIA Primary Health Care Informatics Working Group. Yearb Med Inform. 2015; 10(1): 22–29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim KK, Bell JF, Reed SC, et al.: Chapter 5 - Coordination at the Point of Need. In: Hesse BW, Ahern DK, Beckjord E, editors. Oncology Informatics. Boston: Academic Press; 2016; 81–100. Publisher Full Text\n\nBhatt S, Evans J, Gupta S: Barriers to Scale of Digital Health Systems for Cancer Care and Control in Last-Mile Settings. J Glob Oncol. 2018; 4: 1–3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHartomo Pujosiswanto K, Palutturi S, Ishak H: Policy Implementation of Healthy Indonesia Program Through Family Approach (PIS-PK) In Community Health Center of Polewali Mandar Regency. IJCTR. 2018; 11(8): 199–203. Publisher Full Text\n\nBancin LJ, Putri NA, Rahmayani N, et al.: Gambaran Sistem Rujukan Terintegrasi (SISRUTE) di RSUD Dr. RM Djoelham Binjai Tahun 2019. Jurnal Ilmiah Perekam dan Informasi Kesehatan Imelda. 2020; 5(1): 16–19. Publisher Full Text\n\nMelyana M, Sarotama A: Implementasi Peringatan Abnormalitas Tanda-Tanda Vital pada Telemedicine Workstation. Prosiding Semnastek. 2019. Reference Source\n\nEvaluating the Usability of Mobile JKN the Indonesian App for Universal Healthcare Coverage, Using the Technology Acceptance Model (TAM). 서울대학교 대학원. 2019. Reference Source\n\nIndonesia Internet Service Provider Association: Penetrasi dan Perilaku Pengguna Internet Indonesia. 2017. Reference Source\n\nHandayani PW, Saladdin IR, Pinem AA, et al.: Health referral system user acceptance model in Indonesia. Heliyon. 2018; 4(12): e01048. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJoint Regulation of the Secretary General of the Ministry of Health of the Republic of Indonesia and the Managing Director of the Health BPJS. Hk.01.08/Iii/980/2017 Mar 31, 2017. Reference Source\n\nHandayani PW, Pinem AA, Azzahro F, et al.: The Information System/Information Technology (IS/IT) practices in the Indonesia health referral system. Inform Med Unlocked. 2019; 17: 100263. Publisher Full Text\n\nOnghena P, Maes B, Heyvaert M: Mixed Methods Single Case Research: State of the Art and Future Directions. J Mix Methods Res. 2019; 13(4): 461–480. Publisher Full Text\n\nWaterson P: Health information technology and sociotechnical systems: a progress report on recent developments within the UK National Health Service (NHS). Appl Ergon. 2014; 45(2): 150–161. PubMed Abstract \| Publisher Full Text\n\nAmmenwerth E, Gräber S, Herrmann G, et al.: Evaluation of health information systems—problems and challenges. Int J Med Inform. 2003; 71(2–3): 125–135. PubMed Abstract \| Publisher Full Text\n\nEslami Andargoli A, Scheepers H, Rajendran D, et al.: Health information systems evaluation frameworks: A systematic review. Int J Med Inform. 2017; 97: 195–209. PubMed Abstract \| Publisher Full Text\n\nYusof MM, Kuljis J, Papazafeiropoulou A, et al.: An evaluation framework for Health Information Systems: human, organization and technology-fit factors (HOT-fit). Int J Med Inform. 2008; 77(6): 386–398. PubMed Abstract \| Publisher Full Text\n\nSittig DF, Singh H: A New Socio-technical Model for Studying Health Information Technology in Complex Adaptive Healthcare Systems. Health Informatics. 2015; 59–80.\n\nHandayani PW, Pinem AA, Munajat Q, et al.: Health Referral Enterprise Architecture Design in Indonesia. Healthc Inform Res. 2019; 25(1): 3–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThe Ministry of Health of The Republic of Indonesia: 2018 Report of Directorate of Non Communicable Diseases. 2019.\n\nSuryanto, Plummer V, Boyle M: Healthcare System in Indonesia. Hosp Top. 2017; 95(4): 82–89. PubMed Abstract \| Publisher Full Text\n\nHospital Regulation of The Republic of Indonesia. 2009; 24.\n\nThe Ministry of Health of The Republic of Indonesia: Guidelines for Cancer Management in Health Facilities. 2017.\n\nHospital Classification and Licensing Regulation of The Republic of Indonesia. 2014; 56.\n\nInstitute of Medicine (US) and National Research Council (US) National Cancer Policy BoardHewitt M, Simone JV: Health Care Delivery and Quality of Cancer Care. Ensuring Quality Cancer Care. National Academies Press (US); 1999. Reference Source\n\nKementerian Kesehatan Republik Indonesia: Panduan Penyelenggaraan Pelayanan Kanker di Fasilitas Pelayanan Kesehatan. Reference Source\n\nWardhani V, van Dijk JP, Utarini A: Hospitals accreditation status in Indonesia: associated with hospital characteristics, market competition intensity, and hospital performance? BMC Health Serv Res. 2019; 19: 372. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBadan Pusat Statistik Provinsi D.I. Yogyakarta: Jumlah Penduduk menurut Kabupaten/Kota di D.I Yogyakarta (Jiwa). In: Badan Pusat Statistik Provinsi D.I. Yogyakarta. [cited 26 Jul 2019]. Reference Source\n\nKementerian Kesehatan Republik Indonesia: Peraturan Menteri Kesehatan Republik Indonesia Nomor 56 Tahun 2014 tentang Klasifikasi dan Perizinan Rumah Sakit. 2014. Reference Source\n\nEffendy C, Vernooij-Dassen M, Setiyarini S, et al.: Family caregivers’ involvement in caring for a hospitalized patient with cancer and their quality of life in a country with strong family bonds. Psychooncology. 2015; 24(5): 585–591. PubMed Abstract \| Publisher Full Text\n\nPopay J, Roberts H, Sowden A, et al.: Guidance on the conduct of narrative synthesis in systematic reviews. The ESRC methods programme. 2006; 15: 047–071. Reference Source\n\nAllsop M: SRQR checklist for ‘Protocol for a mixed-methods exploratory investigation of the role of health information technology in the provision of cancer care in Indonesia’. figshare. Online resource. 2020. http://www.doi.org/10.6084/m9.figshare.12656381.v1" }	[ { "id": "85447", "date": "02 Jun 2021", "name": "Niloofar Mohammadzadeh", "expertise": [ "Reviewer Expertise Health information management and health informatics." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 think this subject is very interesting and can be helpful for health information technology experts.\nIn table 1 - what is medical subspecialty?\n\nIn table 2 - the total column is referring to organization number or patient number?\n\nIn article said there is 10 organization but selected 9, what is the reason to choose 9? (Table 2 and figure 1).\n\nIn table 2 - in total column 306 and selected 2 in the next column. Honestly I cannot understand why 2 from 306 selected? Or these columns are not related to each other. Please explain more about table 2.\n\nWhat is the method for sampling patient in figure 1?\n\nIn figure 1 about hospital staff, what is the sampling method? And how many people are selected in each position?\n\nIn table 3: number of health facilities is more than 10?\n\nOn page 9 in second paragraph after reference of 49, you write \"dyads\". What is it?\n\nIn table 6: which of these question asked of children and which of them asked about adults?\n\nConclusion is very short. I suggest explain more for example about limitation of study, compare result with same studies.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "11932", "date": "01 Jul 2024", "name": "Matthew Allsop", "role": "Author Response", "response": "R1 comment: I think this subject is very interesting and can be helpful for health information technology experts. Author response: Thank you for your comments and for your guidance on improving our manuscript. R1 comment: In table 1 - what is medical subspecialty? Author response: Thank you for your comment. This was a repetition of information in the table that has now been removed. We describe basic medical speciality and supporting medical speciality categories in the footnote of the table. R1 comment: In table 2 - the total column is referring to organization number or patient number? Author response: The total column refers to the total number of facilities of that type in the Yogyakarta region. We have now clarified this in the column title. R1 comment: In article said there is 10 organization but selected 9, what is the reason to choose 9? (Table 2 and figure 1). Author response: Thank you for highlighting this. We have amended the word “ten” to “nine” to align with the plans detailed in the table and figures. R1 comment: In table 2 - in total column 306 and selected 2 in the next column. Honestly, I cannot understand why 2 from 306 selected? Or these columns are not related to each other. Please explain more about table 2. Author response: This is correct that we seek to recruit two primary care sites, as detailed in the table. This work is an exploratory study to address gaps in the evidence base. While it may have been helpful to sample a higher number of primary care sites, this is not possible within the confines of the budget available for this study. We have reflected this limitation in the section outlining the methodology relating to health professional interviews. R1 comment: What is the method for sampling patient in figure 1? Author response: We have addressed this omission in our reporting of methods through adding the following text to the Sample Selection section: The research team will liaise with the Head or Director of Patient Services at each facility to support the identification of eligible health professionals. The research will liaise with clinical staff supporting patients with cancer to identify and support the recruitment of patient participants. R1 comment: In figure 1 about hospital staff, what is the sampling method? And how many people are selected in each position? Author response: As part of our response to the prior comment, we have also added details of the sampling method for hospital staff. We will remain flexible around the recruitment across different positions based on availability and willingness to participate across the facilities. We have not provided specific expectations of figures across each position but do specify that we will seek to recruit participants across all positions. R1 comment: In table 3: number of health facilities is more than 10? Author response: Thank you. The figures represent the number of health facilities that have the cancer service type available. For example, 3 of the cancer services have one-day care services, from which we will sample 4 patients at each. This will result in up to 12 participants being recruited across these services. R1 comment: On page 9 in second paragraph after reference of 49, you write \"dyads\". What is it? Author response: Dyad referred to interviewing two participants together to collect data, but we have clarified this in the text to now read “As such we will be flexible about whether interviews are conducted with individual patients or with their caregivers present”. R1 comment: In table 6: which of these question asked of children and which of them asked about adults? Author response: We have clarified in the topic guide which questions are solely for child participants and which are for exploring primarily with caregivers of child participants, but with child participant input encouraged. We have also provided flexibility with the way in which questions can be posed based on the participant type. R1 comment: Conclusion is very short. I suggest explain more for example about limitation of study, compare result with same studies. Author response: Thank you. We have now reflected limitations in responding to prior points raised. In terms of the conclusion, given this is a protocol we do not yet have results to compare to the literature. After we have conducted the research, we will be able to contextualise our findings within existing literature. We have however included an introduction section that provides an overview of the state of evidence to date and the need for the research." } ] }, { "id": "71090", "date": "20 Jun 2024", "name": "Andree Kurniawan", "expertise": [ "Reviewer Expertise Epidemiology", "supportive care", "cancer" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis protocol is fantastic and can be useful for cancer care in Indonesia. We will wait for the subject recruitment and study results.\n\nMy comment is about the sampling methods. How do you ensure that participant recruitment (healthcare provider and cancer patients) can represent the Indonesian population? Is there random sampling in several clusters? The second is about how do you gather data in qualitative methods, is there using focus group discussion or direct interview? The key person should be described to ensure the validity of the information.\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": "11933", "date": "01 Jul 2024", "name": "Matthew Allsop", "role": "Author Response", "response": "Thank you for your time in reviewing the manuscript and for providing your comments. Please find below our response. R2 comment: My comment is about the sampling methods. How do you ensure that participant recruitment (healthcare provider and cancer patients) can represent the Indonesian population? Is there random sampling in several clusters? Authors’ response: Thank you for your comment. We have proposed to undertake an exploratory study that begins to document and understand the types of systems being used for cancer care across the Yogyakarta region. This is a first step in developing the evidence base. We have developed sampling frames for all participant types but do not seek to have a sample that reflects the Indonesian population. For this exploratory work, we are seeking to obtain a wide range of views and perspectives from patients accessing cancer care and their health professionals across a range of settings to begin to understand current practice. R2 comment: The second is about how do you gather data in qualitative methods, is there using focus group discussion or direct interview? The key person should be described to ensure the validity of the information. Authors’ response: Thank you. We will be conducting face-to-face interviews for the qualitative methods, either with individual adult participants or with their caregivers present. We will also undertake face-to-face interviews with child participants with their caregivers present." } ] } ]	1	https://f1000research.com/articles/9-904
https://f1000research.com/articles/13-640/v1	17 Jun 24	{ "type": "Software Tool Article", "title": "Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG", "authors": [ "Jeferyd Yepes-García", "Laurent Falquet", "Jeferyd Yepes-García" ], "abstract": "Background Building Metagenome–Assembled Genomes (MAGs) from highly complex metagenomics datasets encompasses a series of steps covering from cleaning the sequences, assembling them to finally group them into bins. Along the process, multiple tools aimed to assess the quality and integrity of each MAG are implemented. Nonetheless, even when incorporated within end–to–end pipelines, the outputs of these pieces of software must be visualized and analyzed manually lacking integration in a complete framework.\n\nMethods We developed a Nextflow pipeline (MAGFlow) for estimating the quality of MAGs through a wide variety of approaches (BUSCO, CheckM2, GUNC and QUAST), as well as for annotating taxonomically the metagenomes using GTDB-Tk2. MAGFlow is coupled to a Python–Dash application (BIgMAG) that displays the concatenated outcomes from the tools included by MAGFlow, highlighting the most important metrics in a single interactive environment along with a comparison/clustering of the input data.\n\nResults By using MAGFlow/BIgMAG, the user will be able to benchmark the MAGs obtained through different workflows or establish the quality of the MAGs belonging to different samples following the divide and rule methodology.\n\nConclusions MAGFlow/BIgMAG represents a unique tool that integrates state-of-the-art tools to study different quality metrics and extract visually as much information as possible from a wide range of genome features.", "keywords": [ "Metagenomics", "Nextflow", "pipeline", "dashboard", "data analysis." ], "content": "Introduction\n\nThe generation of metagenomics data has increased exponentially within the last ten years, supported by the rapid evolution of next generation sequencing techniques for both short and long reads (Tremblay et al., 2022). Moreover, to perform the analysis of microbiome data the usual approach involves reconstructing genomes, commonly known as Metagenome–Assembled Genomes (MAGs), from fragmented sequences obtained during DNA extraction. The steps to achieve this goal enclose the cleaning and filtering out of low–quality reads, the assembly of the short sequences into longer and contiguous strands (contigs), plus clustering contigs into bins according to multiple genome–level features such as tetranucleotide frequency, similarity in coverage, GC content, among others (Yang et al., 2021).\n\nRoutinely, the recovered MAGs, independently of the selected workflow to assemble them, should be subject to quality measurements by one or several tools. Contiguity, completeness, and contamination are regular metrics used to classify the MAGs in different categories based on arbitrary criteria (Haryono et al., 2022). Common thresholds used to separate low (or simply bins), mid or high-quality MAGs are completeness and contamination values generated by tools such as CheckM or CheckM2, e.g., high-quality MAGs depict levels of contamination below 5% and completeness above 90%. For this manuscript we will use MAGs as a reference to any MAG regardless the category they should be classified in.\n\nFurthermore, given the complexity and abundance of species within some specific environments, i.e., soil or sea sources (Guseva et al., 2022), more sophisticated tools have been developed to detect the presence of specific marker genes, chimerism and duplication. In addition, proper taxonomical annotation of the MAGs allows to report unique insights related to the composition of the community, contributing to ensure the quality of the assembly and the accuracy of the methods employed to bin the contigs (Cornet & Baurain, 2022).\n\nNevertheless, many pipelines or methodologies only include one or two tools to measure the quality of the MAGs (Kieser et al., 2020; Krakau et al., 2022; Uritskiy et al., 2018), and the visualization and/or analysis of the quality data relies entirely on the user who should be familiar with the type of generated files and how to display the information in a pleasant manner. In other cases, the users must develop manually their own methodology to perform this important step during the metagenome assembly, increasing the risk of lack of reproducibility and the difficulty to test and validate the results. This scenario sets interesting challenges that encases maximizing the scope of the quality assessment, the need of pipelines coupled to visualization tools and boosting reproducibility by wrapping the process with workflow managers (Wratten et al., 2021).\n\nAs a result, we designed a framework to measure the quality of the MAGs generated by different methodologies or belonging to different samples, as well as to visualize the metrics through a web–based interface. This framework carries out the analysis through a Nextflow pipeline (MAGFlow) that takes the MAGs as input to measure their completeness and contamination using machine learning through CheckM2 (Chklovski et al., 2023), determine the level of single–copy ortholog (SCO) completeness, duplication and fragmentation using BUSCO (Manni et al., 2021), estimate chimerism and contamination with GUNC (Orakov et al., 2021), perform a full taxonomical classification by GTDB-Tk2 (Chaumeil et al., 2022), and produce a full report of the assembly features by QUAST (Gurevich et al., 2013). After merging the outcomes from these tools, a final.tsv file is compiled by MAGFlow, and the user can use it to render an interactive web–based Dash application (BIgMAG).\n\n\nMethods\n\nMAGFlow\n\nMAGFlow is a pipeline designed to run in any environment, to be portable, easy to install, scalable to the available computational resources and ready to use in local or cloud-based infrastructures. In addition, MAGFlow can be customized through tuning parameters that are available for each tool encompassed in the workflow.\n\nIn order to assess the MAG quality and/or perform the taxonomical annotation, MAGFlow, wrapped by Nextflow (v23.04.0), runs BUSCO (v5.7.0), CheckM2 (v1.0.1), GUNC (v1.0.6), QUAST (v5.2.0) and optionally GTDB-Tk2 (v2.3.2), along with a download of the latest Genome Taxonomy Database (GTDB, current release: 220), to produce a.tsv file that concatenates the outputs from these pieces of software (Figure 1). The external tools enclosed by MAGFlow are Open Access, and they will remain in such status according to the license provided by their developers.\n\nAs input, the pipeline uses genomic files organized in corresponding folders, decompressed (.fna, .fa, .fasta) or compressed (.gz) obtained from a previous process of assembly/binning. Depending on the type of input, the workflow begins by decompressing the files and checking if there are empty files to be removed from the analysis; the original files will not be modified. Afterwards, the tools mentioned above will be run in parallel according to the allocated resources for each job. The taxonomical annotation is optional for each user given the high demand it represents in terms of memory and storage. Once all the processes are finished, MAGFlow will merge the outcomes from each tool, to end up with a unique final_df.tsv file, which is the main input for BIgMAG. Additionally, the pipeline will produce the regular output from each of the tools and HTML execution reports displaying the resource usage, success of each step and timestamps, allowing the user to explore them if required.\n\nIn case the user accounts with previously generated BUSCO, CheckM2, GTDB-Tk2, GUNC or QUAST files and their aim is to use them to explore the metrics using BIgMAG, it is possible to achieve this task by just running an additional script (skip_pipeline.py). This script can recognize and process the files into the required final_df.tsv by BIgMAG. Directions about how to run MAGFlow or use the skip_pipeline.py script are available at https://github.com/jeffe107/MAGFlow.\n\nBIgMAG\n\nBIgMAG consists of an interactive Dash application with Plotly as the rendering engine on a regular modern web browser. The layout is divided into 7 sections, 5 of them being plots dedicated exclusively to the tools executed by MAGFlow. In the case of CheckM2 and BUSCO, scatterplots are used to depict the behavior of genome completeness against contamination levels. Moreover, the results from QUAST and GUNC are displayed through boxplots that show the distribution of the data according to a user–selected parameter.\n\nTo process the outcomes from GTDB-Tk2, BIgMAG generates a presence/absence matrix representation of annotated taxa at the taxonomical level specified by the user, in a novel strategy to extract the core data without showing the complete phylogeny of the annotated MAGs. This approach is valuable in terms of the simplicity it achieves to display complex information, providing an alternative to the time–consuming branch-collapsing methodology that is usually followed through specialized software packages, e.g., iTOL (Letunic & Bork, 2021), as shown by Bayer et al. (2020) to condensate the GTDB-Tk2 output.\n\nFollowing the GTDB-Tk2 plot, as an attempt to compare the features among samples and cluster them according to their similarity using different parameters provided by BUSCO, CheckM2, GUNC and/or GTDB-Tk2, a cluster heatmap is displayed. To render this plot, average values are used, combined with the proportion of MAGs passing the GUNC test and/or the proportion of annotated MAGs by GTDB-Tk2.\n\nAt the bottom of the dashboard, the raw data in a format table is displayed with the possibility for the user of highlighting cells, deleting rows and filtering the columns with keywords.\n\nComplementary to each plot, there is a series of callbacks that exploits the native interactivity of Plotly and Dash. These callbacks allow filtering out the MAGs according to contamination and completeness threshold levels in the CheckM2 plot, or based on complete SCO and duplicated SCO in the case of the BUSCO figure, selecting the parameter to display the data distribution of each sample in GUNC or QUAST plots and zooming in/out in the GTDB-Tk2 plot by selecting the number of samples to show. Also, it is possible to store all the figures individually directly from the dashboard with the in–built function to download the plots locally. More interactive details will be displayed when the cursor hovers each of the plot zones, i.e., on CheckM2 or BUSCO scatterplots, if GTDB-Tk2 data is found in the final_df.tsv file, the taxonomical classification will be also included in the information depicted.\n\nBIgMAG also features the possibility of being compiled as an HTML webpage to be displayed afterwards without requiring any of the processing components installed. However, given that this is not a native feature of Dash, the callbacks cannot be used while the dashboard is stored. Therefore, we developed an additional script (app_lite.py), a lite version of BIgMAG, displaying the same layout as the regular version, although with an additional Save to html button below the heading section, and without the components triggering the callbacks. This lite version of BIgMAG can be customized and adjusted by using command line arguments (tutorial available at the repository https://github.com/jeffe107/BIgMAG).\n\nMAGFlow/BIgMAG is performed on UNIX-based operating systems, e.g., any Linux distribution or macOS; its operation on Windows 10 or 11 is also possible through Windows Subsystem for Linux (WSL2). Specifically, MAGFlow demands the installation of Nextflow (≥23.04.0), which in turn requires Java JDK 17 or 19 (recommended version 17.0.3). In addition, it is necessary to account with a software management tool such as Conda (≥23.3.1), Mamba (≥1.3.1) or any container technology including Docker, Singularity, Apptainer, Podman or Charliecloud. After fulfilling these requirements, the user can start the analysis with MAGFlow by providing the directory path where the MAG files are stored or a.csv file indicating the different file paths. A terminal example command can be as follows:\n\nOr:\n\nThe -profile argument must be set according to the software management tool the system user incorporates, and the path to store the output files is completely arbitrary to the user. Details in regard to the required MAG file structure, an example of the .csv datasheet, and other configuration options can be found at https://github.com/jeffe107/MAGFlow.\n\nOn the other hand, BIgMAG only requires a previous installation of Conda (≥23.3.1), Mamba (≥1.3.1) or pip, plus the availability of any modern browser such as Chrome (≥v124.0.6367.62) or Firefox (≥v124.0.2). Once the user satisfies these requisites, they can install the components and dependencies trough the commands:\n\nOr:\n\nAs a result, the user can access the interactive dashboard by providing the path to the final_df.tsv file generated by MAGFlow through the following terminal command:\n\nThe argument -p is included to display BIgMAG on the port of the user preference. The default value is 8050. Once the command is run, the prompt output will indicate the IP direction the user must type on the browser or copy and paste onto it, i.e., http://127.0.0.1:8050/.\n\n\nResults\n\nWith the aim of demonstrating the usability of MAGFlow/BIgMAG, we used it to benchmark the MAG features recovered from a mock community (ATCC MSA-1003TM, Table 1) by 6 different pipelines, namely ATLAS, DATMA, MetaWRAP, MUFFIN, nf-core/mag and SnakeMAGs (Kieser et al., 2020; Benavides et al., 2020; Uritskiy et al., 2018; van Damme et al., 2021; Krakau et al., 2022; Tadrent et al., 2023). The selected pipelines were performed using short reads only (Illumina), except for MUFFIN which was tested for hybrid assembly (Illumina and PacBio). Additionally, in order to establish the same starting point for all the pipelines Megahit (Li et al., 2016) was set as assembly software, as well as MetaBAT2 (Kang et al., 2019) was selected as the binning tool, excluding DATMA since this workflow follows a different strategy to recover the MAGs that groups first the reads using a specific approach called CLAME (Benavides et al., 2018), to assemble them in batches afterwards.\n\nThe results obtained by MAGFlow and displayed by BIgMAG for this experiment highlight the different behavior the pipelines in their default implementation can depict even if they account with the same tools to assemble the reads and group the contigs. For instance, MetaWRAP and ATLAS show a higher dispersion in terms of the number of contigs assigned per bin (Figure 2a), whilst nf–core/mag depicted a higher proportion of MAGs with higher quality (completeness > 70% and contamination < 5%) (Figure 2b). Likewise, nf-core/mag and MetaWRAP exhibit a trend to produce more MAGs with duplicated SCO with at least 50% of complete SCO (Figure 2c). Another important aspect to consider to compare the pipeline performance is the Clade Separation Score (CSS) calculated by GUNC, a metric that indicates the level of taxonomical chimerism in each contig of a MAG, where MetaWRAP, ATLAS, nf–core/mag and SnakeMAGs show the highest consistency and correspondence between the MAGs passing the GUNC test and the CSS value (Figure 2d). Regarding the taxonomical annotation at species level, it is noticeable that DATMA is not as effective to recover the genomes from the mock community as the rest of the workflows, remaining the main proportion of these unannotated (Figure 2e). Also, MUFFIN outcomes indicate an enhancement in the recovery of less abundant genomes by performing a hybrid assembly with short and long read technologies, since species such as Acinetobacter baumannii, Cutibacterium acnes, Helicobacter pylori and Neisseria meningitidis were only detected by this pipeline; this improvement by achieved hybrid assemblies has been proved by Tao et al. (2023) and Liew et al. (2024).\n\nAs a result, the observations afore-mentioned contribute to the pipeline grouping displayed in the cluster heatmap, in which the metrics of the outcomes from MetaWRAP seem to be closer to the values obtained with ATLAS, and more dissimilar from the cluster that encompasses nf-core/mag and SnakeMAGs; MUFFIN and DATMA represent the most different workflows in regard to the quality features depicted by the MAGs assembled with these pipelines (Figure 2f).\n\nIn terms of performance, MAGFlow takes approximately 18 minutes to analyze the MAGs obtained from the mock community on an HPC cluster with 128 CPUs and 500 GB of available memory using the local executor and the default configuration that can be found on the file MAGFlow/conf/base.config at the repository (https://github.com/jeffe107/MAGFlow). Downloading the GTDB-Tk2 database can take up to 4 hours, while retrieving the GUNC database takes ~1 hour depending on the bandwidth of the user Internet network.\n\nIn order to show another example of the utility of MAGFlow/BIgMAG, we used nf–core/mag to recover MAGs from several public metagenomics datasets generated from different crop rhizospheres or soil including rice, wheat and maize (Table 1). Additionally, two modes of assembly and binning were considered, namely SASB as single assembly/single binning and CACB as co-assembly/co-binning. Considering the intensive computational demands by the co-assembly process, only Megahit was used as assembly software and MetaBAT2 as the binning tool, allowing the same experimental setting for both SASB and CACB modes. Besides, the raw reads were previously cleaned using fastp (Chen et al., 2018), and a host removal was performed with bowtie2 (Langmead & Salzberg, 2012), indexing the proper host genome according to the type of crop the samples were obtained from.\n\nAfterwards, the MAGs retrieved under each condition were used as input for MAGFlow/BIgMAG, and leveraging on these outcomes it is possible to notice how rice samples remarkably allowed to recover a higher number of MAGs, depicting greater quality in terms of percentage of complete SCO (Figure 3a), mainly for the CACB mode even though all the co-assemblies accounted with a similar number of reads (sequencing depth). This situation highlights how the sequencing depth is not the single factor affecting the assembly process and stresses the need to consider how additional conditions can influence the results such as the error rate of the sequencing method, the complexity of soil/rhizosphere samples, and the read length (Sims et al., 2014).\n\nThe names of the samples are represented by merging the origin of the sample (rice, wheat or maize) and the mode used by the pipeline to obtain the MAGs (SASB or CACB).\n\nMoreover, this application of MAGFlow/BIgMAG underlines the advantages CACB permits by increasing both the quality and the number of MAGs obtained per type of sample. This is supported by the obtention of more mid-quality MAGS (completeness > 50% and contamination < 10%) (Figure 3b), as well as by the higher proportion of annotated MAGs at genus levels for all soil/rhizosphere samples treated under CACB mode (Figure 3c). These observations can even lead to cluster samples assembled under CACB in the same group when they belong to different matrices (Figure 3d). Similar outcomes have been published by Vosloo et al. (2021) during experiments set with this type of operational mode, fixing metaSPAdes as assembler and MetaBAT2 as binning software.\n\n\nDiscussion\n\nThe strategy MAGFlow uses to perform the analysis attempts to follow the nf–core guidelines (P. A. Ewels et al., 2020), which allows robustness and reproducibility, and it has been tested using nf–test. This is supported by its Nextflow wrapping, along with its great performance features such as the possibility to run the software independently and in parallel, the chance to couple it to many other Nextflow modules or pipelines and the property to be scalable and adjusted to the available resources on the system user (Di Tommaso et al., 2017). MAGFlow can also be implemented through a wide variety of profiles such as Conda, Mamba, Docker, Singularity and Apptainer, which increases the scope of suitable systems to execute it. In addition, the pipeline can be launched in local environments, HPC clusters featuring executors as SLURM or SGE, or cloud–based solutions such as Azure Batch or AWS Batch (native Nextflow functionality not tested for MAGFlow).\n\nWhen writing this report, there is another specific workflow aiming to run multiple tools to measure the quality of metagenomes called GENcontams.nf, which is part of the GEN–ERA toolbox (Cornet et al., 2022). Among the advantages of this package, we can enumerate the inclusion of tools that MAGFlow currently lacks, such as Physeter, Kraken2 and EukCC, the wide control the user can apply over the parameters to run the software, as well as the integration with the GEN–ERA suite. Nonetheless, GENcontams.nf is written under Nextflow DSL1, which is no longer supported by the developers, it does not incorporate a visualization module, and it is not modularized, meaning that all of the analysis are performed in a single script, increasing the likely to fail, and limiting the possibility to couple it to other Nextflow pipelines. Besides, GENcontams.nf does not perform the taxonomical annotation with GTDB-Tk2, leaving this task to a different module within the GEN–ERA toolbox.\n\nOn the other hand, in terms of visualization and portability of the plots, MultiQC (Ewels et al., 2016) is the top–of–the–notch application that has eased the process of output integration from several pieces of software; however, out of the tools implemented in MAGFlow, MultiQC only accounts with support for QUAST and BUSCO data obtained from their execution elsewhere.\n\nMAGFlow/BIgMAG attempts to fulfil these limitations in the field of metagenomics data analysis given the reproducibility and scalability of its workflow to assess the quality of the MAGs, the complementary functionalities it includes varying from taxonomic classification to assembly metrics passing through structural integrity, the easiness to analyze as many MAG folders as the user decides and the modularization to enclose the software tools in separate Nextflow modules. Furthermore, BIgMAG complements MAGFlow by generating high-quality automatic plots for all the encompassed tools, allowing a high degree of interactivity and customization according to the user needs. As a result, MAGFlow/BIgMAG represents a unique tool to our knowledge that integrates the execution of the software with a visualization module to extract MAG quality information and taxonomical features, making it interestingly useful when targeting comparisons among different metagenomics pipelines or tools to bin contigs. Also, MAGFlow/BIgMAG provides a convenient support during exploratory analyses that involve establishing general differences across samples as we showed with the examples presented in this paper.\n\nFinally, following the principle of divide–and–rule proposed by Lupo et al. (2021), which suggests that genome quality and contamination should be assessed with as many different tools as possible, MAGFlow/BIgMAG scope will be continuously expanded through the inclusion of additional new tools, such as Kraken2, Physeter, EukCC, among others.", "appendix": "Data availability\n\nThe raw sequencing data to test MAGFlow/BIgMAG were retrieved from the Sequence Read Archive (SRA), and they can be accessed through the following identifiers:\n\nSequence Read Archive: NextSeq500 of rice rhizosphere soil: Francis booting rep1. Accession number SRR12687830; https://www.ncbi.nlm.nih.gov/sra/?term=SRR12687830 (Fernández-Baca et al., 2021).\n\nSequence Read Archive: NextSeq500 of rice rhizosphere soil: Francis booting rep2. Accession number SRR12687829; https://www.ncbi.nlm.nih.gov/sra/?term=SRR12687829 (Fernández-Baca et al., 2021).\n\nSequence Read Archive: NextSeq500 of rice rhizosphere soil: Francis booting rep3. Accession number SRR12687818; https://www.ncbi.nlm.nih.gov/sra/?term=SRR12687818 (Fernández-Baca et al., 2021).\n\nSequence Read Archive: AAFC-Pcyc_02A_Pos1_Plot18_noN_noP_2016-08. Accession number SRR7013867; https://www.ncbi.nlm.nih.gov/sra/?term=SRR7013867 (Li et al., 2020).\n\nSequence Read Archive: AAFC-Pcyc_12A_Pos1_Plot73_noN_noP_2016-08. Accession number SRR7013874; https://www.ncbi.nlm.nih.gov/sra/?term=SRR7013874 (Li et al., 2020).\n\nSequence Read Archive: Rhizosphere soil 1. Accession number SRR12192850; https://www.ncbi.nlm.nih.gov/sra/?term=SRR12192850 (Akinola et al., 2021).\n\nSequence Read Archive: Rhizosphere soil 2. Accession number SRR12192849; https://www.ncbi.nlm.nih.gov/sra/?term=SRR12192849 (Akinola et al., 2021).\n\nSequence Read Archive: Rhizosphere soil 3. Accession number SRR12192848; https://www.ncbi.nlm.nih.gov/sra/?term=SRR12192848 (Akinola et al., 2021).\n\nSequence Read Archive: Metagenome_ID964_ATCC. Accession number SRR8359173; https://www.ncbi.nlm.nih.gov/sra/?term=SRR8359173 (Portik et al., 2022).\n\nSequence Read Archive: WGS of ATCC MSA-1003 Mock Microbial Community with PacBio CCS on the Sequel II System. Accession number SRR9328980; https://www.ncbi.nlm.nih.gov/sra/?term=SRR9328980 (Portik et al., 2022).\n\nThe bash scripts with all required configurations to run each pipeline as we performed in this paper, the MAGs recovered by each pipeline using the mock community or soil/rhizosphere samples, as well as the outputs generated by MAGFlow/BIgMAG during the analysis of these MAGs have been made available in a Zenodo repository.\n\nZenodo: Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG (Sup. Material). https://doi.org/10.5281/zenodo.11003957.\n\nThis project contains the following underlying data:\n\n• The recovered MAGs by 6 different metagenomics pipelines (ATLAS, DATMA, MetaWRAP, MUFFIN, nf-core/mag and SnakeMAGs) using a mock community as input (SRR8359173 and SRR9328980), complemented with the output from MAGFlow using these MAGs as input for their quality assessment and taxonomical annotation.\n\n• The MAGs produced by nf-core/mag using rice/rhizosphere sequenced libraries (PRJNA663614, PRJNA448773 and PRJNA645385) in either single assembly/single binning or co-assembly/co-binning mode, complemented with the output from MAGFlow using these MAGs as input for their quality assessment and taxonomical annotation.\n\n• Scripts, commands and configuration files to run the different pipelines (ATLAS, DATMA, MetaWRAP, MUFFIN, nf-core/mag and SnakeMAGs) and reproduce the experimental conditions.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nMAGFlow/BIgMAG is being developed under the support of the Federal Commission for Scholarships for Foreign Students (FCS) through the program Swiss Government Excellence Scholarships.\n\n\nReferences\n\nAkinola SA, Ayangbenro AS, Babalola OO: Metagenomic insight into the community structure of maize-rhizosphere bacteria as predicted by different environmental factors and their functioning within plant proximity. Microorganisms. 2021; 9(7): 1419. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBayer K, Busch K, Kenchington E, et al.: Microbial Strategies for Survival in the Glass Sponge Vazella pourtalesii. MSystems. 2020; 5(4): e00473–e00420. Publisher Full Text\n\nBenavides A, Isaza JP, Niño-García JP, et al.: CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes. BMC Genomics. 2018; 19(Suppl 8): 858. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBenavides A, Sanchez F, Alzate JF, et al.: DATMA: Distributed Automatic Metagenomic Assembly and annotation framework. PeerJ. 2020; 8: e9762. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaumeil P-A, Mussig AJ, Hugenholtz P, et al.: GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics. 2022; 38(23): 5315–5316. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen S, Zhou Y, Chen Y, et al.: fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34(17): i884–i890. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChklovski A, Parks DH, Woodcroft BJ, et al.: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat. Methods. 2023; 20(8): 1203–1212. PubMed Abstract \| Publisher Full Text\n\nCornet L, Baurain D: Contamination detection in genomic data: more is not enough. Genome Biol. 2022; 23(1): 1–15. Publisher Full Text\n\nCornet L, Durieu B, Baert F, et al.: The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics. GigaScience. 2022; 12: 1–10. Publisher Full Text\n\nDi Tommaso P, Chatzou M, Floden EW, et al.: Nextflow enables reproducible computational workflows. Nat. Biotechnol. 2017; 35(4): 316–319. PubMed Abstract \| Publisher Full Text\n\nEwels PA, Peltzer A, Fillinger S, et al.: The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 2020; 38(3): 276–278. PubMed Abstract \| Publisher Full Text\n\nEwels P, Magnusson M, Lundin S, et al.: MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016; 32(19): 3047–3048. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFernández-Baca CP, Rivers AR, Kim W, et al.: Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes. Soil Biol. Biochem. 2021; 156: 108233. Publisher Full Text\n\nGurevich A, Saveliev V, Vyahhi N, et al.: QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29(8): 1072–1075. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuseva K, Darcy S, Simon E, et al.: From diversity to complexity: Microbial networks in soils. Soil Biol. Biochem. 2022; 169: 108604. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHaryono MAS, Law YY, Arumugam K, et al.: Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling. Front. Microbiol. 2022; 13: 869135. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKang DD, Li F, Kirton E, et al.: MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019; 7: e7359. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKieser S, Brown J, Zdobnov EM, et al.: ATLAS: A Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. BMC Bioinformatics. 2020; 21(1): 1–8. Publisher Full Text\n\nKrakau S, Straub D, Gourlé H, et al.: nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning. NAR Genom. Bioinform. 2022; 4(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLangmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012; 9(4): 357–359. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLetunic I, Bork P: Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021; 49(W1): W293–W296. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi D, Luo R, Liu CM, et al.: MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016; 102: 3–11. PubMed Abstract \| Publisher Full Text\n\nLi Y, Tremblay J, Bainard LD, et al.: Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production. Environ. Microbiol. 2020; 22(3): 1066–1088. PubMed Abstract \| Publisher Full Text\n\nLiew KJ, Shahar S, Shamsir MS, et al.: Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation. Environ. Microbiome. 2024; 19(1): 1–20. Publisher Full Text\n\nLupo V, Van Vlierberghe M, Vanderschuren H, et al.: Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics. Front. Microbiol. 2021; 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nManni M, Berkeley MR, Seppey M, et al.: BUSCO: Assessing Genomic Data Quality and Beyond. Curr. Protoc. 2021; 1(12): e323. PubMed Abstract \| Publisher Full Text\n\nOrakov A, Fullam A, Coelho LP, et al.: GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 2021; 22(1): 1–19. Publisher Full Text\n\nPortik DM, Brown CT, Pierce-Ward NT: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets. BMC Bioinformatics. 2022; 23(1): 1–39. Publisher Full Text\n\nSims D, Sudbery I, Ilott NE, et al.: Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet. 2014; 15(2): 121–132. PubMed Abstract \| Publisher Full Text\n\nTadrent N, Dedeine F, Hervé V, et al.: SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes. F1000Res. 2023; 11: 1522. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTao Y, Xun F, Zhao C, et al.: Improved Assembly of Metagenome-Assembled Genomes and Viruses in Tibetan Saline Lake Sediment by HiFi Metagenomic Sequencing. Microbiology Spectrum. 2023; 11(1): 1–18. Publisher Full Text\n\nTremblay J, Schreiber L, Greer CW: High-resolution shotgun metagenomics: the more data, the better? Brief. Bioinform. 2022; 23(6): 1–16. Publisher Full Text\n\nUritskiy GV, Diruggiero J, Taylor J: MetaWRAP - A flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018; 6(1): 1–13. Publisher Full Text\n\nvan Damme R , Hölzer M, Viehweger A, et al.: Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PLoS Comput. Biol. 2021; 17(2): 1–13.\n\nVosloo S, Huo L, Anderson CL, et al.: Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes. Microbiol. Spectr. 2021; 9(3): e0143421. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWratten L, Wilm A, Göke J: Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nat. Methods. 2021; 18(10): 1161–1168. PubMed Abstract \| Publisher Full Text\n\nYang C, Chowdhury D, Zhang Z, et al.: A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Comput. Struct. Biotechnol. J. 2021; 19: 6301–6314. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "300031", "date": "18 Jul 2024", "name": "Abraham Gihawi", "expertise": [ "Reviewer Expertise microbial bioinformatics and metagenomics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nJeferyd Yepes-García and Laurent Falquet present the article entitled: \"Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG\". This article describes two pieces of software. Firstly MAGFlow, which is concerned with the quality control and taxonomy of contigs. Secondly BIgMAG presents a solution to visualising these results.\nOverall the pipeline is similar to others available, but could still offer considerable use to the community if it is a well written and a well maintained piece of software. Care needs to be taken in the manuscript, particularly with results that points are backed up by figures and statistical tests.\nDespite investing a significant amount of time trying, I have not been able to get the pipeline to run. Every time it seems to be a different error arising.\nThe MAGflow software doesn't seem to work with my own gtdb-tk v2 database. The tool seems to want to re-download it despite giving it a valid absolute file path, it raised an error in downloading the database. I updated line 6 ((gtdbtk2_download_db.sh) to \"wget https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/auxillary_files/gtdbtk_package/full_package/gtdbtk_data.tar.gz\". Despite this, I still couldn't get the GTDB-tk step to run. Separately, there seem to be a range of other bugs that keep cropping up and I invested a significant amount of time to try and resolve each one. Having been unable to resolve all of them I am raising it in this review that I recommend that the authors carry out some additional user testing of the software. I am using the singularity profile on a linux based computing environment and launching it with:\n\"nextflow run MAGFlow/main.nf -profile singularity --files 'samples/' --outdir /path/to/magflow_test/mag_output -qs 1\"\nResulting Error: \" ERROR ~ Error executing process > 'MAGFlow:BUSCO (XXXXXXXX)'\nCaused by:\n\nProcess `MAGFlow:BUSCO (XXXXXXXX)` terminated with an error exit status (1)\nCommand executed:\n\nbusco -i XXXXXXXX\n\n-o busco\n\n-m genome -c 8 --force\n\n-l bacteria_odb10\n\ncat <<-END_VERSIONS > versions.yml\n\n\"MAGFlow:BUSCO\":\n\nbusco: $( busco --version 2>&1 \| sed 's/^BUSCO //' )\n\nEND_VERSIONS\nCommand exit status:\n\n1\nCommand output:\n\nthis version of pandas is incompatible with numpy < 1.17.3\n\nyour numpy version is 1.16.4.\n\nPlease upgrade numpy to >= 1.17.3 to use this pandas version\n\nThere was a problem installing BUSCO or importing one of its dependencies. See the user guide and the GitLab issue board (https://gitlab.com/ez$\nCommand error:\n\nthis version of pandas is incompatible with numpy < 1.17.3\n\nyour numpy version is 1.16.4.\n\nPlease upgrade numpy to >= 1.17.3 to use this pandas version\n\nThere was a problem installing BUSCO or importing one of its dependencies. See the user guide and the GitLab issue board (https://gitlab.com/ez$ \"\nAs I could not carry out the first step, I was unable to test BIgMAG. I have also included some suggestions for the manuscript below.\n\nSuggestions:\n- \"high-quality MAGs depict levels of contamination below 5% and completeness above 90%\" - I feel it would be appropriate to cite Bowers et al. here that established the MIMAG standards - https://doi.org/10.1038/nbt.3893\n\n- \"Nevertheless, many pipelines or methodologies only include one or two tools to measure the quality of the MAGs\" - then cite Krakau et al. 2022 [Ref-1]- This tool has several evaluation tools including the ones that this proposed pipeline offers - GTDB-tk, BUSCO, CheckM, GUNC, QUAST. This is more than 'one or two tools' to measure MAG quality. Similarly, Tadrent et al. details CheckM, GUNC, GTDB-Tk and CoverM which is also more than 'one or two tools'. The text would benefit from expanding upon these tools and state clearly how the work of the authors distinguishes from these. Is it purely the additional visualisation that the authors provide?\n- It has been shown that single sample metagenome assembly can cause extensive hidden contamination. Mattock J, et al., 2023 [Ref-2] - How does the pipeline proposed by the authors handle or investigate this?\n- \"Following the GTDB-Tk2 plot, as an attempt to compare the features among samples and cluster them according to their similarity using different parameters provided by BUSCO, CheckM2, GUNC and/or GTDB-Tk2, a cluster heatmap is displayed. To render this plot, average values are used, combined with the proportion of MAGs passing the GUNC test and/or the proportion of annotated MAGs by GTDB-Tk2\" - Perhaps it's just me. I find this paragraph unclear at describing what exactly is being compared. Are you comparing the completeness/quality for the same features? Does this cluster the samples, or the features?\nOverall, the results need values and statistical tests to support the claims that the authors are making. A few examples are in the points below.\n- \"For instance, MetaWRAP and ATLAS show a higher dispersion in terms of the number of contigs assigned per bin (Figure 2a)\" - This sentence indicates that MetaWRAP and Atlas demonstrate a higher variation in terms of the number of contigs compared to all other tools. Looking at the plot, this might not be entirely true. SnakeMAGS and nf_core_mag also seem similar. This statement should be backed up with values and statistical tests.\n- Similarly the following sentence should be backed up by values and statistics: \"whilst nf core/mag depicted a higher proportion of MAGs with higher quality (completeness > 70% and contamination < 5%) (Figure 2b).\". Currently, this can not be interpreted from the plot. This should also be considered for sentence afterwards: \"Likewise, nf-core/mag and MetaWRAP exhibit a trend to produce moreMAGswith duplicated SCO with at least 50% of complete SCO\".\n- \"where MetaWRAP, ATLAS, nf – core/mag and SnakeMAGs show the highest consistency and correspondence between the MAGs passing the GUNC test and the CSS value (Figure 2d).\" - What do the authors mean by this? Surely it would be preferably to compare the number of results passing/failing the GUNC filter? This graph currently could suggest that more contigs are failing chimerism checks than passing?\n- \"increasing the likely to fail\" - Revise grammar. Additionally I don't necessarily know if something is more likely to fail because it's written in a single script. Can the authors expand on this point or back it up?\n- \"MultiQC is the top of the notch application\" - The grammar here needs revising and also it reads as quite informal for a manuscript. What do the authors mean by 'top of the notch'? highly cited? highly used? There is no context to this statement.\n- \"making it interestingly useful when\" - revise grammar\n- Methods: Thank you to the authors for uploading code on Zenodo repositories. As a minor suggestion, it might be nice for reproducibility purposes if the authors state what version of each tool they used in their analysis.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "12351", "date": "23 Sep 2024", "name": "Jeferyd Yepes", "role": "Author Response", "response": "Dear Dr. Abrahm Gihawi, We appreciate the time you took to review our manuscript and tool, and we are grateful for the valuable comments and suggestions you provided us. Please find below our answers to each of them in the same order you stated your comment/suggestion: Response 1: Dear reviewer, the link from which the database is downloaded was broken; it was corrected, and it is working properly now. We apology for the inconvenience. In addition, we would like to share with you a small but important detail when providing different versions of GTDB to MAGFlow using the parameter --gtdbtk2_db: Notice that when you untar any GTDB dabatase, it is stored under the name release; please keep the word release in the name to guarantee a proper detection by the pipeline. This and other important tips are given in the README file of the pipeline (https://github.com/jeffe107/MAGFlow). Response 2: Dear reviewer, to ensure the functionality of the pipeline, we carried out several tests of MAGFlow under the following settings: Rocky Linux version 8.10 with profiles Apptainer and Mamba. WSL running with Ubuntu 22.04.4 with profiles Singularity, Docker and Mamba. Within these environments the pipeline worked appropriately using the recommended versions of Java and Nextflow in the manuscript. Also, the versions of the profile software in which MAGFlow was tested is now indicated in the new version of the manuscript. Response 3: The error related to pandas and Numpy incompatibility is quite rare since the pipeline runs under either containerized versions of the software or Conda/Mamba environments to ensure precisely that this kind of errors does not happen. From what we could tell, it may be possible that in your system there is an available version of BUSCO and hence the pipeline is crashing by trying to use that version which is incompatible. As we stated previously, we tested in different environments and profiles, and the pipeline worked properly. Response 4: We appreciate your suggestion, and we included this reference in the new version of the manuscript. Response 5: Indeed, the mentioned pipelines have evolved throughout time to include more tools and not only one or two. This statement has been changed in the manuscript the demonstrate that the power of our tool relies in the practical integration with a dashboard and the possibility it offers to compare the output from different pipelines or binning software. The mentioned pipelines, nf-core/mag, ATLAS and others, include these tools to measure the quality of the obtained bins, but they are available only if running the entire workflow. We have highlighted this advantage of our approach in the text as well. Response 6: The challenge researchers face when building bins from assemblies of metagenome samples has been pointed out widely, and in general terms, it has been advised to carry out a co-assembly/co-binning of the samples. Our tool MAGFlow/BIgMAG can help during the investigation of MAG hidden contamination by offering quality metrics and comparisons among tools run under different binning settings. For instance, we carried out a comparison using MAGFlow/BIgMAG among two different settings to reconstruct the MAGs: single-assembly/single-binning and co-assembly/co-binning for soil-associated samples. This utility of MAGFlow/BIgMAG has been highlighted in the discussion of the manuscript. Response 7: We thank the reviewer for this comment. This paragraph has been modified to clarify the purpose of the plot. The cluster heatmap attempts to show how similar or dissimilar the samples are using as many features as possible from CheckM2, BUSCO, GUNC and if performed, GTDB-Tk2. Response 8: Dear reviewer, to backup this and other statements in regard to the outcomes of our experiments, we have added the result of a Welch ANOVA to the plot that shows the QUAST metrics distribution. This test helps to detect if there are significant variations in at least one of the samples, and it was chosen because it might be possible that the user does not account with the same sample size for all of their samples. This aspect has been also included and discussed in the new version of the manuscript. Response 9: We acknowledge the reviewer for this comment, and we have reformulated our analysis of the benchmarking among pipelines by modifying this and other statements according to the new version of BIgMAG, in which we carried out a statistical analysis using features such as Number of bins, Number of unique annotated bins, Number of mid-quality MAGs, Number of high-quality MAGs and the Number of bins passing GUNC. As a result, the dashboard now accounts with a Summary section to display the results of a Kruskal-Wallis test and a Duncan test. In addition, BIgMAG is mainly thought to be an exploratory analysis tool that can assist the researchers in identifying important aspects to consider from their samples, highlighting features that can be further studied. Response 10: The GUNC plot attempts to show the distribution of the selected parameter for each sample, discriminated by bins that passed or failed the GUNC filter. In the case of the Clade Separation Score (CSS), it can be noticed that in general terms for the bins that did not pass the filter, the CSS presented a higher dispersion and non-uniform distributions compared to the bins that passed the filter. The percentage of bins passing/failing the test can be visualized in the new plot included at the Summary dashboard. This graph does not suggest that more contigs are failing/passing the test, it only tries to show the distribution of the CSS parameter according to the bins that failed/passed the test. Response 11: We acknowledge the reviewer for this suggestion, and therefore the phrase was modified to: “This single-script configuration increases the difficulty to track and monitor the pipeline execution, disables the feature to resume the pipeline given the lack of checkpoints, and limits the possibility to couple it to nf–core pipelines”. Response 12: The phrase was modified to: “MultiQC represents the most used and widespread visualization tool, commonly included many metagenomics pipelines”. Response 13: The phrase was modified to: “…featuring MAGFlow/BIgMAG as a helpful piece of software when…” Response 14: The authors have modified the manuscript to depict the version used for the analysis in the manuscript. Finally, we kindly invite you to review our paper after applying the discussed changes. In addition, in case of persisting inconveniences with the tool, please open an issue on the github repository." } ] }, { "id": "300036", "date": "29 Jul 2024", "name": "Fotis Baltoumas", "expertise": [ "Reviewer Expertise Bioinformatics", "metagenomics", "sequence analysis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article by Yepes-Garcia and Falquet, titled \"Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG\" presents a new, nextflow-based pipeline for the analysis and assessment of MAGs.\nAlthough a number of similar workflows exist, I believe MAGflow/BIgMAG to be a welcome addition, especially since their combination seems to offer a number of visualization and analysis schemes not available by other solutions.\nThe manuscript is well-written and in good English. The methodology, case studies, and discussion are presented in adequate detail, including statistical analysis and interpretation. Overall, the presentation of the workflow is sound.\nHowever, I do have one major point that needs to be addressed, before I can consider the manuscript to be 100% acceptable for MEDLINE indexing:\nI was not able to initiate and run the MAGflow workflow, even the test runs. The reason for this is that at least some of the dependencies of the workflow either don't exist anymore, at least publicly or their name/version/installation method has been updated. For example, this happens with the \"biocontainers/checkm2\" dependency. I have tried to test MAGflow using conda, mamba AND docker, and in ALL 3 cases, the workflow fails saying that the aforementioned package either doesn't exist or it is not publicly available.\n(specifically, docker gives the following error report:\nCommand error:\n\nUnable to find image 'biocontainers/checkm2:1.0.1--pyh7cba7a3_0'\n\ndocker: Error response from daemon: pull access denied for biocontainers/checkm2, repository does not exist or may require 'docker login': denied: requested access to the resource is denied. )\nI have tried to run this in 3 different machines, all of which have run other nextflow pipelines successfully, and all of which have conda/mamba and docker installations that work as intended. The authors need to update the dependencies and setup scripts of their pipeline, and make sure that:\n1. it depends solely on publicly available dependencies. If something is proprietary or requires access to be provided by the authors of the package, it should be stated explicitly. Can be run successfully, without any troubleshooting required by the end user.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "12352", "date": "23 Sep 2024", "name": "Jeferyd Yepes", "role": "Author Response", "response": "Dear Dr. Fotis Baltoumas, We appreciate the time you took to review our manuscript and tool, and we are grateful for the valuable comments and suggestions you provided us. We are sorry that you didn’t manage to run MAGFlow. For this reason, we carried out many more tests of MAGFlow under the following settings: Rocky Linux version 8.10 with profiles Apptainer and Mamba. WSL running with Ubuntu 22.04.4 with profiles Singularity, Docker, and Mamba. Within these environments the pipeline worked appropriately using the recommended versions of Java and Nextflow in the manuscript. Also, the versions of the profile software in which MAGFlow was tested is now indicated in the new version of the manuscript. Finally, we kindly invite you to review our paper after applying the discussed changes. In addition, in case of persisting inconveniences with the tool, please open an issue on the github repository." } ] }, { "id": "300029", "date": "31 Jul 2024", "name": "Juliette Hayer", "expertise": [ "Reviewer Expertise Bioinformatics", "Metagenomics", "Bacterial genomics", "Antimicrobial 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\nThe authors present a new and very useful workflow, MAGFlow, coupled with a visualization tool (BIgMAG) for assessing the quality of Metagenome Assembled Genomes (MAGs). These tools allow not only to assess the quality of the MAGs by combining several metrics including the completeness and the contamination rate, but also to assign the taxonomy of the MAGs using the latest GTDB-Tk2. In the manuscript, the authors also show the utility of MAGFlow and BIgMAG for comparing various workflows for MAG reconstruction, but also various strategies of assembly and binning for metagenomes.\nThe workflow seems well designed and makes use of nf-core modules, which highly valuable. The way it is coded and the use of Nextflow and containers for the different processes makes the analyses performed with this workflow scalable and reproducible.\nMy comments are below, organised by section.\nIntroduction: I think that another similar tool exists in Anvi'o, maybe the authors could add some words about it.\nMethods: I think the fact that several different kind of inputs can be used for MAGFlow is great, therefore it is not clear if the user should input bins or assemblies (paragraph 3 in the Methods for MAGFlow => assembly/binning). What would happen if the user provides the assembly without binning step? Please clarify about the different inputs.\nRegarding the Methods section for BIgMAG, the sentence: \"To process the outcomes from GTDB-Tk2, BIgMAG generates a presence/absence matrix representation of annotated taxa at the taxonomical level specified by the user, in a novel strategy to extract the core data without showing the complete phylogeny of the annotated MAGs.\" I would appreciate if the authors could provide more details about the \"novel strategy to extract the core data without showing the complete phylogeny\".\nResults: I am wondering why only MUFFIN was tested for hybrid assembly, while nf-core/mag can also do it?\nI think it would bring interesting information to also compare the binning from different binning tools in the same pipeline (ex: nf-core/mag). Also, have the authors considered comparing the results obtained from binning refinement methods like DAStool (now included in nf-core/mag), which can refine bins from different binning methods on the same datasets. I think it would bring even more interesting data to provide the community, using MAGFlow and BIgMAG to show it's utility. Maybe something to include for the comparison presented in Fig3?\nFig2. I think the legend for c) and d) are inverted.\nRegarding BIgMAG and the plot displayed on Figure 2 e): I think that the presence/absence matrix would benefit from removing the black lines that are misleading (ex. DATMA has the line going over absent taxa that are in grey...). The dots are sufficient in my opinion.\nFor the crop MAGs comparison with nf-core/mag (fig3), it might be useful to provide the accession numbers of the reference genomes used for mapping out the host genome reads (reproducibility).\nMinor comments on the Discussion: Paragraph2 - sentence 1: a word is probably missing, the sentence is unclear, please rephrase. Paragraph4 - sentence 1 is too long and unclear. The authors should break in several sentences and clarify.\nA last question: would the authors consider adapting MAGFlow/BIgMAG for an integration directly with nf-core/mag for example? if the developers are up for it of course.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? 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? Yes", "responses": [ { "c_id": "12353", "date": "23 Sep 2024", "name": "Jeferyd Yepes", "role": "Author Response", "response": "Dear Dr. Juliette Hayer, We appreciate the time you took to review our manuscript and tool, and we are grateful for the valuable comments and suggestions you provided us. Please find below our answers to each of them in the same order you stated your comment/suggestion: Response 1: The authors have noticed the power and utility of anvi’o for a wide variety of analysis in the metagenomics field. Nonetheless, anvi’o does not account with workflow nor artifact to carry out the quality measurement of bins or MAGs since anvi’o current metagenomics workflow does not include binning software. Therefore, MAGFlow/BIgMAG wouldn’t be useful to process contigs artifacts from the anvi’o suite. Response 2: The design and purpose of BIgMAG and MAGFlow is the analysis of bins or MAGs obtained after different pipelines or binning software. Eventually, files with assemblies can used as input (in essence they are the same type of file), albeit software such as CheckM2, BUSCO or GUNC are designed to analyze “ideally” one single genome at a time. As a result, and since an assembly is a mixture of multiple genomes, the calculated contaminated portion of the input files would be over-represented, and the values of completeness and contig heterogeneity would lead to erroneous conclusions based on false estimations. The text was modified to clearly state that the input for MAGFlow is genomic files of the MAGs. Response 3: Traditionally, to visualize the output from GTDB-Tk2, the researchers use tools such as iTOL or TreeViewer in which a work of branch collapsing should be carried out to reach the desired plot that depicts the phylogeny and annotation of the input genomes. In the case of BIgMAG, the output from GTDB-Tk2 is handled in the sense of processing only the annotation of the input genomes (the .tsv summary) and not using the entire phylogeny, this is translated into a matrix of presence/absence at the taxonomical level selected by the user. Consequently, we consider that this strategy allows for a cleaner view of the taxonomy across samples. Response 4: Indeed, nf-core/mag is able as well to perform hybrid assembly. In order to complement the scope of our comparison, we tested nf-core/mag performing a hybrid assembly of the mock community. Therefore, the manuscript result section was modified to include these outcomes. Response 5: Precisely, among the advantages of MAGFlow/BIgMAG is to compare different binning tools in terms of their performance to provide more complete and less contaminated bins. To expand this utility, we have performed a comparison among MetaBAT2, SemiBin and Metabinner using the same assembly. The results from this comparison are now included in the new version of the manuscript. Response 6: We thank the reviewer for spotting this inversion. It has been reviewed and corrected for the new version of the manuscript. Response 7: In some cases, the line connecting the dots can be misleading when the length of the list of the taxonomical group is short. Nonetheless, when the users have a long list of taxonomical groups, i.e., genus, the plot is depicted quite compacted in the default state, and the user has to use the sliding window, the line shows that there is still genus present in a specific sample. Response 8: We acknowledge the reviewer for this suggestion, and hence the manuscript has been modified to include this accession numbers. Response 9: We modified that sentence to provide more clarity to the reader. Response 10: We thank the reviewer for the comment, and we modified this specific sentence to provide more clarity to the reader. Response 11: We have considered the integration with nf-core/mag since our pipeline is Nextflow based and we attempt to follow the nf-core guidelines. In this sense, we would be interested in integrating our tool by developing a parallel application (similar to our app_lite.py script implementation) to maintain the possibility for the user to run MAGFlow/BIgMAG separately from nf-core/mag to analyze the outcomes from different pipelines or binning software, and not force them to use only nf-core/mag. As a result, we could develop an nf-core module able to process the output from nf-core/mag to generate a single dashboard html file displaying the plots and metrics calculated by the pipeline." } ] } ]	1	https://f1000research.com/articles/13-640
https://f1000research.com/articles/13-275/v1	15 Apr 24	{ "type": "Research Article", "title": "Effect of ethanol extract of nigella sativa L seeds and propofol on BDNF protein level as neuroplasticity and neuroprotection of traumatic brain injury in rats", "authors": [ "Kulsum Kulsum", "Syahrul Syahrul", "Kartini Hasbalah", "Ummu Balqis", "Kulsum Kulsum", "Kartini Hasbalah", "Ummu Balqis" ], "abstract": "Background Traumatic brain injury (TBI) is a change in brain function or evidence of brain pathology caused by external mechanical forces. Brain Derived Neurotrophic Factor (BDNF) is a neurotropin that functions as a neuron protective. Nigella sativa L is reported to have an antioxidant effect, administration of Nigella Sativa L to rats treated with ischemia-reperfusion brain injury. Propofol is an anesthetic agent frequently used intravenously in the management of TBI. The effect of propofol on brain tissue after TBI may be neuroprotective. We aimed to compare the potential of Nigella sativa L and propofol as neuroplasticity and neuroprotection in rats with TBI.\n\nMethods This was a laboratory experimental animal model with the post-test only control group design, namely measuring the effect of treatment by comparing the five groups of rats consisting of 30 rats. BDNF levels in rat brain tissue were collected at day 7 of treatment and measured by ELISA.\n\nResults The average BDNF protein levels per group, namely G1 (221,243 pg/mL), G2 (172,139 pg/mL), G3 (255,483 pg/mL), G4 (227,089 pg/mL), and G5 (272,603 pg/mL) respectively. Based on the ANOVA statistic, p-value = 0.032 (there was a significant difference between groups), with the Levene Test (0.077) or having variance between the same groups, sequentially the difference in average BDNF protein levels of the five groups is G5>G3>G4>G1>G2, meaning that the combination of Nigella sativa and propofol has more potential to increase BDNF protein levels than Nigella sativa, and Nigella sativa has more potential than propofol.\n\nConclusion We concluded that both nigella sativa and propofol have the potential to increase BDNF protein levels. Nigella Sativa L had a better effect than propofol in repairing damaged neuron cells (neuroplasticity) and increasing BDNF protein levels (neuroprotection) for 7 days of administration in rat traumatic brain injury.", "keywords": [ "BDNF", "Nigella Sativa L", "Propofol", "Traumatic brain injury" ], "content": "Introduction\n\nIn the community, there are health problems such as traumatic brain injury (TBI) causing neurocognitive and psychological disorders such as impaired attention, inability to form visuospatial associations, poor executive function, and depression1,2 A total of sixty-nine million (95% Confidence Interval (CI) 64-74 million) people are estimated to experience TBI every year worldwide. The highest proportion of TBI due to traffic accidents occurred in Southeast Asia and Africa (both around 56%) and the lowest in North America (25%). The incidence of TBI is also highest in Southeast Asia (1.5% of the population per year) and Europe (1.2%). The overall incidence of TBI per 100,000 people is highest in North America and Europe with 1299 cases in America and 1012 cases in Europe and the least in the Eastern Mediterranean (897 cases) and Africa (801 cases).3\n\nBrain Derived Neurotrophic Factor (BDNF) is a neurotropin that is useful as a neuroprotective. BDNF is an important molecule in brain plasticity. The increase in BDNF is related to the progress of improvement in nerve function. However, after ischemia of the brain injury occurs, BDNF will decrease either spontaneously or by induction of rehabilitation so that neuroplasticity or repair of nerve cell function will change.4,5 The central and peripheral nervous systems are the working areas of BDNF. BDNF also stimulates the growth of new neurons and their ability to survive. The hippocampus, cortex, and frontal lobe in the base of the brain are where BDNF works actively.4–7\n\nNigella sativa oil is reported to have antioxidant, antihistamine, anti-inflammatory, immunomodulatory, antitussive, antidiabetic, antihypertensive, antipyretic, analgesic, anticancer, and antimicrobial effects.8–14 Protecting nerve cells from damage due to disease processes or chemicals has also been widely reported.15–18 In a study conducted by Zadeh et al., Nigella sativa significantly increased BDNF levels in depressed patients. This study indicates the importance of administering Nigella sativa to cure depression. This study was statistically significant comparing Nigella sativa with placebo. In this study, decreased BDNF increased the risk of Alzheimer’s disease, stress, depression, and anxiety. There have been many reports that state BDNF levels can be a predictor of a neuropsychiatric disease.7 BDNF functions as a growth and development protein in the central nervous system and peripheral nervous system and is very active in the hippocampus and parts of the brain cortex.7–9\n\nThe results of a study by Hosseinzadeh et al., stated that administration of Nigella sativa L oil to rats treated with ischemia-reperfusion brain injury in the hippocampus. The active ingredient of Nigella sativa L oil is thymoquinone. Timoquinone, the main constituent of essential oil from Nigella sativa seeds, is reported to have antioxidant properties that can increase protection and resistance to oxidative stress.18 Another study from Abbasnezhad et al. stated that thymoquinone as an antioxidant can significantly reduce oxidative stress which damages hippocampal neurogenesis. A previous study has been conducted on Nigella Sativa L as a potential antioxidant because its chemical compounds have the potential to be effective in capturing OH radicals during non-enzymatic lipid peroxidation and deoxyribose degradation.12\n\nPropofol is a fast-acting intravenous induction anesthetic agent and is widely used in the treatment of TBI because of its good induction ability.19 BDNF is useful in reducing the density of propofol synapses followed by activation of growth factor receptors p75NTR and RhoA, namely actin depolymerization, loss of microtubules, and disruption of axon transport resulting in inhibition of BDNF traffic.20,21 Propofol is an intravenous anesthetic agent used as an anesthetic induction agent and is also widely used to sedate patients in intensive care units. Many preliminary studies suggest that propofol has a neuroprotective effect against brain ischemia.22 However, in the study of Kotani et al., the evidence that propofol can reduce ischemic brain damage is inconclusive, and further research is needed.23\n\nYusriyani’s research found that there was an effect of propofol on the percentage of caspase 3 expression in the hippocampus in mice that had experienced traumatic brain injury. This study used different doses of propofol starting from doses of 10 mg, 25 mg, and 50 mg/kg body weight intravenously. The results of the study found significant differences between treatment groups. The most effective dose to reduce the percentage of caspase 3 expression in the hippocampus in mice is a dose of 50 mg/kg body weight intravenously. Of the statement above, the author’s interest arose to research the effect of Nigella sativa seed extract and propofol on BDNF as neuroplasticity and neuroprotection of traumatic brain injury in rats (Rattus novergicus). This study will later assess the amount of BDNF levels in the cerebrospinal fluid using the Enzyme-linked immunosorbent assay (ELISA) method in the treatment group compared to the control group.24 The results of research on propofol in vivo and in vitro have not been able to explain with certainty the mechanism of propofol as neuroplasticity and neuroprotection of the brain. Therefore researchers want to analyze the effect of giving propofol to BDNF on traumatic brain injury so that it can be used as the basis for an effective treatment.\n\n\nMethods\n\nThis was a laboratory experiments animal model with the post-test only control group design, namely measuring the effect of treatment by comparing the five groups. G1 = Negative control (without TBI treatment), G2 = Positive control (TBI without drug administration), G3 = TBI with Nigella sativa 500 mg/kgBW P. O. administration, G4 = TBI with Propofol 10 mg/kgBW I. M. administration, G5 = TBI by administering a combination of Nigella sativa 500 mg/kgBW P. O. and Propofol 10 mg/kgBW I. M. The data was collected from April 2023 to May 2023.\n\nThe subjects of this study were Rattus novergicus rats, adult males, aged 4-8 weeks, weighing 150-200 grams, obtained from the Faculty of Veterinary Medicine, University of Syiah Kuala. The sample selection technique used in this study is the Federer formula.\n\nLaboratory data including BDNF protein level were collected on day 8 of the TBI treatment. In total, 30 rats were selected during the study period.\n\nPreparation of animal model\n\nPrior to the treatment, the fur was assigned a specific number for use in the straightforward randomization procedure. This hair shaving can cause wounds but this has to be anticipated by shaving carefully and using a very sharp razor to avoid damage to the animal’s skin. Following this, 10 days period of adaptation took place, homogenization was conducted in the cage. The temperature in the cage was adjusted to room temperature, and the rats were fed with BR I on a daily basis.\n\nAdministration of TBI\n\nThe Feeney weight drop mode was carried out using male Rattus norvegicus rats. These rats were shaved and had a 4 mm incision made on their right frontoparietal area to expose the bone. The skin opening’s center was positioned 1.5 mm posterior to the bregma and 2.5 mm lateral from the midline. Subsequently, the rats were dropped from a 1 meter height, with a weight diameter of 2.5 mm. Earlier research had previously conducted initial trials to create experimental animal models. The results from these earlier studies with the Feeney TBI model demonstrated an increase in inflammatory levels of TF Alpha and elevated MDA ischemic levels.\n\nSurgical procedure\n\nOn the 7th day following the rats exposure to TBI, the rats were euthanized using the cervical dislocation technique. Subsequent to euthanasia, craniotomy was performed on the rats, allowing for the extraction of brain tissue. The collected brains were weighed and their weights were documented. The entirety of the process was executed by the same operator utilizing microsurgical tools.\n\nBDNF protein level with ELISA method\n\nBrain Tissue Protein Isolation. Fresh rat brain tissue was cut into small pieces and then rinsed with cold PBS (0.01 M, pH 7.4) to remove blood that was carried away during the collection process. The tissue was weighed ± 0.1 gram and added assay buffer with a ratio of 1:9 (w/v) then homogenized using a paste followed by a freeze-thaw cycle to optimize the destruction of brain tissue cells. The rat brain tissue homogenate was then centrifuged at 5,000×g at 40C for 10 minutes.\n\nBDNF levels in rat brain tissue were measured using a commercial kit (Elabscience Rat BDNF Catalogue number E-EL-R1235) using standard concentrations of 0, 31.25, 62.5, 125, 250, 500, 1000, and 2000 pg/ml. The initial stage of the ELISA examination begins with adding 100 ul of sample and standard into each well plate that has been coated with a specific antibody. The Elisa plate was then incubated at 37oC for 90 minutes. The sample/standard solution on the Elisa plate was then removed and then 100 ul of Biotinylated detection AB solution was added and incubated at 37°C for 60 minutes. Next, the Elisa plate was washed 3 times using an Elisa washer followed by the addition of 100 ul HRP conjugate working solution and incubated at 37°C for 30 minutes. The ELISA well plates were then washed again 5 times and then 90 ul of reagent substrate was added to each Elisa well plate. At this stage, a color change reaction occurs after the Elisa plate is incubated for 15 minutes. To stop the color change reaction, 50 ul stop solution was added to each Elisa well plate, the addition of the solution would change the color of the reaction from blue to yellow. The color was then measured at a wavelength of 450 nm using a microplate spectrophotometer. Step by step description of BDNF procedures can be found on Protocols.io, DOI: dx.doi.org/10.17504/protocols.io.ewov1q3w2gr2/v1.\n\nData analysis in this study used one-way ANOVA (Analysis of Variance) to test the hypothesis of the study with a significance level of 0.05 (α = 5%). Before data analysis, the ANOVA prerequisite test was carried out, namely the normality test and homogeneity test which were calculated with the help of a software application by using SPSS (IBM, New York, US). The normality test was carried out on the residual results of the ANOVA model using the Shapiro-Wilk test because the number of samples was < 50.\n\nThis study was approved by the Veterinary Research Ethics Committee of the Faculty of Veterinary, Universitas Syiah Kuala, Banda Aceh, Indonesia, No. 208/KEPH/III/2023.\n\n\nResult\n\nThe results of the ELISA to determine BDNF protein levels in rat brain tissue can be seen in Table 1.\n\n* Shapiro-Wilk test.\n\n** ANOVA test.\n\nThe data shown in Table 1. shows data on BDNF protein levels in rat brain tissue using the ELISA method in all groups that appear to be normally distributed. G2 rats had the lowest level of BDNF protein in brain tissue compared to the other groups, while G5 had the highest score. The results of analysis of BDNF protein levels in rat brain tissue using the ELISA method between groups showed that there were significant differences. Post hoc analysis for analysis between groups of rats is presented in Table 2 as follows:\n\nBased on the results of the analysis between groups, the levels of BDNF protein in brain tissue that showed a significant difference (P < 0.05) were between G2 compared to G3 and G5, while the levels of the other groups did not differ significantly. It can be concluded that the BDNF protein levels in the brain tissue of rats using the ELISA method in positive control rats were significantly lower when compared to the group of rats given Nigella sativa 500 mg/kgBW P. O. and the group of rats given a combination of Nigella sativa 500 mg/kgBW P. O. and Propofol 10 mg/kgBW I.M. Based on Figure 1, the longest interval of BDNF protein levels is obtained at G3 and the shortest at G2. The highest BDNF protein level was found in G5 with a level of 377,300, followed in G3 with a total level of 333,279 and the lowest was in G2 with a BDNF protein level of 141,146. However, qualitatively based on Figure 1 it can be seen that the highest peak of the median is G3, followed by G5, G4, G1, and G2 sequentially.\n\nThe results obtained based on this test were at a significance level of 1% and based on the output of the normality test, the Shapiro-Wilk values were all greater than 0.01 (Table 3), so it can be concluded that the residual values are normally distributed. The homogeneity test was carried out using the Levene test (Table 4). The results obtained are as follows: with a significance level of 1% and based on Levene’s test output, a p-value of 0.077 is obtained. This value is greater than 0.01 so it can be concluded that the variance of the variables is the same or homogeneous. Because the normality and homogeneity assumptions have been fulfilled, the one-way ANOVA test can be carried out. The results of one-way ANOVA calculations in this study can be seen in Table 5.\n\na Lilliefors significance correction.\n\n* This is a lower bound of the true significance.\n\nBased on Table 5 p-value <0.05 (p-value = 0.000) and F count (3.140) > F table (2.98) then H0 is rejected and H1 is accepted. This means that there is a difference in the average results of the ELISA examination in each group. Based on the ANOVA statistic, the test results obtained were p = 0.032 (there was a significant difference between groups), with the Levene Test (0.077) or having variance between the same groups, Post hoc test with LSD test showed G1 did not have a significant difference with other groups, G2 was significantly different G3 and G5 were significantly different, G3 was significantly different from G2, G4 was not significantly different from all groups, and G5 was significantly different from G2. Then a Post hoc test was carried out as a follow-up test from the ANOVA test to find out which variable had the average difference. significant. Further test results with the Post hoc test method can be seen in Table 6.\n\n* The mean difference is significant at the 0.05 level.\n\nThe results of the ANOVA test were p = 0.032 (there were significant differences between groups), with the Levene Test (0.077) having the same variance between groups. The post hoc test with the LSD test showed that Group 1 had no significant difference from the other groups, group 2 was significantly different from Groups 3 and 5; Group 3 was significantly different from Group 2; Group 4 was not significantly different from all groups; and Group 5 is significantly different from group 2.\n\nTable 6 shows that with a significance level of 5% (α = 5%), the average G5 is significantly different from G2 (p = 0.003, p < 0.05). The mean of G3 was significantly different from that of G2 (p = 0.012, p < 0.05), and the mean of G3 was not significantly different from that of G4 (p = 0.363, p > 0.05). Based on these results it can also be seen that the average difference between G5 and G2 is 100.46383 (the BDNF protein content of G5 is 100 points greater than G2), the average difference between G5 and G4 is 45.51467 (G5 is 45 points greater than G4), followed by the average difference between G5 and G3 is 17.12017 (G5 is 17 points bigger than G3), while the average difference between G3 and G4 is 28.39450 (G3 is 28 points bigger than G4). Thus sequentially the difference in average BDNF protein levels from the five groups is G5 > G3 > G4 > G2, meaning that the combination of Nigella sativa and propofol has more potential to increase BDNF protein levels than Nigella sativa, and Nigella sativa has more potential than propofol.\n\n\nDiscussion\n\nThe present study was conducted on 30 Rattus novergicus rats treated with BDNF examination after 7 days of TBI. Within seven days after administration of Nigella sativa and propofol, changes in the levels of the BDNF gene were found. This present study has comparable results with the results of research conducted by Hutagalung,25 this present study was carried out with Nigella sativa extract, in contrast to Hutagalung using curcumin. Hutagalung’s study proves that the administration of curcumin from turmeric extract can increase mBDNF expression in rats that have experienced traumatic brain injury. Rats model were divided into 3 groups and each group consisted of 11 rats. All rats were observed after 24 hours after being treated for traumatic brain injury. In the Hutagalung study, it was found that curcumin from turmeric extract orally can increase mBDNF expression in brain cells that have experienced traumatic head injury.25\n\nIn contrast to a study conducted by Zhou et al., using 120 Sprague-Dawley rats to look at the mechanism of the effect of propofol on cognitive function.26 As a comparison, a BDNF study in humans was conducted by Dharmajaya. Based on the results of statistical analysis on 16 samples of patients with head injuries, significant values were obtained on examination of BDNF levels. There was an increase in BDNF in the first 24 hours after TBI, then it increased at 48 and 72 hours after TBI and decreased in levels 120 hours after injury.6\n\nBDNF is a neurotrophic factor that helps the maturation, differentiation, and survival of neurons in the nervous system. In addition, in bad conditions, BDNF can show neuroprotective effects in the form of glutamatergic stimulation, hypoglycemia, cerebral ischemia, and neurotoxicity. BDNF functions to stimulate and control neurogenesis. BDNF can be found in most areas of the brain such as the cortex, hippocampus, mesencephalon, hypothalamus, olfactory bulb, basal forebrain, brainstem, and spinal cord. BDNF levels in neurodegenerative diseases such as multiple sclerosis (MS), Parkinson’s, and Huntington’s disease. In addition, BDNF also plays a role in the process of homeostasis.5–7,27 The rat’s BDNF gene consists of eight exons, each with its promoter, and one 3’ exon encoding the active BDNF protein. Rat BDNF is very similar in structure to human BDNF. Exons I-III are located mainly in the brain, whereas exons IV are identified in the lung and heart, resulting in the transcription of eight different mRNAs. BDNF mRNA is highly expressed in the brain, according to in situ hybridization investigations. BDNF expression levels are very low during fetal development, increase after birth, and decrease in adults.28\n\nThis present study is in line with the results of research by Wu et al. Based on the research results of Wu A, et al., there is an increase in BDNF levels in head injuries which serves as an indicator of healing and as a sign of an increase in the ability to form nerve cells and a reduction in the impact of cognitive decline. In this study, the researchers showed that the presence of endogenous BDNF and pro-BDNF were also replaced by additional nutrition.29\n\nThe conclusion from the study of Elfving et al. shows that the determination of BDNF in plasma samples is affected by temperature, caution should be exercised when interpreting the results where BDNF levels have been determined in plasma samples. Comparing BDNF measurements in mouse brain and mouse serum led to the conclusion that the BDNF ELISA kit has better accuracy, yield, and inter- and intra-test variation in serum samples compared to brain samples.30\n\nResearch by Hicks et al. states that BDNF and its receptor, trkB, can provide trauma-related neuroprotection in the central nervous system. However, several other studies suggest that BDNF is a contributing factor to neurodegenerative events in trauma. This study aims to determine the role of BDNF in neuroprotection. Research conducted by Hicks et al. Regarding neurotrophins, especially BDNF in head injuries, it was found that the time for an increase in BDNF was between the first 24−72 hours post-traumatic.31\n\nJuananda et al’s research states that BDNF is believed to have a neuroprotective effect involved in synaptic plasticity and cognitive function. This function is mediated by intracellular signaling cascades via the mitogen-activated protein kinase (MAPK) and PI3K pathways. In the cerebellum, BDNF is involved in granular cell neurogenesis. BDNF can also increase neuronal growth, maturation, and differentiation of nerve cells and can protect cerebellum granular cells from apoptosis due to loss of glucose or hypokalemia.28\n\nBased on the results of a study conducted by Bathina et al., BDNF is a neurotrophin that has a neuroprotective effect against ischemic brain injury. BDNF increases in the area around the lesion which is related to the progress of nerve function improvement. However, after brain ischemia injury occurs it causes a decrease in the level of BDNF which results in changes in the ability of neuroplasticity or repair of nerve cell function, spontaneously or by inducing rehabilitation BDNF is an important molecule in brain plasticity.4\n\nIn present study, from the results of statistical analysis on the ELISA in determining the BDNF protein level, it can be stated that the peak potential for increasing BDNF in all treatment groups is G3 > G5 > G4 > G1 > G2 respectively, meaning that administration of Nigella sativa L extract is better at increasing BDNF levels than giving the combination of Nigella sativa L + propofol, and propofol alone so that it can be stated that giving Nigella sativa L extract increases the potential for neuroplasticity.\n\nThe results of this study are in line with the research of Nazwar et al. A study conducted by Nazwar et al., found that giving Nigella sativa (black cumin) extract to rats with head trauma increased BDNF levels. In experimental rats with head injury, injection of black cumin extract reduced apoptosis, although not significantly. In experimental rats with head injury, black cumin extract treatment led to an association between BDNF and apoptosis. Further research is needed to determine the mechanism or method used by black seed extract to increase BDNF expression. It is necessary to carry out pharmacological studies of various black cumin extraction methods to increase understanding of thymohydroquinone. To learn more about thymohydroquinone, it is necessary to do pharmacological research on black cumin extraction methods. This is because the administration of black cumin extract orally to humans requires clinical trials.32\n\nIn a study conducted by Zadeh et al., Nigella sativa significantly increased BDNF levels in depressed patients. This study indicates the importance of administering Nigella sativa to cure depression. This study was statistically significant comparing Nigella sativa with placebo. In this study, decreased BDNF increased the risk of Alzheimer’s disease, stress, depression, and anxiety. There have been many reports that state BDNF levels can be a predictor of a neuropsychiatric disease. BDNF functions as a growth and development protein in the central nervous system and peripheral nervous system and is very active in the hippocampus and parts of the brain cortex.7\n\nThis present study was carried out with Nigella sativa extract, in contrast to Motaghinejad et al’s research using curcumin. Motaghinejad et al’s study also investigated the role of curcumin in vivo in protecting rat hippocampal cells against alcohol-induced neuroapoptosis, oxidative stress, neuroinflammation, and reduced cell density and aimed to study the potential involvement of phospho-CREB-BDNF signaling in curcumin-mediated neuroprotection.33 It could be argued that Nigella sativa has the same neuroprotective potential as curcumin.\n\nThis present study is similar to that of Wu et al. because Nigella sativa contains the active substance Docosahexaenoic Acid (DHA). According to the research of Wu et al., Docosahexaenoic Acid (DHA) is one of the main omega-3 polyunsaturated fatty acids in the brain which plays an important role in neurological development, maintenance of learning, and memory, and increases fluidity and signal transduction function and regulates gene expression. The DHA supplement diet is expected to protect against reduced plasticity and side effects that occur after injury. Wu et al’s research concludes that supplementation of omega-3 fatty acids can restore cognitive function and normalize the action of BDNF, synapsin I, and CREB as well as oxidative damage after traumatic brain injury.34\n\nSlightly different from this present study. If the intake of certain nutrients in the form of Nigella sativa was given in this study, then in the study by Oliveira et al. the subjects in this study were not given dietary rules with special replacements. for healing to continue. Several studies have shown that BDNF is a key molecule for neuroplasticity. Oliveira et al’s study showed that increased BDNF in the central nervous system is a particular response to inflammatory stimuli, namely as a special neuroprotector.35\n\nIn this present study, propofol (G4) was also able to increase BDNF protein levels in the brains of traumatic brain-injured rats compared to the positive control group (G2), although its potency was lower than that of Nigella sativa L (G3). TBI increases oxidative stress, and reduced levels of BDNF, synapsin I, and cAMP. Responsive Element-Binding Protein (CREB) in the brain. TBI causes a decrease in BDNF levels, but within 48 hours the BDNF levels will rise. BDNF stimulates the mitogen-activated protein kinase/extractcellular signal-regulated kinase (MAPK/ERK), phosphoinositide-3 kinase (PI3K), and phospholipase C (PLC)-gamma pathway through activation of the receptor tyrosine kinase B (TrKB), a high-affinity receptor for BDNF.26\n\nThe present study has produced evidence that propofol may exert a neuroprotective effect. In line with the results of Kotani et al’s study, propofol has been reported to have a neuroprotective effect that can reduce bleeding and intracranial pressure.23\n\nIn line with the present study, a study conducted by Jacques et al. stated that propofol is a highly hydrophobic intravenous hypnotic in the form of a lipid emulsion. Like many intravenous anesthetics, propofol can decrease brain oxygen consumption, decrease glutamate release, and modulate GABA-A receptor activity. In vitro, propofol reduces oxidative stress.36\n\nThe study by Hausburg et al., found that in a rabbit model of cerebral IRI, propofol increased plasma SOD activity, which was associated with increased neuronal survival. Furthermore, in the rat model of IRI, ischemic infarct size was reduced by 21% in animals anesthetized with propofol. In addition, the neurological outcome in the rat model of incomplete ischemia was significantly improved in the rats anesthetized with propofol.37\n\nWhite et al.’s study demonstrated that propofol exhibits a neuroprotective effect in improving neurological function in brain-traumatized rats, which is independent of intralipid. In addition, propofol treatment can effectively reduce the expression of pro-inflammatory cytokines in the injured cortex of late-phase brain trauma.38 The neuroprotective effects of propofol have long been recognized in animal studies such as ischemia/reperfusion models and brain trauma models, which have largely focused on the mechanism complex of propofol. to relieve brain edema, neuronal apoptosis, inflammatory response, and so on.39 Through a rat model of ischemia, Shi’s research showed that propofol reduces inflammatory reactions and brain damage in focal cerebral ischemia in rats.40\n\nThe study by Zhou et al. showed that the neuroprotective effect of propofol on brain trauma-induced brain damage was attributed to its anti-inflammatory properties. However, this study did not demonstrate the effect of propofol on cytokine expression in late-phase brain trauma. This study, to our knowledge, is the first time to show that the increased expression of IL-1β, IL-6, and TNF-ɑ genes on days 3 and 7 after brain trauma can be inhibited remarkably by propofol administration. Changes in IL-1β expression were most prominent among the three cytokines after propofol treatment on days 1 and 3. These results suggest that IL-1β may play a more important role than IL-6 and TNF-α under propofol administration after brain trauma. The results of this study provide new evidence for overcoming cytokine changes in brain-traumatized rats by time-delayed administration of propofol after brain trauma, Regarding the effect of propofol on neurologic function, in a model of cerebral ischemia, propofol was found to improve neurologic function.41\n\n\nConclusions\n\nWe concluded that both nigella sativa and propofol have the potential to increase BDNF protein levels. Nigella Sativa L had a better effect than propofol in repairing damaged neuron cells (neuroplasticity) and increasing BDNF protein levels (neuroprotection) for 7 days of administration in rat traumatic brain injury.", "appendix": "Data availability\n\nZenodo: BDNF Dataset, https://doi.org/10.5281/zenodo.10276418. 42\n\nZenodo: ARRIVE checklist for “Effect of ethanol extract of nigella sativa L seeds and propofol on BDNF protein level as neuroplasticity and neuroprotection of traumatic brain injury in rats, https://doi.org/10.5281/zenodo.10276505. 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\nSastrodiningrat AG: Traumatic brain injury: primary brain damage, secondary brain damage, management, and neuro critical care. Book. Medan: Sumatera Utara University Press; 2012; pp. 125–182.\n\nDas M, Mohapatra S, Mohapatra SS: New perspectives on central and peripheral immune responses to acute traumatic brain injury. J.Neuroinflammation. 2012; 9(236): 1–12.\n\nDewan MC, Rattani A, Gupta S, et al.: Estimating the global incidence of traumatic brain injury. J.Neurosurg. 2018; 1(1): 1–18.\n\nBathina S, Das UN: Brain-derived neurotrophic factor and its clinical implications. Arch. Med. Sci. 2015; 11(6): 1164–1178. PubMed Abstract \| Publisher Full Text\n\nSalehi Z, Mashayekhi F: Brain-derived neurotrophic factor concentrations in the cerebrospinal fluid of patients with Parkinson’s disease. J. Clin. Neurosci. 2009; 16: 90–93. PubMed Abstract \| Publisher Full Text\n\nDharmajaya R: Brain Derived Neurotrophic Factor (BDNF) post-severe head injury as a predictor of disease course. Indones. J. Clin. Pathol. Med. Lab. 2014; 21: 61–66. Publisher Full Text\n\nZadeh AR, Eghbal AF, Mirghazanfari SM, et al.: Nigella sativa extract in the treatment of depression and serum Brain-Derived Neurotrophic Factor (BDNF) level. J. Med. Res. Sci. 2022; 27(28): 26–28. Publisher Full Text\n\nAzzubaidi MS, Al-Ani IM, Saxena AK, et al.: Prevention of brain hypoperfusion-induced neurodegeneration in rat’s hippocampus by black cumin fixed oil treatment. IIUM Med. J. Malaysia. 2018; 17(1): 1–4. Publisher Full Text\n\nTavakkoli A, Hosseinzadeh H: Nigella sativa L., and thymoquinone as neuroprotective antioxidants. Chapter 21. Oxidative stress and dietary antioxidants in neurological disease. 2020; pp. 1–17.\n\nLanducci E, Mazzantini C, Buovicino D, et al.: Neuroprotective effects of thymoquinone by the modulation of ER stress and apoptotic pathway in in vitro model of excitotoxicity. Molecules. 2021; 26: 1–11. Publisher Full Text\n\nIslam MH, Ahmad IZ, Salman MT: Neuroprotective effects of Nigella sativa extract during germination on central nervous system. Pharmacogn. Mag. 2015; 11(42): 182–190. Publisher Full Text\n\nAbbasnezhad A, Hayatdavoudi P, Niazmand S, et al.: The effects of hydroalcoholic extract of Nigella sativa seed on oxidative stress in hippocampus of STZ-induced diabetic rats. Avicenna J. Phytomedicine. 2015; 5(4): 333.\n\nMarwan K, Boom CE, Ruslami R: Statins as brain protectors in traumatic brain injury. J. Neuroanestesi Indones. 2017; 6(1): 48–57. Publisher Full Text\n\nIstikomah I, Purwanto B, Ardiyanto TD: The effect of date palm juice and green tea supplementation on reducing plasma malondialdehyde (MDA) levels in children with thalassemia. J. Kesehat Kusuma Husada. 2018; 162–167. Publisher Full Text\n\nIsaev NK, Chetverikov NS, Stelmassok EV, et al.: Thymoquinone as a potential neuroprotector in acute and chronic forms of cerebral pathology. Biokhimiya. 2020; 85(2): 167–176. Publisher Full Text\n\nBabar ZU, Azad AK, Sulaiman WMAW, et al.: Neuroprotective properties of Nigella sativa (L.) seeds extract in Sprague dawley rats model. Dhaka Univ. J. Pharm. Sci. 2018; 17(1): 113–121. Publisher Full Text\n\nAsiei F, Fazel A, Rajabzadeh AA, et al.: Neuroprotective effect of Nigella sativa extract upon the hippocampus in PTU-induced hypothyroidism juvenile rats: a stereological study. Metab. Brain Dis. 2017; 32: 1755–1765. Publisher Full Text\n\nHosseinzadeh L, Monaghash H, Ahmadi F, et al.: Bioassay guided isolation of neuroprotective fatty acid from Nigella sativa L. against 1-methyl -4-phenylpyridium-induced neurotoxicity. Pharmacogn.Mag. 2017; 13: 627–633. PubMed Abstract \| Publisher Full Text\n\nWoldegerima N, Rosenblatt K, Mintz CD: Neurotoxic propoerties of propofol sedasion following traumatic brain injury. Crit. Care Med. 2016; 44(2): 455–456. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOzer A, Ozcan S: Anesthetic neurotoxycity and neuroplasticity in pediatric patients. Curr. Top. Anesthesiol. 2017; 1–10. Publisher Full Text\n\nEllen McCann M, Soriano SG: General anesthetics in pediatric anesthesia: influences on the developing brain. Curr. Drug Targets. 2012; 13: 944–951. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeck K, Arumuhum A, Veronese M, et al.: N-methyl-D-aspartate receptor availability in first episode psychosis: a PET-MR brain imaging study. Trans. Psychiatry. 2021; 11(425): 1–8. Publisher Full Text\n\nKotani Y, Shimazawa M, Yoshimura S, et al.: The experimental and clinical pharmacology of propofol, an anesthetic agent with neuroprotective properties. CNS Neurosci. Ther. 2008; 14: 95–106. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYusriyani TA: Effect of intravenous propofol administration on hippocampal caspase 3 expression in balb/c mice with head injury. J. Neuroanestesi. Indones. 2013; 2: 81–88.\n\nHutagalung TR: Effect of administration of turmeric extract (curcuma domestica val.) on the expression of mature brain derived neurotrophic factor (m-BDNF) in male rats Sprague-Dawley strain after traumatic brain injury. Tesis, Universitas Sumatera Utara.2018.\n\nZhou J, Wang F, Zhang J, et al.: The interplay of BDNF-TrkB with NMDA receptor in propofol induced cognition dysfunction. BMC Anesthesiol. 2018; 18(35): 1–8. Publisher Full Text\n\nLin PH, Kuo LT, Luh HT: The roles of neurotrophins in traumatic brain injury. Life. 2022; 12: 1–22. Publisher Full Text\n\nJuananda D, Cahyani D, Sari R, et al.: Effects of chronic stress on the brain: biomolecular study of glucocorticoid hormones and post-regulation Brain-Derived Neurotrophic Factor (BDNF) in the Cerebellum. FK UGM. 2015; 9: 65–70. Publisher Full Text\n\nWu A, Ying Z, Pinilla FG: Dietary Omega-3 Fatty Acids Normalize BDNF Levels, Reduce Oxidative Damage and Counteract Learning Disability after Traumatic Brain Injury in Rats. J. Neurotrauma. 2004; 21(10): 1457–1467. Publisher Full Text\n\nElfving B, Plougmann PH, Wegener G: Detection of brain-derived neurotrophic factor (BDNF) in rat blood and brain preparations using ELISA: Pitfalls and solutions. J. Neurosci. Methods. 2010; 187(1): 73–77. PubMed Abstract \| Publisher Full Text\n\nHicks RR, Li C, Zhang L, et al.: Alterations in BDNF and trkB mRNA levels in the cerebral cortex following experimental brain trauma in rats. J. Neurotrauma. 2019; 16: 501–510. Publisher Full Text\n\nNazwar TA, Balafif F, Wardhana DW, et al.: Potential of Nigella Sativa on Anti or Pro-apoptotic Pathway After Brain Injury Via Brain-derived Neurotrophic factor on Rattus Norvegicus Wistar. Teikyo Med. J. 2023; 46(01): 7683–7696.\n\nMotaghinejad M, Motevalian M, Fatima S, et al.: Curcumin confers neuroprotection against alcohol-induced hippocampal neurodegeneration via CREB-BDNF pathway in rats. Biomed. Pharmacother. 2017; 87: 721–740. PubMed Abstract \| Publisher Full Text\n\nWu A, Ying ZHE, Gomez-pinilla F: Dietary Omega-3 Fatty Acids Normalize BDNF Levels, Reduce Oxidative Damage, and Counteract Learning Disability after Traumatic Brain Injury in Rats. J. Neurotrauma. 2004; 21: 1457–1467. PubMed Abstract \| Publisher Full Text\n\nOliveira CO, Ikuta N, Regner A: Outcome Biomarkers Following Severe Traumatic Brain Injury. Rev. Bras. Ter. Intensiva. 2008; 20(4): 411–421. PubMed Abstract \| Publisher Full Text\n\nJacquens A, Needham EJ, Zanier ER, et al.: Neuro-inflammation modulation and post-traumatic brain injury lesions: from bench to bed-side. Int. J. Mol. Sci. 2022; 23(19): 11193. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHausburg MA, Banton KL, Roman PE, et al.: Effects of propofol on ischemia-reperfusion and traumatic brain injury. J. Crit. Care. 2020; 56: 281–287. Publisher Full Text\n\nWhite TE, Ford GD, Surles-Zeigler MC, et al.: Gene expression patterns following unilateral traumatic brain injury reveals a local pro-inflammatory and remote anti-inflammatory response. BMC Genomics. 2013 Apr 25; 14: 282. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXi HJ, Zhang TH, Tao T, et al.: Propofol improved neurobehavioral outcome of cerebral ischemia-reperfusion rats by regulating Bcl-2 and Bax expression. Brain Res. 2011 Sep 2; 1410: 24–32. Publisher Full Text\n\nShi SS, Yang WZ, Chen Y, et al.: Propofol reduces inflammatory reaction and ischemic brain damage in cerebral ischemia in rats. Neurochem. Res. 2014 May; 39(5): 793–799. PubMed Abstract \| Publisher Full Text\n\nZhou R, Yang Z, Tang X, et al.: Propofol protects against focal cerebral ischemia via inhibition of microglia-mediated proinflammatory cytokines in a rat model of experimental stroke. PLoS One. 2013 Dec 9; 8(12): e82729. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKulsum K: BDNF Dataset. [Dataset]. In F1000research. Zenodo. 2023. Publisher Full Text\n\nKulsum K: ARRIVE checklist for research entitled: Effect of ethanol extract of nigella sativa L seeds and propofol on BDNF protein level as neuroplasticity and neuroprotection of traumatic brain injury in rats. In F1000Research. Zenodo. 2023. Publisher Full Text" }	[ { "id": "293532", "date": "15 Jul 2024", "name": "Li Liu", "expertise": [ "Reviewer Expertise Perioperative brain protection" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe title of this article is \"Effect of ethanol extract of Nigella sativa L seeds and promotion on BDNF protein level as neuroplasticity and neuroprotection of traumatic brain injury in rates\", which is an interesting study. This article uses advanced statistical methods to discover the advantageous effects of ethanol extract from Nigella sativa L seeds in traumatic brain injury. However, there are several aspects that need to be addressed before indexing:\n1. This article only uses BDNF as an indicator for observation. Although the role of BDNF in neuroprotection is well-known, it has not been reflected in the neuroprotection and neuroplasticity aspects of this experiment.\n2. Propofol is a commonly used anesthetic in clinical anesthesia and intensive care units. In this study, it is unreasonable for clinical application that is continuous intravenous infusion of traumatic rats for 7 days.\n3. Why is there no statistical significance between the G1 group and the G2 group in Table 6? This is very confusing.\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": "12194", "date": "23 Sep 2024", "name": "Syahrul Syahrul", "role": "Author Response", "response": "Dear Prof. Li Liu, Harbin Medical University, Harbin, Heilongjiang, China Thank you very much for your generous comment. I was greatly helped by your suggestions, and I revised our article manuscript according to your suggestions. In the introductory section, we have provided information about the benefits of BDNF as an indicator of neuroprotection, as well as neuroplasticity, in which section it has been mentioned that BDNF is an important molecule in neuroplasticity. In our study, the effects of Nigella sativa and Propofol were tested using the ELISA method to determine the effects of neuroplasticity and neuroprotection by observing the increase in BDNF protein levels. In this study, neuroplasticity was reflected in the increase in BDNF protein levels, while neuroprotection was reflected in the average BDNF protein levels. We agree with your view that propofol has been widely used in anaesthesia services and ICU management. We need to add information that: In this study, propofol was not given intravenously for 7 days but was given intravenously only once at the beginning of the study so as not to cause a prolonged hypoxic head effect. Thank you for your correction. We agree to add information about the level of significance between groups G1 and G2 to the narrative at the end of the results section. In Table 6, it is listed, but not narrated. Here is the additional information: Group G1 differs on average above G2 by 49.10350 points but is not statistically significantly different between G1 and G2 (p = 0.122, p > 0.05).Thus sequentially the difference in average BDNF protein levels from the five groups is G5>G3>G4>G1>G2. Best regards Syahrul" } ] }, { "id": "315110", "date": "03 Sep 2024", "name": "Mohamad Sofyan Harahap", "expertise": [ "Reviewer Expertise stress", "inflammation and brain protection" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, the author has a good idea and will enrich the view of brain protection. The author has tried to find a simple method with easily obtained materials, and made a comparison with Propofol which is considered by researchers as the gold standard, because Propofol is used clinically in the fields of anesthesia and intensive care. In developing new materials (Nigella Sativa extract), it is correct to use animal trials, with the rules that have been attempted properly, but the technique of administering Propofol to mice must be in accordance with the correct method so that it can be reworked by other researchers. Likewise, regarding the model for creating artificial head injuries, the method must be clear so that it can be replicated by other researchers. I think the two things above are my major corrections that need to be clarified by the author. My suggestion to help improve this research and hopefully increase the quality of the research results is the use of anatomical pathology examination of the brains of mice that have been euthanized, so that it can be assessed pathologically with the right method, the level of damage or protective effects of the two test materials, (Propofol and Nigella Sativa).\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? Partly", "responses": [ { "c_id": "12442", "date": "23 Sep 2024", "name": "Syahrul Syahrul", "role": "Author Response", "response": "Dear: Prof. Mohamad Sofyan Harahap, Diponegoro University, Semarang, Indonesia Thank you very much for your generous comment. I was greatly helped by your suggestions, and I revised our article manuscript according to your suggestions. Reviewer comment: The technique of administering Propofol to rats must be in accordance with the correct method so that it can be reworked by other researchers. Author response: We agree with the suggestion, here we add information in the study design and subjects’ section, namely propofol is an anesthetic and intensive therapy drug, for the technique of administering propofol is by intravenous injection or continuous syringe pump. In this study, propofol was given to the tail of the rat because there are many blood vessels there so that it can quickly reach the systemic blood circulation, in addition, oxygen saturation monitoring was carried out through pulse oximetry because the side effect of propofol is falling asleep until apnoea so that oxygen saturation monitoring here is to prevent oxygen desaturase. Reviewer comment: Likewise, regarding the model for making artificial head injuries, the method must be clear so that it can be replicated by other researchers. Author response: We agree with the suggestion. We will add information in the administration of TBI section, in this study, artificial head injuries were carried out using the Feeney weight drop mode. The stages of this method are sequential, first, the Rattus norvegicus head hair is shaved then given local anaesthesia to reduce pain in the animal model, then a 4 mm incision is made above the right frontoparietal bone area. Second, the centre of the scalp was then opened at a position of 1.5 mm from the posterior part of the bregma and 2.5 mm from the lateral midline. Third, Rattus norvegicus was dropped from a height of 1 meter with the head down, the part of the head that was exposed was the right frontoparietal bone. Reviewer comment: To help improve this research and hopefully improve the quality of research results is to utilize pathological anatomical examination of the brains of euthanized rats, so that it can be assessed pathologically with the right method, the level of damage or protective effects of the two test materials, (Propofol and Nigella Sativa). Author response: We strongly agree with your suggestion, we have done this from another side of this research, namely by examining the effects of Propofol and Nigella Sativa on the histopathological picture of post-traumatic brain injury as an indicator of neuroprotection. Best regards Prof.Syahrul" } ] } ]	1	https://f1000research.com/articles/13-275
https://f1000research.com/articles/13-689/v1	25 Jun 24	{ "type": "Study Protocol", "title": "Internet-based cognitive behavioral therapy for individuals with gambling disorder in Indonesia: protocol for a pilot and feasibility study", "authors": [ "Kristiana Siste", "Enjeline Hanafi", "Belinda Julivia Murtani", "Michael Baigent", "Ben J Riley", "Jayne Sessions", "Lee Thung Sen", "Hans Christian", "Astria Aryani", "Kevin Surya Kusuma", "Enjeline Hanafi", "Belinda Julivia Murtani", "Michael Baigent", "Ben J Riley", "Jayne Sessions", "Lee Thung Sen", "Hans Christian", "Astria Aryani", "Kevin Surya Kusuma" ], "abstract": "Background Gambling disorder (GD) has become a wide concern in Indonesia, as many negative consequences arise from this psychiatric condition. Prompt treatment with an appropriate method of delivery is required to achieve optimal outcomes in GD patients. This protocol paper outlines a study to determine the effectiveness, acceptability, and feasibility of internet-based cognitive behavioral therapy (iCBT) in treating GD in Indonesia.\n\nMethods This non-randomized pilot and feasibility study will recruit 20 people with GD. All participants will receive the iCBT intervention through self-learning videos and guided weekly group sessions. The effectiveness of the intervention will be assessed at baseline (week 0), post- treatment completion (week 10), and 6 weeks post-treatment (week 16). The outcomes measured will be the change in gambling symptoms, gambling urges, cognitive distortions, readiness to change, emotional problems, and quality of life of the participants.\n\nDiscussion The feasibility of iCBT for GD patients in Indonesia will be assessed by this study. The study's results will give an indication of the acceptability of the intervention and the feasibility of a subsequent conclusive trial. The delivery of iCBT may help to address the issue of treatment access in an extensive geographical region and provide immediate implications as a treatment resource for GD in practice.", "keywords": [ "gambling disorder", "internet based", "cognitive behavioral therapy", "treatment", "Indonesia" ], "content": "Introduction\n\nAccording to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), gambling disorder is defined as a persistent and recurrent problematic gambling behavior that results in substantial clinical impairment or distress.1 The issue of gambling disorder (GD) is growing worldwide. In recent years, more people have access to both offline and online gambling. In addition, the COVID-19 pandemic corresponded with an increase in online gambling platforms.3,4 A study in Indonesia during the pandemic found the prevalence of GD in Indonesia is estimated to be 1% in 2021.2 This is an enormous figure as Indonesia comprised up to 278 million people.3Low public awareness and a lack of effective regulation could eventually cause the number of individuals experiencing GD to rise in the future.3,5\n\nGambling disorder causes major impacts in life including unemployment, interpersonal problems, financial difficulties, and an increased risk of other mental disorders such as depression, anxiety disorders, stress-related and somatoform disorders, along with substance use disorder.2 Therefore, it is essential to provide suitable treatment for gambling disorders. Early intervention and appropriate management have been shown to significantly improve outcomes for individuals with gambling disorders.6,7\n\nThe goal of GD treatment is symptom remission and functional recovery. To date, no pharmacological treatment has been approved for GD. However, some studies have demonstrated positive outcomes when pharmacological and psychotherapy treatments are combined.8 Cognitive behavioral therapy (CBT) is an effective treatment modality for GD.8,9 Studies reveal that CBT reduces gambling-related symptoms and problematic behavior whilst also improving the overall functioning and quality of life of people with GD.7,9 In recent years, internet-based cognitive behavioral therapy (iCBT) has been suggested as a means of lowering barriers to professional help seeking by showing equally promising outcomes with increased accessibility, convenience, and cost-effectiveness.10–12 Studies of help-seeking among individuals with gambling problems consistently report very few (less than 10%) gamblers seek formal help.13–15 Similar findings also come from an Indonesian study that indicated only 15.5% of people seek treatment for GD.2 Problem gambling and its consequences can remain hidden within families, usually over extended periods, and help-seeking is often the last resort after significant adverse events or crises such as family breakdown, loss of employment, legal issues, or deterioration of mental health.16,17 Since delivering treatment for gambling disorders is challenging in Indonesia due to its vast and varied territory, iCBT appears to be a promising treatment option. However, research regarding the effectiveness of iCBT is still very scarce in Indonesia. This pilot study aims to examine the acceptability and feasibility of iCBT for GD in Indonesia.\n\nPROTOCOL\n\n\nMethods\n\nThis study is a pilot and feasibility study with a quasi-experimental design. The protocol adheres to the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist (Extended data: Supplementary file 1).18 After intake screening, participants will undergo baseline assessment (T1) and will be given treatment for 10 weeks. This will be followed by follow up assessment immediately after treatment (T2) and follow up assessment 6 weeks after treatment (T3) (Figure 1).\n\nA total of 20 participants will be recruited using online advertisements via social media and through consecutive sampling by directly approaching current and former patients in inpatient and outpatient services in Cipto Mangunkusumo Hospital, Indonesia.\n\nThe inclusion criteria include age between 18-59 years old, fluent in Bahasa Indonesia, be screened as probable pathological gambler (indicating severe and pervasive problem gambling) based on South Oaks Gambling Screen (SOGS), and do not have comorbid severe psychiatric disorder (i.e., psychotic disorders, severe mood disorders, and intellectual disability). Exclusion criteria are no history of gambling in the past six months, history of neuropsychiatric disorders (e.g., seizures), and inability to access web browsers and online conferencing platforms. Drop-outs are defined as those who miss three consecutive sessions of the 10-week therapy program for any reason.\n\nThe South Oaks Gambling Screen is chosen as a screening tool because of its widespread use internationally.19 The adaptation to Indonesian version in community setting yielded a good validity and reliability testing, indicating SOGS as a good instrument to screen for GD in Indonesia.2\n\nParticipant eligibility will be assessed by medical doctors at Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia. A psychiatric assessment utilizing the ICD-11 criteria for gambling disorders will be carried out to confirm the patient's diagnosis of GD.\n\nFollowing the determination of a participant’s eligibility for the study, the Indonesian version of Gambling Symptom Assessment Scale (G-SAS), Gambling Urge Scale (GUS), Gambling Related Cognitions Scale (GRCS), and Barratt Impulsiveness Scale-11 (BIS-11) will be administered to evaluate the participants' symptoms, gambling urges, cognitive distortions and impulsivity, respectively. The University of Rhode Island Change Assessment Scale (URICA) will be used to evaluate the participants’ readiness to change. The World Health Organization Quality-of-Life Scale (WHOQOL-BREF) will be used to evaluate quality of life and the Self Rating Questionnaire-20 (SRQ-20) will be used to assess emotional problems.20–30 In order to evaluate the treatment outcome, a direct psychiatric assessment of GD using ICD-11 criteria will also be conducted at the end of treatment. The assessment schedule is presented in Table 1 and Figure 2.\n\nThe iCBT module was developed by researchers from Department of Psychiatry, Faculty of Medicine, Universitas Indonesia and Department of Psychiatry, Flinders Centre for Gambling Research, South Australia. This module consists of 6 parts which will be used as a guide for the therapist in the therapy sessions. The module content for each session is described in Table 2.\n\nThe contents of iCBT module are largely derived from The Flinders/Statewide Gambling Therapy Service (SGTS) Model of Treatment for Gambling Disorders, a manualized CBT treatment program.31,32 The beginning of the program addresses topics such as the severity of gambling, the level of motivation, comorbidities, money management, and support systems. The intervention approach then provides psychoeducation and outlines objectives of the therapy for the participants and their significant others, aiding them with the understanding of gambling behavior, and how to identify distorted gambling thoughts and correct them. Exposure therapy including guided imagery is introduced and used to extinguish urges. Relapse prevention strategies are also included with ways to implement a balanced lifestyle, managing lapses and relapses, and ongoing money management.\n\nAll participants will undergo 10 therapy sessions (once-weekly) with each session lasting for 40-60 minutes. They will be divided into four small groups, each comprising five participants and a therapist. The therapy module will be given as an online self-learning source via videos in a website specifically developed for this training. The videos will divide the module content into several parts with each video lasting about 10 minutes. To confirm the participants have watched the videos, there will be a post-test measurement with no passing mark as the purpose is to assert the important points contained in the videos. The participants will then be encouraged to discuss things they understand or do not understand from their online self- learning sessions during each therapy session. There will also be several tasks that must be completed by the participants and then discussed with the therapist during each therapy session (e.g., ‘please identify the urges you feel over the next week’). Participants who miss three consecutive sessions over 10 weeks will be considered dropped out. Researchers from Flinders Centre for Gambling Research and Universitas Indonesia will meet online every two weeks to discuss participants and to provide input on treatment.\n\nTwo psychiatrists with expertise in GD from Department of Psychiatry, Faculty of Medicine, Universitas Indonesia will facilitate each group session in this study. The roles of the therapist are to: (1) lead and moderate iCBT sessions based on (but not limited to) the module, (2) establish a safe and warm environment, (3) provide consultation, including out-of-session, and (4) contact absent participants to encourage attendance.\n\nThe following descriptive data will be obtained via a self-administered questionnaire: age, gender, education level, ethnicity, religion, approximate residential location, marital status, employment status, monthly income, last gambling session, age during first instance of gambling, frequency of gambling in a month, first person to introduce gambling, other people around the patient who also have gambling problems, media used to gamble, types of device used, types of gambling played, average duration of gambling during weekday and weekend, lowest and highest bet ever placed, total money lost to gambling, purpose of gambling, negative impacts from gambling, help seeking behaviors, substance use history, usage of substance during gambling session, and (if ever) rehabilitation due to substance use history.\n\nThe sample size for this study was determined using the formula for one sample, continuous outcome study: 𝑛 = (Z ∗ σ/E)2, where Z is the value from the standard normal distribution reflecting the confidence level that will be used (Z = 1.96 for 95%), σ is the standard deviation score, which is 10.46 from a previous study.33 Margin of error was determined to be 5 units. The sample size needed using the above formula is 17 samples, which is then rounded to 20 samples to accommodate the group therapy sessions.\n\nEvaluation of the response to CBT will be measured using repeated measures ANOVA. Statistical analysis will be carried out using the Statistical Package for the Social Sciences (SPSS) software version 23.0. The raw data obtained in this study only be accessible to the authors. Missing data will be handled on whether they are at random.\n\nData on adverse events, including hospitalization, arrest, and death, will be collected from the participants’ contact person, treating physician or medical staff. In addition, participants will be interviewed at T2 to determine whether they have experienced any subjective harmful effects (e.g., withdrawal syndrome, increased cravings) after joining this program.\n\nAt the time of submission, the study had not begun any recruitment.\n\nThe results of this study will be disseminated via peer-reviewed journals and international academic conferences. All procedures of this study will be independent from the sponsor. Participant-level dataset will not be made publicly available. Any authors included in the publications will be determined according to authorship guideline of the International Committee of Medical Journal Editors (ICMJE).\n\n\nDiscussion\n\nThe aim of our study is to evaluate the feasibility of an online CBT intervention for patients with GD in Indonesia. Previous studies found that only few of those with gambling problems seek professional help.2,13–15,26 Multidimensional factors including social, cultural, and personal could be contributing to their reluctance to seek treatment. There are a number of obstacles that inhibit help-seeking such as pressure from others to continue gambling, the desire to handle the issues on their own, stigma, secrecy, shame, not admitting problems, practical concerns (such as lack of availability and cost of treatment), worries about treatment, uncertainty, and avoidance.34–36 Gambling is strictly prohibited under the Indonesian Criminal Code and engaging in such activities is punishable by law.37 Although there is currently no research on the subject, it is possible that the illegality of GD is one of the contributing factors to the low rate of help-seeking in GD. Internet-based therapies have the potential to overcome these obstacles through the following means: (i) fostering a greater sense of anonymity; (ii) promoting transparency and honesty; and (iii) overcoming practical barriers like travel time to treatment facilities, conflicts between treatment and other time-constrained obligations like childcare or paid work, and (iv) provision of treatment relevant to cultural or language needs.38\n\nTo our knowledge, our study will be the first to examine the effectiveness and feasibility of a CBT program which will be delivered online for patients with GD in Indonesia. The outcome of this study will provide valuable data for the development of iCBT for individuals with addiction, particularly GD in LMIC. This established module may be a beneficial addition to the resources of treatment for GD in practice.\n\nEvidence-based treatments for GD in Indonesia and LMICs in general remain sparse. The proposed study may provide an alternative to conventional CBT when physical accessibility is an issue (as many experienced during the COVID-19 pandemic), or when the patients have limited access to professional help locally. As a result of this study's findings, iCBT might be applied in a more widespread context and utilized as a module to assist psychiatrists in engaging and treating more GD patients throughout Indonesia.\n\nThe study protocol was approved by the Research Ethical Committee of Faculty of Medicine, Universitas Indonesia (approval number: KET-992/UN2.F1/ETIK/PPM.00.02/2023) which was issued on 24th of July 2023. The study protocol was registered at ClinicalTrials.gov (NCT number: NCT06171516 on 14th December 2023). The study will be conducted in accordance with the Declaration of Helsinki 1969, revision 2013.\n\nAll participants will be provided with and asked to sign a patient information and consent form (PICF). The results will be submitted for publication after finalizing the study. Personal data will be protected by separating the study data from the participants’ identifiable information and importantly, written agreement will be obtained from participants to never share others’ information with any third party even after the therapy is finished.\n\n\nContributors\n\nKS and EH conceptualised the study. KS, EH and BJM are the main developers of the iCBT module. MB, BJR, and JS reviewed the iCBT module. LTS and HC helped in designing study methodology. BJM, LTS, HC, AA, and KSK wrote the protocol and initial manuscript. KS, MB, BJR and JS reviewed and edited the final manuscript. KS supervised the whole study and procured grants. All authors have read and approved the final manuscript.\n\n\nEthics and dissemination\n\nThe study protocol was reviewed and approved by the Research Ethical Committee of Universitas Indonesia on 24th of July 2023 (approval number: KET-992/UN2.F1/ETIK/PPM.00.02/2023). All participants will be provided with and asked to sign a patient information and consent form (PICF). The study will adhere to the Declaration of Helsinki 1964, revision 2013. The results will be submitted for publication after finalizing the study.\n\n\nTrial Registration\n\nThe trial is registered on the 14th of December 2023 at the ClinicalTrials.gov database with the identifier number NCT06171516.", "appendix": "Data availability\n\nNo data is associated with this protocol article.\n\nReporting guideline\n\nOSF: Internet-based cognitive behavioral therapy for individuals with gambling disorder in Indonesia: protocol for a pilot and feasibility study, https://doi.org/10.17605/OSF.IO/JB7F5. 39 Licensed under CC-BY 4.0 International.\n\nThe project includes:\n\n• Spirit checklist\n\n\nAcknowledgements\n\nWe would like to thank the Flinders Centre for Gambling Research for their participation in designing the iCBT module.\n\n\nReferences\n\nAssociation American Psychiatric: Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5®). Washington DC: American Psychiatric Publishing; 2013; 59.\n\nSinambela Y: Instrument Validity and Reliability test: South Oaks Gambling Screen (SOGS). Jakarta: Faculty of Medicine Universitas Indonesia; 2021.\n\nHealth TLP: Gambling: a neglected public health issue. Lancet Public Health. 2021 Jan 1; 6(1): e1. Publisher Full Text\n\nHodgins DC, Stevens RMG: The impact of COVID-19 on gambling and gambling disorder: emerging data. Curr. Opin. Psychiatry. 2021; 34(4): 332–343. Publisher Full Text Reference Source\n\nBijker R, Booth N, Merkouris SS, et al.: Global prevalence of help-seeking for problem gambling: A systematic review and meta-analysis. Addiction. 2022 Dec 1; 117(12): 2972–2985. Publisher Full Text\n\nStefanovics EA, Potenza MN: Update on Gambling Disorder. Psychiatr. Clin. N. Am. 2022; 45(3): 483–502. Publisher Full Text Reference Source\n\nPotenza MN, Balodis IM, Derevensky J, et al.: Gambling disorder. Nat. Rev. Dis. Prim. 2019; 5(1): 51. Publisher Full Text\n\nRibeiro EO, Afonso NH, Morgado P: Non-pharmacological treatment of gambling disorder: a systematic review of randomized controlled trials. BMC Psychiatry. 2021; 21(1): 105. Publisher Full Text\n\nRizeanu S: Cognitive-Behavioral Therapy for Gambling Addiction.Şenormancı Ö, Şenormancı G, editors. Cognitive Behavioral Therapy and Clinical Applications. Rijeka: IntechOpen; 2018; Ch. 9. Publisher Full Text\n\nCasey LM, Oei TPS, Raylu N, et al.: Internet-Based Delivery of Cognitive Behaviour Therapy Compared to Monitoring, Feedback and Support for Problem Gambling: A Randomised Controlled Trial. J. Gambl. Stud. 2017; 33(3): 993–1010. Publisher Full Text\n\nvan der Maas M , Shi J, Elton-Marshall T, et al.: Internet- Based Interventions for Problem Gambling: Scoping Review. JMIR Ment Health. 2019; 6(1): e65. Publisher Full Text Reference Source\n\nMolander O, Lindner P, Ramnerö J, et al.: Internet-based cognitive behavior therapy for problem gambling in routine care: protocol for a non-randomized pilot and feasibility trial. Pilot Feasibility Stud. 2020 Jul 21; 6(1). Publisher Full Text\n\nSuurvali H, Hodgins DC, Cunningham JA: Motivators for Resolving or Seeking Help for Gambling Problems: A Review of the Empirical Literature. J. Gambl. Stud. 2010; 26(1): 1–33. Publisher Full Text\n\nCunningham JA: Little Use of Treatment Among Problem Gamblers. Psychiatr. Serv. 2005 Aug 1; 56(8): 1024-a–1025. Publisher Full Text\n\nBraun B, Ludwig M, Sleczka P, et al.: Gamblers seeking treatment: Who does and who doesn’t? J. Behav. Addict. 2014 Sep 1; 3(3): 189–198. Publisher Full Text\n\nProductivity Commission: Gambling, Report No.50. Canberra: Productivity Commission; 2010.\n\nEvans L, Delfabbro PH: Motivators for Change and Barriers to Help-Seeking in Australian Problem Gamblers. J. Gambl. Stud. 2005; 21(2): 133–155. Publisher Full Text\n\nChan A-W, Tetzlaff JM, Gøtzsche PC, et al.: SPIRIT 2013 Explanation and Elaboration: Guidance for protocols of clinical trials. BMJ. 2013; 346: e7586. Publisher Full Text\n\nBattersby MW, Thomas LJ, Tolchard B, et al.: The South Oaks Gambling Screen: A Review with Reference to Australian Use. J. Gambl. Stud. 2002; 18(3): 257–271. Publisher Full Text\n\nKim SW, Grant JE, Potenza MN, et al.: The Gambling Symptom Assessment Scale (G-SAS): A reliability and validity study. Psychiatry Res. 2009 Mar 31; 166(1): 76–84. Publisher Full Text\n\nMiller DG, Kim SYH: Euthanasia and physician-assisted suicide not meeting due care criteria in the Netherlands: a qualitative review of review committee judgements. BMJ Open. 2017 Oct 1; 7(10): e017628. Publisher Full Text Reference Source\n\nSmith D, Pols R, Battersby MW, et al.: The Gambling Urge Scale: Reliability and validity in a clinical population. Addict. Res. Theory. 2013; 21: 113–122. Publisher Full Text Reference Source\n\nRaylu N, Oei TPS: The gambling urge scale: Development, confirmatory factor validation, and psychometric properties. Psychol. Addict. Behav. 2004 Jun; 18(2): 100–105. Publisher Full Text\n\nGanihartono I: Psychiatric Morbidity Among Patients Attending the Bangetayu Community Health Centre in Indonesia. Indonesian Bulletin of Health Research. 1996; 24(4).\n\nWorld Health Organization: WHOQOL-BREF: Introduction, Administration, Scoring and Generic Version of the Assessment: Field Trial Version. 1st ed. Geneva: World Health Organization; 1996; vol. 1. : 3–12.\n\nSaputro C, Siste K, Kusumaningrum P, et al.: Validation and Reliability Study of the Barratt Impulsiveness Scale 11 Indonesian version. Jakarta: Faculty of Medicine Universitas Indonesia; 2024.\n\nSiste K: Psychometric Properties of Indonesian Gambling Related Cognitions Scale (GRCS). Jakarta: 2024. (3). Report No.: 1.\n\nSiste K: Psychometric Properties of Indonesian Gambling Urge Scale (GUS). Jakarta: 2024. (2). Report No.: 1.\n\nSiste K: Psychometric Properties of Indonesian Gambling Symptom Assessment Scale (G-SAS). Jakarta: 2024. (1). Report No.: 1.\n\nDevi A, Kusumawardhani A, Budiman R, et al.: Validity and reliability test of University of Rhode Island Change Assessment Scale instrument on substance abusers at LIDO treatment and Rehabilitation Centre National Narcotics Board. Jakarta: Faculty of Medicine Universitas Indonesia; 2013.\n\nBaigent M, Riley B, Harris S, et al.: The Flinders/SGTS Model of treatment for Gambling Disorders. Flinders Centre for Gambling Research; 2022.\n\nSmith DP, Battersby MW, Harvey PW, et al.: Cognitive versus exposure therapy for problem gambling: Randomised controlled trial. Behav. Res. Ther. 2015; 69: 100–110. Publisher Full Text\n\nWall H, Magnusson K, Hellner C, et al.: The evaluation of a brief ICBT program with therapist support for individuals with gambling problems in the context of a gambling helpline: a randomized pilot trial. Pilot Feasibility Stud. 2023 Dec 1; 9(1). Publisher Full Text\n\nItäpuisto M: Problem Gambler Help-Seeker Types: Barriers to Treatment and Help-Seeking Processes. J. Gambl. Stud. 2019; 35(3): 1035–1045. Publisher Full Text\n\nEvans L, Delfabbro PH: Motivators for Change and Barriers to Help-Seeking in Australian Problem Gamblers. J. Gambl. Stud. 2005; 21(2): 133–155. Publisher Full Text\n\nSuurvali H, Cordingley J, Hodgins DC, et al.: Barriers to Seeking Help for Gambling Problems: A Review of the Empirical Literature. J. Gambl. Stud. 2009; 25(3): 407–424. Publisher Full Text\n\nAgung M: Kitab Undang-Undang Hukum Pidana. Jakarta: Biro Hukum dan Humas Badan Urusan Administrasi Mahkamah Agung Republik Indonesia; 1st ed2023; vol. 1. .\n\nSagoe D, Griffiths MD, Erevik EK, et al.: Internet-based treatment of gambling problems: A systematic review and meta-analysis of randomized controlled trials. Journal of Behavioral Addictions. Akademiai Kiado ZRt. 2022; 10: 546–565. Publisher Full Text\n\nSiste K, Hanafi E, Murtani BJ, et al.: iCBT for Gambling Disorder. OSF. 2024. Publisher Full Text" }	[ { "id": "300646", "date": "30 Aug 2024", "name": "Simone N Rodda", "expertise": [ "Reviewer Expertise Internet delivered interventions", "help seeking and gambling 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\nThank you for the opportunity to review this protocol for iCBT for an Indonesian cohort of people with Gambling Disorder. An interesting study and well-written protocol. Some minor points of clarification are listed below. Citations 13-15 are individual studies on help-seeking, but this is superseded by a meta-analysis on population prevalence studies from around the world which reported one in five people with problem gambling had sought treatment and one in 25 at moderate risk, so the suggestion that it is 10% is not entirely correct. See (Bijker R,et al., 2022 [Ref 1]) Methods Figure 1 refers to ‘groups of 5’ under treatment, suggesting the treatment is group-based, which so far hasn't been stated. Figure 2 also refers to groups – but there’s nothing in the text on it until well into the methods under delivering the intervention. The delivery section suggests in-person treatment, but this is not reported anywhere earlier in the introduction or aims. It is also discussed that it is group therapy with iCBT consisting of videos and activities. This is really interesting and novel but hasn’t been stated in the background, aims, or study design. I’m not sure I know of other treatments that blend in-person with iCBT – so really novel – and if not, then the previous studies should be reported. I note under sample size it is referred to as group therapy – if so, what BCTs are being delivered then and how does this relate to the iCBT content?\nIt would be great to have a table of the specific BCTs being delivered, when and how frequently, and how they are being delivered (therapist, video, written, other) and then link that to the outcome measures. For instance, I see an outcome measure of impulsivity, and it would be good to know exactly which BCT is expected to change that variable, etc. I don’t think Table 2 is sufficient for replication or to be able to map intervention components to outcomes. TREND reporting guidelines state that sufficient intervention information should be provided so as to allow for replication.\nI wonder, given the intervention is exploratory, whether it is appropriate to describe participants who do not complete the entire 10 weeks as drop-out? Perhaps an alternative is to use the feasibility study as a way of determining the optimal duration/configuration of the iCBT. Looking later at the manuscript, it looks like drop-out is from in-person treatment rather than the iCBT?\nGiven the ICD-11 is being used in the interview, I wonder if it is necessary to burden participants with the SOGS given it is screening only. Perhaps consider a briefer screen – there are meta-analyses on brief screens to detect GD.\nDiscussion Given that gambling is illegal, perhaps there needs to be a stronger case made for group therapy, which by its very nature sounds problematic for anonymity, legal and criminal issues, and chances of sharing gambling information.\nThe discussion again refers to the treatment being delivered online. It would be good to be very clear on who is delivering what behaviour change technique and how (see Michie work on BCTs if not familiar).\nMinor Instead of ‘pathological gambler’ – consider person with pathological gambling or similar.\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": "12454", "date": "23 Sep 2024", "name": "Kristiana Siste", "role": "Author Response", "response": "Citations 13-15 are individual studies on help-seeking, but this is superseded by a meta-analysis on population prevalence studies from around the world which reported one in five people with problem gambling had sought treatment and one in 25 at moderate risk, so the suggestion that it is 10% is not entirely correct. See (Bijker R,et al., 2022 [Ref 1]). Answer: We have revised the number of treatment-seeking gamblers according to Bijker R et al., 2022 in the last paragraph of the Introduction. Figure 1 refers to ‘groups of 5’ under treatment, suggesting the treatment is group-based, which so far hasn't been stated. Figure 2 also refers to groups – but there’s nothing in the text on it until well into the methods under delivering the intervention. Answer: We added the suggestion in the paragraph above figure 1. The delivery section suggests in-person treatment, but this is not reported anywhere earlier in the introduction or aims. Answer: We added the suggestion in the study design section. It is also discussed that it is group therapy with iCBT consisting of videos and activities. This is really interesting and novel but hasn’t been stated in the background, aims, or study design. Answer: The treatment will consist of individual online learning sessions delivered through pre-recorded videos, followed by weekly online group therapy sessions with a therapist. Each group therapy session will include five participants and will occur over a 10-week period. It would be great to have a table of the specific BCTs being delivered, when and how frequently, and how they are being delivered (therapist, video, written, other) and then link that to the outcome measures. For instance, I see an outcome measure of impulsivity, and it would be good to know exactly which BCT is expected to change that variable, etc. Answer: We have now specified them in Table 2. Given the intervention is exploratory, whether it is appropriate to describe participants who do not complete the entire 10 weeks as drop-out? Perhaps an alternative is to use the feasibility study as a way of determining the optimal duration/configuration of the iCBT. Looking later at the manuscript, it looks like drop-out is from in-person treatment rather than the iCBT? Answer: There will be no drop out criteria in this study. Adherence to the treatment will be evaluated to optimize the configuration of the iCBT for future studies. Given the ICD-11 is being used in the interview, I wonder if it is necessary to burden participants with the SOGS given it is screening only. Perhaps consider a briefer screen – there are meta-analyses on brief screens to detect GD. Answer: We will be using SOGS as it is validated and proven reliable in Bahasa Indonesia. Given that gambling is illegal, perhaps there needs to be a stronger case made for group therapy, which by its very nature sounds problematic for anonymity, legal and criminal issues, and chances of sharing gambling information. Answer: Group therapy design was chosen as this format better supports the purpose of this study: to provide a resource effective means of quality therapy in LMIC and geographically difficult terrains for gambling disorder. We deleted the anonymity benefits in Discussion. In ethical consideration, we mentioned that sharing personal information is forbidden among participants, even after the therapy sessions have concluded. The discussion again refers to the treatment being delivered online. It would be good to be very clear on who is delivering what behaviour change technique and how (see Michie work on BCTs if not familiar). Answer: Specified in Table 2. Instead of ‘pathological gambler’ – consider person with pathological gambling or similar. Answer: We added the suggestion, except for “probable pathological gambler” classification in SOGS." } ] }, { "id": "320594", "date": "06 Sep 2024", "name": "David C Hodgins", "expertise": [ "Reviewer Expertise Gambling disorders", "including intervention." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting and well written proposal. I am very eager to hear about the results and conclusions as we have lots to learn about how to provide effective treatment. I was able to review the comments of the first reviewer, Dr. Rodda, and I concur with all her points. I have several additional queries and suggestions. Design: First, the protocol would benefit from identifying the primary and secondary outcomes. The goals in the abstract are threefold -assessing effectiveness, acceptability, and feasibility. (The article text identifies only 2 aims - acceptability and feasibility - although effectiveness is implicitly assumed by the methods). It would be helpful to identify how these goals will be assessed and evaluated as successful or unsuccessful. One primary outcome for effectiveness should be identified. The sample size calculation refers to a standard deviation, but the instrument/variable is unspecified. Participants:\n\nOne method of recruitment is approaching current patients in inpatient and outpatient services. Would these patients be receiving treatment for gambling disorder, which seems like an unnecessary confound? Eligibility includes ICD-11 Gambling Disorder assessed by a psychiatrist. Unfortunately, no standardized instrument exists for assessing these ICD criteria. The lack of an instrument may be problematic for reliably assessing status at follow-up. Perhaps an assessment of DSM-5 Gambling Disorder criteria with a standardized instrument such as the NODS might be more reliable? Will the psychiatrists that provide the treatment also be conducting the follow-up diagnostic assessments? Statistical Analysis: The analytic plan is briefly described. Repeated measure ANOVA is proposed. Given that there are three time points, a mixed model analyses would better handle missing data. This analytic model would also allow inclusion of a nested “group” variable. It is unclear whether “dropouts” will be followed but they should be included if possible. I agree with Dr. Rodda that the definition of dropout seems arbitrary given that this is a pilot study. Discussion: A minor point is that the discussion describes internet interventions as possibly fostering a sense of anonymity. Given that one of the novel aspects of this intervention is the group sessions, this advantage is unlikely to apply here.\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": "12455", "date": "23 Sep 2024", "name": "Kristiana Siste", "role": "Author Response", "response": "First, the protocol would benefit from identifying the primary and secondary outcomes. The goals in the abstract are threefold -assessing effectiveness, acceptability, and feasibility. (The article text identifies only 2 aims - acceptability and feasibility - although effectiveness is implicitly assumed by the methods). It would be helpful to identify how these goals will be assessed and evaluated as successful or unsuccessful. One primary outcome for effectiveness should be identified. The sample size calculation refers to a standard deviation, but the instrument/variable is unspecified. Answer: The primary outcomes will be GUS, G-SAS, and GRCS. The secondary outcomes will be BIS-11, WHOQOL-BREF, SRQ-20, and URICA. The primary outcome used for sample size calculation is GUS. Feasibility: adherence to the protocol by the participants. Acceptability: 5-point Likert scale for satisfaction after each iCBT session. Effectiveness: measurement of pre- and post- outcomes. One method of recruitment is approaching current patients in inpatient and outpatient services. Would these patients be receiving treatment for gambling disorder, which seems like an unnecessary confound? Eligibility includes ICD-11 Gambling Disorder assessed by a psychiatrist. Unfortunately, no standardized instrument exists for assessing these ICD criteria. The lack of an instrument may be problematic for reliably assessing status at follow-up. Perhaps an assessment of DSM-5 Gambling Disorder criteria with a standardized instrument such as the NODS might be more reliable? Will the psychiatrists that provide the treatment also be conducting the follow-up diagnostic assessments? Answer: All participants will be allowed to continue their prior treatment as indicated. Deleted the post-treatment icd-11 interview as no standardized instruments are available to assess this outcome. Moreover the time duration of the diagnostic criteria (12 months) make it so that it is unreasonable to reassess the participants in 10 weeks. The analytic plan is briefly described. Repeated measure ANOVA is proposed. Given that there are three time points, a mixed model analyses would better handle missing data. This analytic model would also allow inclusion of a nested “group” variable. It is unclear whether “dropouts” will be followed but they should be included if possible. I agree with Dr. Rodda that the definition of dropout seems arbitrary given that this is a pilot study. Answer: Suggestion accepted, all participants' data will be analyzed whether they finish the study or not. A minor point is that the discussion describes internet interventions as possibly fostering a sense of anonymity. Given that one of the novel aspects of this intervention is the group sessions, this advantage is unlikely to apply here. Answer: Group therapy design was chosen as this format better supports the purpose of this study: to provide a resource effective means of quality therapy in LMIC and geographically difficult terrains for gambling disorder. We deleted the anonymity benefits in Discussion. In ethical consideration, we mentioned that sharing personal information is forbidden among participants, even after the therapy sessions have concluded. Thank you for your invaluable feedback." } ] } ]	1	https://f1000research.com/articles/13-689
https://f1000research.com/articles/13-201/v1	21 Mar 24	{ "type": "Review", "title": "Review of Deep Learning Performance in Wireless Capsule Endoscopy Images for GI Disease Classification", "authors": [ "Tsedeke Temesgen Habe", "Keijo Haataja", "Pekka Toivanen", "Keijo Haataja", "Pekka Toivanen" ], "abstract": "Wireless capsule endoscopy is a non-invasive medical imaging modality used for diagnosing and monitoring digestive tract diseases. However, the analysis of images obtained from wireless capsule endoscopy is a challenging task, as the images are of low resolution and often contain a large number of artifacts. In recent years, deep learning has shown great promise in the analysis of medical images, including wireless capsule endoscopy images. This paper provides a review of the current trends and future directions in deep learning for wireless capsule endoscopy. We focus on the recent advances in transfer learning, attention mechanisms, multi-modal learning, automated lesion detection, interpretability and explainability, data augmentation, and edge computing. We also highlight the challenges and limitations of current deep learning methods and discuss the potential future directions for the field. Our review provides insights into the ongoing research and development efforts in the field of deep learning for wireless capsule endoscopy, and can serve as a reference for researchers, clinicians, and engineers working in this area inspection process.", "keywords": [ "Wireless capsule endoscopy", "Deep learning", "Transfer learning", "Attention mechanisms", "Multi-modal learning", "Automated lesion detection", "Interpretability and explainability", "Data augmentation", "Edge computing." ], "content": "Introduction\n\nWireless capsule endoscopy (WCE) is a minimally invasive diagnostic imaging modality that is used to examine the digestive tract. The procedure involves swallowing a small capsule equipped with a camera, which takes images of the digestive tract as it travels through the body. The images obtained from WCE are an important source of information for diagnosing and monitoring digestive tract diseases. However, the images are of low resolution and often contain a large number of artifacts, making their analysis a challenging task.\n\nArtificial intelligence has shown remarkable diagnostic abilities in a variety of gastrointestinal medical image sectors1 and health care sector.2 Wireless capsule endoscopy is regarded as a valuable tool for diagnosing intestinal illnesses. Due to the millions of training constraints, existing DL (Deep Learning) approaches for pathology detection in WCE (Wireless Capsule Endoscopy) image are complex and computationally intensive.3 Color and texture have a significant role in prominence target feature that aid in the recognition of abnormalities.3 One of the WCE’s primary limitations has been that it captures many snapshots that should be sent to the attached screen and evaluated by physician: this takes a lot of time. Another drawback is the unclear line between lesions and normal tissues.4\n\nDeep learning techniques offer a lot of promise for helping doctors detect, find, and diagnose gastrointestinal disease with wireless capsule endoscopy. Several researchers have created image processing5–7 and deep learning methods for finding and diagnosing disease from gastrointestinal tract problems using wireless capsule endoscopes over the last ten years. The main problem with capsule endoscopy is that images are obtained with inadequate lighting and the capsule camera moves around throughout the digestive tract, resulting in inadequate quality frames.1\n\nThe most popular application of existing machine learning improvements in healthcare is Computer Aided Detection (CAD),8,9 which is used to detect lesions, such as those present in the gastrointestinal tract.\n\nDeep learning approaches, Supervised learning, and Transfer Learning methods were investigated in this study to better understand the situation and which types of CNN blocks and features can improve the classification and detection of GI pathology. To arrive at this conclusion, we first reviewed various recent papers in Table 1, held a discussion, and then compared accuracy in Tables 2 and 3.\n\nThe Wireless capsule Endoscopy Deep Learning implementation detected, red spots, vascular lesionsulcers, small bowel lesions, mucosal lesions, polyps, celiac disease, bleeding, and hookworm. In most existing papers, Deep Learning applications with various CNN features were used to detect all 14 colorectal diseases. Because Deep Learning in Artificial Intelligence plays a significant role and performs well in medical image identification and processing, it has gained impressive performance improvements in the identification of a variety of diseases in Wireless Capsule Endoscopy.\n\nThe CNN models with Xception and ImageNet features show reliable performance of transforming the color space, which completely transforms one image into a new one and then the CNN1 can extract features for classification.\n\nThe texture, color, and shape qualities3,10,11 were used in the training. Since color can influence training results, image processing (e.g., white balance adjustment) was needed to reduce color alterations.10 HSV-S, Gray, and Lab-b components were employed as source data for training in the HSV, RGB, and Lab color models, respectively.10 CNN in WCE images with YOLO-v411 feature showed high-accuracy, fast, and error-free method for finding intestinal anomalies in WCE images and classification. The models constructed with CNN with Xception and ImageNet yield the extracted features and three classifications. The performance was evaluated by using sensitivity and specificity. In the future the researcher plans to improve the performance of the deep neural network by using effective networks construction (architecture), scale of datasets, initial variables, and NN algorithm generalization.12\n\nOn-the-fly data augmentation and color space transformation are performed by TICT-CNN, accompanied with binary classification of the frames.3 The use of Deep learning to wireless capsule endoscopy3 and Device-assisted enteroscopy13 could have a significant impact on how patients with gastrointestinal hemorrhage are treated.\n\nAI features, including LeNet, AlexNet,14,15 VGGnet,14 GoogLeNet,14 and ResNet,14,16,17 DenseNet121,14,18 Xception,14,18,19 have been recently the most used in wireless capsule endoscopy image. The most widely improved convolutional CNN architecture is Alexnet.15,20,21 In some application AlexNet has outperformed architectures in terms of improving CNN performance.\n\nIn the absence of pixel-level labels, TICT-CNN3 is used when datasets-level in WCE image labels are used as weakly annotated-data for training. Self-supervised learning17 is a practical method for dealing with the problem of insufficient training data and annotations. SSL performance is good in the ResNet-50 design with dense layer.17\n\nThe performance of CNN in wireless capsule image pathology detection/classification is typically restricted because of the small, labeled CE (capsule endoscopy) image datasets. Transfer learning (TL)22,23 is beneficial for several tough pathology identification operations, and it is one solution to machine-vision problems when only restricted CE images are typically available due to patient medical imaging data privacy concerns. We should research the best ways to learn and verify pathology detection with a few datasets to solve such problems.\n\nTransfer learning approaches with a pre-trained model were applied with ImageNet datasets, and the rectified linear unit (ReLU),14,17,24 dense layer17 was used as a transfer function for transfer learning. The VGG16 model really does have the highest Matthews Correlation result of 95% and Cohen’s Kappa score of 96% when compared to other algorithms.23 During the training datasets of the amplified Kvasir-version-2 datasets, fine-tune three key pre-trained CNN are VGG-16,25 ResNet-18,23 and GoogLeNet.23 VGG-16 consists of 16 layers, 3 of which are 3 dense layers and 13 convolution layers.23 In comparison to ResNet-18 and GoogleNet, VGG16 has performed better in this architecture in.23 Using a larger dataset that has been labeled by a larger group of specialists is one way to improve pathology detection.23 However, to overcome the challenges of obtaining a huge dataset, we need use the best transfer learning techniques available, such as the few shots learning approach, which can learn new things from current datasets.\n\nAlthough the dataset in22 is 30 times larger than in,23 the author’s result in 6 is better than in 7 because with a few datasets, the researcher used a better architecture than in,23 which solved the issues of gathering large medical datasets. However, a huge dataset23 helped to improve the effectiveness of CNN features in wireless capsule endoscopy. Xception model with ImageNet10,13,26,27 was able to reach higher levels of accuracy than23 when we compare as well as great image processing results with superior performance. We hope that their findings will contribute to the wider adoption of AI (Artificial Intelligence) technology in the field of WCE for researcher who wants to work on Deep learning with transfer learning approaches. The researcher employed the EFAG-CNN4 with three branches: branch 1, branch 2, and branch 3. Initially, AI DenseNet1214 built on ImageNet was trained using branch 1 and branch 2, then fine-tuning approach was employed to improve performance and convergence speed. Branch1 has been used to concentrate the lesion region, branch 2 has been used to extract useful features from the lesion area, and branch 3 has been used to combine global and local features to get the final prediction result.4\n\nWhen the available labeled datasets are insufficient to produce a supervised model with improved performance, weakly supervision1,28 is seeking to gather more labeled data for supervised training and modeling. The labeled data that is accessible is noisy or comes from an unreliable source. Weakly supervise learning used by most researchers for the long video localization in wireless capsule endoscopy. GCNN (Graphical Convolutional Neural Network),1 unlike CNN, is designed to work with non-Euclidean structured data. The author gathered extensive videos, which will be converted into nodes Count. GCNN1 performed a node count in the form of non-Euclidean structured data (space). For the AI characteristics and architecture, most of the researchers employed CNN, which means they used Euclidean space. The challenge of poorly labeled data is addressed by weakly labeled datasets.28 The film produced by Wireless Video Capsule Endoscopy (WCE) holds up to 52000 images. Labeling these datasets takes a long time, which is why doctors do not do it. They can make a remark about a certain frame (and that this label is for a time-region in the video). This writes down that the data is poorly labeled. There is also a substantial correlation between frames that can be exploited. Spatial and temporal features, as well as memory (LSTM (Long Short-Term Memory) and attention, used in.28\n\nGraphSAGE1 is good at predicting the encoding of a new node without the need for re-training. This feature is used to manage CNN training by shortening the time it takes, but only for capsule endoscopy video, not images. The researcher begins, with temporary segmentation of the long video into consistent, similar. Then they represented as a graph, the frame in the capsule endoscopy video as the node by connected the relation by the graph’s edges.1 To make this relationship we used a variety of identical measures such as correlation, cosine similarity, and Euclidean distance among the nodes of the graph.1 In weakly supervise learning with GCNN used pretrained VGG191 trained on huge ImageNet datasets after that finetuned to remove inadequate lighting and inferior quality in the video frames. On large graphs, GraphSAGE1 offers interactive and dynamic learning. LSTM, Mean, and max pool, are examples of aggregation functions that can be used in GCNN. Long Sort term memory1 and max-pooling for few-shot learning24 outperformed competitors in.\n\nThe protection of patient information is one of the most difficult aspects of data acquisition. As a result, we are unable to gate huge datasets from medical fields. To deal with data scarcity, most researchers use the augmentations feature, and transfer learning techniques can also be used to reduce datasets or train CNN networks with minimal datasets. To generate extra new supplementary datasets with varied features of the images, augmentation approaches1,3 are applied. Few-shot learning24 is another method for improved classification by training a limited number of labeled datasets. As summarized in Table 2 some authors employed Transfer learning algorithms and functions to tackle dataset scarcity.10,20,21,29 The largest datasets were 400,000 with Inception- Resnet-V2 architecture22 and performed 98.1 accuracy, while the smallest datasets were 201 with VGG 16 network architecture25 and performed 93.4 accuracy in this systematic investigation.\n\nA Few-Shots Learning is a core solution to the delinquency of classifying wireless capsule endoscopy (WCE) images with few labeled data.24 To increase the performance of the Abnormal Feature Attention Relation Network a few-shot learning applied in24 with a few datasets. In wireless capsule endoscopy, feature addition, feature concatenation, and bilinear merging improve this learning architect for foreground abnormal feature enhancement methods.24 When compared to the bilinear merging strategy, the abnormal feature attention module (AFA)24 is more effective, improved by 10.74% across Relation Network (RN). Recognize small polyp boundary in WCE photos using the Multiscale pyramidal FSSD (Fusion Single Shot Detector)25 approach as the underlying architecture, balancing precision, and speed.\n\n\nMethods\n\nThe ultramodern survey began with an analysis of relevant keywords based on subjects or topics. For searching similar and relevant publications from official databases, we found key terms. CNN, Deep learning, Transfer learning, and wireless capsule Endoscopy are just a few main key terms. We used a combination of key terms with “AND” and “OR” logical operations to find related articles. Using the University of Eastern Finland article searching database platform link https://primo.uef.fi/, we obtained 222 peer-reviewed publications from Association for Computing Machinery, PubMed and other international publishers based on the search strategies. The peer review papers were collected from the last 10 years of publication, which began in 2013 and ended in 2022. However, for our inquiry, we chose the most relevant and recent 30 open articles.\n\nMost peer-reviewed papers were from MedPub publishers. Most of the publications investigated on CNNs (Convolutional Neural Networks), which are a type of DL technology that is widely used for WCE images. As a result, we chose the most recent and most relevant journal articles for the survey. We primarily focused on how to overcome the challenges of low light, shadow, low resolution, and noise in wireless capsule endoscopy for enhanced pathology identification using Deep learning algorithms.\n\nAI features, we construct a summary of the methods, with outcomes based on Accuracy, Sensitivity, and Specificity. We compare the results of the top 18 articles development models based on dataset scale and transfer learning features in the next steps.\n\nFinally, we compare the top five findings to decide which AI features and CNN architecture to propose for improved pathology in WCE image using Deep learning methods. Sensitivity and specificity had been evaluated as a group. We can look at CNN’s network design and summary in Table 2 for more information. This will aid in figuring out the best wireless capsule endoscopy feature and procedures.\n\n\nDiscussion\n\nUsing wireless capsule endoscopy images, deep learning models have shown promising accuracy in the classification of gastrointestinal disorders. Research findings indicate that the average accuracy of these models is 99%, demonstrating their potential to support precise diagnosis. But managing nuanced illness symptoms and intricate anatomical variances presents difficulties, necessitating ongoing model reliability development. The pathology map estimator and the classification network are cooperatively tested and trained to enhance detection results by employing ResNet-50 (self-attention) and convolutional stem mechanism features.1 Performance of the model is greatly influenced by the features of the dataset. A stronger generalization is facilitated by large, diverse datasets with well-annotated images. Performance might be impacted by problems including unequal disease representation and differences in imaging conditions, which emphasizes the need for well selected datasets. The lesion part or border is very thin in the wireless capsule endoscopy image, making it difficult to distinguish between the lesion and the normal part of the image in the WCE image. To illustrate the anomalous pattern, most of the researchers concentrated on the entire wireless capsule endoscopy photos. To distinguish this exceedingly small lesion boundary from the rest of the image, as the researcher said in,1 you must use the best representation learning approaches by focusing on the lesion regions. The authors used the CNN features with a unique lesion attention map estimator model1 and ResNet-50 (self-attention)1,28 to solve this anomalous pattern. Some of the researchers also use balancing network depth, image resolution, model performance, and parameter complexity reduction to improve the binary classification of WCE images.19 Some scientists presented a unique pathology sensitive deep learning methods for frame level variance identification and multi label categorization of diverse colon diseases in CE data.6 Weekly supervised model1,28 mostly used for multi-label disease identification. According to the work, attention-based deep MIL28 was trained end-to-end on poorly labeled image using video labels rather than comprehensive frame by frame annotation, but the results are poor based on LSTM.28 The proposed approaches include ResNet50-designed for spatial features and residual LSTM blocks for temporal features,28 a learned temporal attention module for final label identification, and self-supervision1,28 method to enlarge the distance between pathological classes, as well as a self-supervision method to maximize the remoteness between pathological classes. AlexNet possesses these features or architecture are good approaches for Endoscopy pictures because it is hard to obtain a significant quantity of datasets.21 So, if we have a little dataset, we can increase CNN network performance by utilizing ResNet and AlexNet20 and if we have a huge dataset, we should utilize xception and DensNet121.4 However, DensNet121 in (4) also performs well with limited datasets outperformed architectures in terms of improving CNN performance about image processing problems. Addition of CNN layers, number of datasets, number of Epoch, image size, color channel (reduction), transfer learning using pre-trained models such as YOLO and ResNet14,30 are some of the elements affecting the performance of deep learning progress that must be examined in the research. Table 2 shows how the Xception26 design helps CNN achieve high accuracy (99%) with datasets 53555. With DenseNet1214 network design and 1000 datasets, the highest accuracy is 98.17%. Transfer learning techniques were used by both researchers.22,25 However, according to the journal study, 93.4% accuracy was achieved due to the researcher’s employment of data-efficient learning methods with tiny datasets. Comparative studies show that deep learning outperforms classical techniques in identifying complex patterns in capsule endoscopy images. Even if deep learning is superior for feature learning, conventional techniques are still useful in situations when there is less data. Comprehending the advantages and drawbacks of every methodology is vital for making knowledgeable therapeutic judgments.\n\nTo advance the research, disciplinary collaboration is crucial. Creating knowledge-sharing platforms, publicly available datasets, and uniform assessment metrics encourages collaboration to advance deep learning in wireless capsule endoscopy. Collaboration among researchers, clinicians, and tech developers fosters a more comprehensive understanding of the problems at hand and speeds up progress.\n\n\nResult\n\nTable 3 summarizes the final five best-performing articles based on the accuracy and techniques described in Table 2.\n\nAccording to the researchers, two selected strategies in the above table show the best results. However, the approaches chosen take advantage of the largest database, 5355525 and 1000 images for DensNet121,4 as well as data-efficient learning methods. 400,000 images with an Inception-ResNet-v2 feature score of 98.1% are the largest datasets in this state of the art. This method requires more datasets to achieve 99 to 100% accuracy, since 400,000 photos can get 98.1 when compared to the first two articles, which needs many datasets and a revision of the current method. With 6000 photos, ResNet and AlexNet20 supply 98.05 percent and 97.50% accuracy, respectively. Finally, utilizing AlexNet and ResNet,22 the researcher achieves high accuracy with a limited dataset. Table 3 (shown below) has more information about the results.\n\nThere are challenges in integrating deep learning models with current workflows, ethical concerns, and regulatory compliance when moving these models from research to clinical application. In order to develop guidelines for safe and efficient deployment, researchers, healthcare providers, and regulatory bodies must work together to address these challenges. In order to solve present issues, future developments might make use of cutting-edge technology like federated learning and explainable AI.\n\nWorking toward a future in which deep learning models are useful instruments for decision support, frameworks for cooperation between AI and medical professionals are taking shape. Efficient decision-making and improved diagnostic precision can result from combining the analytical power of AI with the clinical expertise of medicine.\n\n\nConclusion and future work\n\nDeep learning techniques have been employed to analyze Wireless capsule Endoscopy images in recent years and they have proved impressive performance in a variety of applications, such as segmentation and registration.\n\nHowever, according to our ultramodern study stein this paper, there are still improvements to be made in the detection/classification of pathology in the GI tract.\n\nOne such way is to investigate data-efficient learning and popular and advanced AI features.\n\nBecause medical data annotation is costly and time-consuming, data-efficient learning is essential. For efficient use of the produced dataset, semi-supervised algorithms, learning from few-samples, and structural understanding of the data were used by some researchers.\n\nLabeling video in wireless capsule endoscopy is easier than labeling individual frames. As a result, learning approaches for inferring the spatiotemporal location of diseases from video labels were created by some researchers. To save review time, video anomaly detection should also be looked at for automated video trimming. In WCE, deep learning has demonstrated remarkable precision in identifying various ailments. Deep learning has shown amazing accuracy in detecting a range of illnesses in WCE. Regardless, the current study is based on past research that is prone to inaccuracy. Future systematic, global studies are called for this technology to be used in the clinical use of WCE.\n\nIn the future work we will investigate quality issues in Wireless Capsule Endoscopy to find the important attributes that can be improved and their potential for improvement pathology detection. Using the knowledge gained from the investigation of quality issues, we will adapt or propose a new enhancement technique and assess the performance of Deep Learning applications for Wireless capsule Endoscopy. This evaluation will be conducted by medical professionals. We planned some interesting directions for the enhancement strategy (this can also include machine learning based techniques). Certain aspects could be specified or excluded. For example, we will not want to go into resolution enhancement, which means no need to increase resolution or upscaling in the enhancement process because it has no effect on Deep Learning datasets training enhancement, but instead focus on contrast or texture enhancement in future work.\n\nFinally, by utilizing the best-chosen AI characteristics, including transfer learning strategies, video localization, and data-efficient learning strategies, we hope to further enhance deep learning approaches based on CNN in the future. This is demonstrated by the comparison presented in Table 3. Using deep learning and machine vision techniques, we plan to broaden our survey on the impact of video improvement on wireless capsule endoscopy in the future.", "appendix": "Data availability\n\nWe did not make use of any resources for datasets. The result under the outcome topic is based on the investigation conducted in the article. We examine and contrast the results based on the number of datasets and the CNN features used in the articles. We did not use any data sources in this survey and there was no need to use extra datasets.\n\n\nReferences\n\nAdewole S, Fernandes P, Jablonski J, et al.: Graph Convolutional Neural Network For Weakly Supervised Abnormality Localization In Long Capsule Endoscopy Videos. Piscataway: IEEE; 2021; pp. 388–399. Reference Source\n\nVäänänen A, Haataja K, Vehviläinen-Julkunen K, et al.: AI in healthcare: A narrative review [version 2; peer review: 1 not approved]. F1000 Res. 2021; 10: 6. Publisher Full Text\n\nGoel N, Kaur S, Gunjan D, et al.: Investigating the significance of color space for abnormality detection in wireless capsule endoscopy images. Biomed. Signal Process Control. 2022; 75: 103624. Publisher Full Text\n\nCao J, Yao J, Zhang Z, et al.: EFAG-CNN: Effectively Fused Attention Guided Convolutional Neural Network for WCE Image Classification. IEEE; 2021; pp. 66–71. Reference Source\n\nMajtner T, Brodersen JB, Herp J, et al.: framework for autonomous detection and classification of Crohnʼs disease lesions in the small bowel and colon with capsule endoscopy. Endosc. Int. Open. 2021; 09(09): E1361–E1370. Publisher Full Text\n\nAmiri Z, Hassanpour H, Beghdadi A: A Computer-Aided Method for Digestive System Abnormality Detection in WCE Images. J. Healthc Eng. 2021; 2021: 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNam JH, Oh DJ, Lee S, et al.: Development and Verification of a Deep Learning Algorithm to Evaluate Small-Bowel Preparation Quality. Diagnostics (Basel). 2021; 11(6): 1127. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nStoleru CA, Dulf EH, Ciobanu L: Automated detection of celiac disease using Machine Learning Algorithms. Sci. Rep. 2022; 12(1): 4071. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDe Maissin A , Vallée R, Flamant M, et al.: Multi-expert annotation of Crohn’s disease images of the small bowel for automatic detection using a convolutional recurrent attention neural network. Endosc. Int. Open. 2021; 09(07): E1136.\n\nMascarenhas M, Ribeiro T, Afonso J, et al.: Deep learning and colon capsule endoscopy: automatic detection of blood and colonic mucosal lesions using a convolutional neural network. Endosc Int Open. 2022; 10(02): E171.\n\nBiradher S, Aparna P: Classification of Wireless Capsule Endoscopy Bleeding Images using Deep Neural Network. Piscataway: IEEE; 2021; pp. 1–4. Reference Source\n\nToonmana C, Numpacharoen K, Wiwatwattana N, et al.: Bleeding Region Segmentation in Wireless Capsule Endoscopy Images by a Deep Learning Model: Initial Learning Rate and Epoch Optimization. Piscataway: The Institute of Electrical and Electronics Engineers, Inc. (IEEE); 2022. Reference Source\n\nSaraiva MM, Ribeiro T, Afonso J, et al.: Deep Learning and Device-Assisted Enteroscopy: Automatic Detection of Gastrointestinal Angioectasia. Medicina (B Aires). 2021; 57(12).\n\nKora P, Ooi CP, Faust O, et al.: Transfer learning techniques for medical image analysis: A review. Biocybern Biomed Eng. 2022; 42(1): 79–107. Publisher Full Text Reference Source\n\nSunitha S, Sujatha SS: An Improved Bleeding Detection Method for Wireless Capsule Endoscopy (WCE) Images Based on AlexNet. IEEE; 2021; pp. 11–15. Reference Source\n\nMuruganantham P, Balakrishnan SM: Attention Aware Deep Learning Model for Wireless Capsule Endoscopy Lesion Classification and Localization. J. Med. Biol. Eng. 2022; 42(2): 157–168. Publisher Full Text\n\nPascual G, Laiz P, García A, et al.: Time-based self-supervised learning for Wireless Capsule Endoscopy. Comput. Biol. Med. 2022; 146: 105631. PubMed Abstract \| Publisher Full Text\n\nSaeed T, Loo CK, Kassim MSS: Ensembles of Deep Learning Framework for Stomach Abnormalities Classification. Comput. Mater. Contin. 2022; 70(3): 4357–4372. Publisher Full Text\n\nGoel N, Kaur S, Gunjan D, et al.: Dilated CNN for abnormality detection in wireless capsule endoscopy images. Soft Comput. (Berlin, Germany). 2022; 26(3): 1231–1247. Publisher Full Text\n\nOzturk S, Ozkaya U: Residual LSTM layered CNN for classification of gastrointestinal tract. J. Biomed. Inform. 2021; 113: 103638. PubMed Abstract \| Publisher Full Text\n\nOzturk S, Ozkaya U: Gastrointestinal tract classification using improved LSTM based CNN. Multimed. Tools Appl. 2020; 79(39–40): 28825–28840. Publisher Full Text\n\nKim SH, Hwang Y, Oh DJ, et al.: Efficacy of a comprehensive binary classification model using a deep convolutional neural network for wireless capsule endoscopy. Sci. Rep. 2021; 11(1): 17479. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nYogapriya J, Chandran V, Sumithra MG, et al.: Gastrointestinal Tract Disease Classification from Wireless Endoscopy Images Using Pretrained Deep Learning Model. Comput. Math. Methods Med. 2021; 2021: 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao Q, Yang W, Liao Q: AFA-RN: An Abnormal Feature Attention Relation Network for Multi-class Disease Classification in gastrointestinal endoscopic images. IEEE; 2021; pp. 1–4. Reference Source\n\nSouaidi M, El Ansari M : A New Automated Polyp Detection Network MP-FSSD in WCE and Colonoscopy Images Based Fusion Single Shot Multibox Detector and Transfer Learning. IEEE access. 2022; 10: 47124–47140. Publisher Full Text\n\nSaraiva MJM, Afonso J, Ribeiro T, et al.: Deep learning and capsule endoscopy: automatic identification and differentiation of small bowel lesions with distinct haemorrhagic potential using a convolutional neural network. BMJ Open Gastroenterol. 2021; 8(1).\n\nRibeiro T, Saraiva MM, Ferreira JPS, et al.: Artificial intelligence and capsule endoscopy: automatic detection of vascular lesions using a convolutional neural network. Ann. Gastroenterol. 2021; 34(6): 820–828. PubMed Abstract \| Publisher Full Text\n\nMohammed A, Farup I, Pedersen M, et al.: PS-DeVCEM: Pathology-sensitive deep learning model for video capsule endoscopy based on weakly labeled data. Comput. Vis. Image Underst. 2020; 201: 103062. Publisher Full Text Reference Source\n\nSaraiva MM, Ferreira JPS, Cardoso H, et al.: Artificial intelligence and colon capsule endoscopy: automatic detection of blood in colon capsule endoscopy using a convolutional neural network. Endosc. Int. Open. 2021; 09(08): E1264–E1268. Publisher Full Text\n\nGan T, Yang Y, Liu S, et al.: Automatic Detection of Small Intestinal Hookworms in Capsule Endoscopy Images Based on a Convolutional Neural Network. Gastroenterol. Res. Pract. 2021; 2021: 1–8. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "306936", "date": "16 Sep 2024", "name": "Gulshan Kumar", "expertise": [ "Reviewer Expertise AI techniques and its applications area", "Intrusion Detection", "Network Security" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 a comprehensive review of the current trends and future directions in deep learning for wireless capsule endoscopy (WCE). While it covers important advancements such as transfer learning, attention mechanisms, multimodal learning, automated lesion detection, interpretability and explainability, data augmentation, and edge computing,. The discussion on challenges and limitations is insightful, yet the paper would benefit significantly from a more explicit statement of how it advances the state of the art, addresses existing gaps, Additionally, more detailed comparisons of the methodologies and their practical implications for clinical practice would enhance the paper's relevance and impact. Therefore, a major revision is necessary to clearly define the paper's contribution and strengthen its analysis and conclusions.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [ { "c_id": "12464", "date": "23 Sep 2024", "name": "Tsedeke Temesgen Habe", "role": "Author Response", "response": "Thank you for your valuable feedback, which has greatly helped us enhance the clarity and impact of our paper. Below is our response to the major points raised: Advancing the State of the Art: We have updated the conclusion section to explicitly highlight how our paper advances the state of the art in applying deep learning techniques to Wireless Capsule Endoscopy (WCE). We have added a detailed discussion on how our review addresses existing gaps in the literature, particularly in lesion detection, segmentation, and classification, which are underexplored areas in current research. Comparison of Methodologies: In response to your suggestion, we expanded the Result section comparing deep learning methodologies. The updated section now includes a more detailed analysis of the practical implications for clinical practice, considering factors such as computational efficiency, model interpretability, and how each method could impact real-world clinical workflows. Strengthening Analysis and Conclusions: We have reworked the conclusions to better align with the current research literature, providing a clearer summary of how the methods reviewed in the paper can directly contribute to advancing WCE technology. This revision also includes more concrete recommendations for both researchers and clinicians. We appreciate your constructive feedback and believe these changes have strengthened the overall quality and relevance of the paper." } ] }, { "id": "280170", "date": "16 Sep 2024", "name": "Reena Gunjan", "expertise": [ "Reviewer Expertise Deep Learning", "Medical Imaging" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nBrief Description and Relevance:\nThis paper presents a comprehensive review of the current trends and future directions in applying deep learning techniques to wireless capsule endoscopy (WCE). The paper addresses challenges such as low-resolution images, artifacts, and annotation difficulties while discussing deep learning methodologies such as transfer learning, attention mechanisms, and semi-supervised learning. Given the increasing use of AI in medical diagnostics, this review is highly relevant for researchers, clinicians, and engineers aiming to leverage AI advancements in GI tract diagnostics.\nMajor Points:\n1) Clarifying Challenges and Limitations: The paper does a good job of highlighting some of the challenges faced by deep learning in WCE, such as data annotation and artifacts. However, it could be more explicit about how current methods fall short in specific areas. For example, while deep learning has demonstrated success in segmentation and lesion detection, what are the common pitfalls in classification tasks. Recommendation: Provide concrete examples of how deep learning models currently underperform in specific GI tract disease classifications and what factors contribute to these limitations. 2) Future Directions: The section on future directions offers an optimistic outlook but could benefit from more concrete and actionable steps. For instance, while data-efficient learning is a promising direction, how can researchers practically implement semi-supervised algorithms in WCE datasets, given the unique challenges of this field? Recommendation: Include more specific methodologies or frameworks that could be adopted for data-efficient learning and video anomaly detection in future research. 3) Encouraging Collaborative Efforts: The paper briefly touches upon the role of researchers, clinicians, and engineers in advancing WCE technology, but it could further emphasize the need for interdisciplinary collaboration. Engaging these diverse fields will be crucial for ensuring that deep learning models are both technically sound and clinically relevant. Recommendation: Highlight the importance of collaboration between AI researchers, gastroenterologists, and medical imaging experts and suggest ways in which such partnerships could be fostered.\nMinor Points:\nSome of the terminology used, particularly in relation to deep learning concepts (e.g., \"structural understanding of data,\" \"spatiotemporal location of diseases\"), may be unclear to readers unfamiliar with the field. Simplifying or briefly explaining these terms would improve the paper's accessibility. Recommendation: Include a brief glossary or explanations of key terms, particularly those related to deep learning and AI, to make the article more accessible to a wider audience. Improvement Suggestions for Image Quality Section: The authors mention that resolution enhancement may not be necessary but suggest focusing on contrast and texture enhancement. This is a valid point, but more detail could be provided about the specific challenges that low contrast or poor texture causes in deep learning models for WCE. Recommendation: Expand the discussion on how contrast and texture improvements can directly benefit the performance of deep learning models, potentially through quantitative examples or referencing specific studies that have addressed these image quality issues\nOverall Evaluation: The article provides an insightful review of the current state and future potential of deep learning in wireless capsule endoscopy. With revisions to clarify complex concepts, integrate technical comparisons earlier, and provide more actionable future directions, this paper can serve as a valuable resource for advancing research and clinical applications in WCE.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [ { "c_id": "12463", "date": "23 Sep 2024", "name": "Tsedeke Temesgen Habe", "role": "Author Response", "response": "Thank you for your insightful comments. We have carefully addressed all the points raised, and our responses are as follows: Clarifying Challenges and Limitations: We have revised the section on challenges and limitations to provide specific examples of how current deep learning models underperform in GI disease classification. The updated section now includes a discussion on misclassification between similar-looking lesions and the role of dataset imbalance, which contributes to these limitations. This expansion provides more concrete insights into the pitfalls of current methods. Future Directions: The future directions section has been expanded to include more actionable steps for researchers. We have added specific methodologies and frameworks for implementing semi-supervised learning and video anomaly detection, particularly in the context of WCE datasets. These revisions offer clearer guidance on how future research can tackle the unique challenges of WCE. Encouraging Collaborative Efforts: We have added a new section that emphasizes the importance of interdisciplinary collaboration between AI researchers, clinicians, and engineers. This section discusses the necessity of fostering partnerships and provides practical suggestions for encouraging such collaboration, including shared datasets and interdisciplinary projects. Image Quality Section: We have expanded the discussion on how contrast and texture improvements can benefit the performance of deep learning models, referencing specific studies that address these image quality challenges. This revision adds depth to the image quality section, illustrating how preprocessing techniques can directly enhance model performance." } ] } ]	1	https://f1000research.com/articles/13-201
https://f1000research.com/articles/12-705/v1	20 Jun 23	{ "type": "Research Article", "title": "Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study", "authors": [ "Eghosa Ekhaese", "Ifeanyi Ezeora", "Ifeanyi Ezeora" ], "abstract": "Background: In a rehabilitation centre designed for drug and alcohol recovery, the therapeutic environment may enhance the psychosocial well-being of sufferers and facilitate a speedy recovery. This study aims to investigate the psychosocial well-being needs (PWNs) of users in an alcohol and drug rehabilitation centre (ADRC) and how therapeutic architectural solutions (TASs) can promote a healing environment through design. Methods: The study employed a mixed research method (qualitative and quantitative). The research strategy was a case study of four rehabilitation centres in Nigeria’s busiest cities; Lagos, Abuja, Port Harcourt, and Enugu. Data were collected via survey questionnaires, an in-depth interview guide, an observation guide, and a checklist of TACs in a healthcare facility. We first investigated what the PWNs of alcohol and drug sufferers (ADSs) are, then identified the therapeutic architectural components (TACs) of an ADRC, before determining what effect TACs have on the recovery process of substance abuse patients. Results: The findings identify eight PWNs and nine TACs essential in an ADRC. The result indicates that TACs have a significant effect on the recovery process of ADSs. However, based on the study results, a framework (framework here refers to using an intelligent and sensitive conceptual design structure as a standard guide for the building archetype rehabilitation facility, which supports mental health service delivery) may be recommended for rehabilitation facilities with TASs for Substance Abuse Disorder (SUD). Conclusion: The study result presents a correlation between ADSs' recovery rates and a well-designed therapeutic environment. So, there is a need for evidence-based design (EBD) of rehabilitation centres with full compliments of a therapeutic architectural environment and integration of mental health services into routine care in sub-Saharan Africa. Limitations include that analyses were cross-sectional and thus may not deduce causal directions, and the authors based the result on self-report.", "keywords": [ "Psychosocial Well-Being Needs", "Substance Use Disorder", "Therapeutic Architecture", "Rehabilitation Centre", "Evidence-based design" ], "content": "Introduction\n\nToday, the world is confronted with the difficulty of dealing with the ever-increasing number of drug addicts (World Drug Report, 2018). As drug misuse and alcohol addiction spreads, the global budgetary health allocation for treatment and rehabilitation has increased significantly (Gale, 2017; Merz, 2018). According to the World Health Organization (WHO), 3.3 million people succumb to alcohol-related deaths worldwide yearly, which accounts for about 5.5% of all death (Mondiale de la Santé and World Health Organisation, 2022; Legg and Newman, 2022). A 2019 survey revealed that 271 million people have taken an illicit drug at least once in their lives, with 31 million suffering from drug addiction (Zarei et al., 2020; Simpson, 2021). On average, 38.3% of the global population drinks alcohol. Global Statistics show average alcohol consumption per person amounts to 9.5 drinks per week and 1.35 drinks per day. Less than half the global population (38.3%) drinks alcohol, this means that those who do drink consume on average 17 litres of pure alcohol annually (World Drug Report, 2019). In Nigeria about 10.8% (22.7 million people) consume cannabis, 10.6% (22.3 million people) consume psychotropic drugs such as benzodiazepines and amphetamine-type substances, 1.6% (3.4 million people) take heroin and 1.4% (2.9 million people) take cocaine (Aweh, Bello and Omemu, 2022). Of those who take drugs, 94.2% are male while only 5.8% are female and the first exposure incidence is between the ages of 10 and 29 for both sexes (Osayomi, Iyanda, Adeleke and Osadolor, 2021). According to various reviews, alcohol accessibility among young adults has increased in recent years (Lasebikan et al., 2018; Obadeji et al., 2020). The average initiation age for alcohol usage in all studies ranged from 13.5 to 20.5 years (Adeloye et al., 2019a). In Nigeria, the rural and urban occurrence of hazardous alcohol consumption was 34.3%, with a higher prevalence in males (43.9%, 31.1–56.8 mean age range) than in females (23.9%, 16.4–31.4 mean age range) (Adeloye et al., 2019b, 2020). Rural inhabitants had a greater prevalence of hazardous alcohol consumption, at 40.1% (24.2–56.1 mean age range) compared with urban dwellers, at 31.2% (22.9–39.6 mean age range) (Ani, Ngwu and Ani, 2020). Drug treatment facilities should have a cheery, engaging atmosphere and a compassionate and therapeutic setting (Zhang, Tzortzopoulos and Kagioglou, 2019; Missouridou et al., 2022). Rehabilitation means returning victims to productivity in society (Timm, Thuesen and Clark, 2021). Rehabilitation services help functionally impaired sufferers to recover from losses, whether that is a physical, mental, social, or vocational impairment (Metzger, Anderson, Are and Ritchwood, 2021). Against this background, it is vital to design an alcohol and drug rehabilitation centre (ADRC) with therapeutic architectural solutions (TACs) for the substance abuse population. An ADRC is a facility where persons addicted to drugs or alcohol or suffering from mental illness can get therapeutic and social care. An ADRC includes medical, psychiatric, administrative, and other support departments. Therefore, such a healthy environment should be designed to have some healing features that combine nature and architecture to facilitate therapy, early recovery, and patients’ psychosocial well-being. The quality of design spaces in such facilities may influence medical treatment outcomes and the healing process. This study focuses on sustainable development goals (SDGs) 3, 9, and 11, which are the 2030 targets of strengthening the WHO framework, namely the convention on tobacco control operations, upgrading infrastructure for better acceptance of environmentally sound technologies, and providing universal access to safe, inclusive, and accessible, green and public spaces. To correctly contextualize this work in the present literature, the next section will undertake a thorough, integrative, and historical review of the literature.\n\nIbrahem, Abouelmagd and Amer (2021) agreed that drug rehabilitation centres should provide an inviting ambience and a caring healing environment. In Nigeria, most rehabilitation centres are designed and built with a focus on the arrest approach rather than treatment, making the centres punitive rather than curative. The techniques or values used in rehabilitation facilities that improve the lives of addicts are not employed in these centres. According to Phillips, Turner-Stokes, Wade and Walton (2020), in some rehabilitation centres, substance abuse therapy is individualised through a collective procedure of judging the patients, planning, arranging, and adjusting the treatment model to meet the exact needs of each patient. Subject to patient needs, treatment involves the following processes.\n\nAccording to Fusar-Poli (2022), the pre-treatment phase entails assessments and treatment planning. The opening assessment is the patient’s first assessment to identify problems and needs and decide eligibility for the program. It involves obtaining the patient’s medical history, piloting a physical check-up, conducting the WHO alcohol, smoking and substance involvement test (ASSIST), and executing urine screening. Some patients also undertake character assessments and psychiatric evaluation IQ tests. To accept a patient for management, they must be willing to undergo treatment and not be psychotic. A patient is either for cure or referral based on the early assessment. Those for treatment are either inpatient or outpatient. As outpatients, they must not be reliant on substances. However, most patients experience the treatment as inpatients since substance abuse disorder (SUD) is at an advanced stage (Smyth et al., 2018).\n\nTay et al. (2019) claimed that treatment planning begins after a patient accepts a cure. Afterwards acceptance, patients undergo tests and assessments that provide an inclusive understanding of their problems and needs. This exercise helps staff to prioritise their problems by recognising salient concerns and guides the advancement of therapy approvals. The treatment plan is a written report of treatment progression and type. It is individualised and designed to meet patient-specific needs. Pergolizzi Jr, Raffa and Rosenblatt (2020) agree that only patients that depend on substances and suffer frank withdrawal symptoms undergo the detoxification phase. In this phase, patients are sedated, hydrated, prescribed analgesics, and managed symptomatically by health professionals. Patients experiencing withdrawal symptoms are isolated, and the interval varies from patient to patient. This phase manages patients’ withdrawal symptoms and stabilises and prepares them for therapy.\n\nStaton et al. (2022) explained that the rehabilitation phase improves the overall functionality and well-being of patients and prevents relapse by assisting them in developing values, lifestyles, morals, skills, and conducts that prevent or control the urge for substance abuse. The patient’s final discharge from the cure centre ends the rehabilitation phase. The program staff strictly determine discharge criteria depending on the patient’s treatment progress. However, the standards for release include family-supported positive therapy completion, factors that determine a reasonable improvement in the patient’s willpower level, personal and career plan development, and the client’s confidence about wants. According to Kennedy (2022), the aftercare treatment phase is for discharged patients that have finished the rehabilitation process. It is scheduled on an outpatient basis and involves regular contact with the patient and their family over the phone and through direct visits. At six weeks post-rehabilitation the social worker visits a patient; at nine weeks, three months and six months post-rehabilitation the patient visits the centre. Ebada and Mohamed (2021) believe that patients are assessed, advised, and provided with other essential support services during regular and ad hoc visits. The aftercare phase aims to offer unending support to discharged patients, monitor their post-rehabilitation improvement, and sense early threats or signs of relapse.\n\nMarques, Freeman and Carter (2021) opined that addressing the healing settings in healthcare institutions requires therapeutic architecture design as an architectural solution. Therapeutic architecture is a people-centred and evidence-based built environment discipline that finds ways of integrating spatial features that relate to people, physically and mentally, into the design. A therapeutic environment is a physical space that helps individuals handle medical difficulties (Reitz and Scaffa, 2020). Healthcare designs encourage and develop cutting-edge research and technology, patient safety, and high-quality health treatment, and welcome patients, families, and caregivers into a psychosocial well-being environment. The physical environment where patients get treatment influences their health results, happiness, serenity, welfare, personnel performance, staff satisfaction, and operational outcomes (Gupta, Howell, Yannelis and Gupta, 2021). The process is beneficial when scientific knowledge is applied in the cure of ailments, patients and their families have support, staff psychosocial and spiritual needs are met, and there is a measurable positive impact on the health conditions of patients and the productivity of personnel.\n\nAccording to Lombardi (2018), people with drug or alcohol addiction can benefit from a healing environment through architectural design. Architecture, scenery, and location can contribute to the healing process of patients. Recovery is faster and more successful for patients in a therapeutic setting. Rehabilitation facilities offer a vital visual link to recovery in the immediate environment (McIntosh, Rodgers, Marques and Gibbard, 2019). When designing a therapeutic facility, the building form, shape, or spaces can mimic the landscape through a relationship ambience between nature and architecture. Natural building materials are required in architecture to create a symbiosis with nature. TACs are elements that promote positive health, well-being, and social connection in rehabilitation institutions. The landscape delivers mental and physical advantages to well-being. TACs incorporated into a rehabilitation facility can reduce anxiety/stress and phobias and assist in meeting the psychosocial well-being needs of patients.\n\n\nMethods\n\nResearch bias can develop during the research process, from the initial planning stage, theory development, data collection and analysis. Therefore, for this study, the effort to control potential sources of bias included: the researchers created a thorough research plan, used an appropriate statistical method, defined a target population and a sampling frame, employed simple random sampling for data collection, avoided convenience sampling, accounted for dropouts or missing data, obtained complete data, avoided generalisation, placed interview or survey topics into separate categories, created data analyst blinding, intention-to-treat analysis, maintained detailed records, completed reporting of all prespecified outcomes.\n\nThe issues guiding research method selection included the topic investigated, the aim and objectives of the study, the research problem, and philosophy. Considering the above, the mixed-method research was determined to be most appropriate for this study. A mixed analysis involves using quantitative and qualitative data analysis techniques within the same study, as shown in Figure 1. A mixed method entails gathering and measuring data using parallel constructs for both data types, separately analysing both data types, and relating results through a side-by-side contrast in a discussion, converting the qualitative data set into quantitative scores, or equally displaying both data (Wisdom and Creswell, 2013). This method is adequate for understanding gaps between both data, reflecting participants’ views and promoting scholarly interaction by improving data validity and reliability. Since psychosocial well-being and therapeutic architectural solutions are multi-faceted issues, this article employed the sequential explanatory mixed-method approach to investigate the psychosocial well-being needs of users in an ADRC that requires TASs to promote a healing environment through design. The research philosophy is pragmatism which adopts both the positivist and interpretivist paradigms. The research strategy is a case study of four selected rehabilitation facilities in four cities (Lagos, Abuja, Port Harcourt, and Enugu) in Nigeria.\n\nThe authors extracted data from both primary and secondary sources. The primary data collection instruments consisted of survey questionnaires, an in-depth interview guide, an observation guide, and a checklist of TACs in a rehabilitation facility. The authors distributed 100 questionnaires among the users of four rehabilitation centres and industry specialists within the study areas, as shown in Table 1. Of the 100 questionnaires distributed, the researchers retrieved 77. The authors interviewed twelve selected sufferers and specialists from the four rehabilitation centres, and 3 interviewees from each of the rehabilitation facilities. The 12 participants were purposely selected from the four randomly selected rehabilitation facilities in the four busiest cities (Lagos, Abuja, Port-Harcourt and Enugu) across four (south-west, north-central, south-south and south-east) of the six geopolitical zones in Nigeria. The authors selected 3 out of the 12 participants from the four facilities. The three participants comprised: 1. the chief consultant, 2. a specialist nurse and 3. an alcohol drug sufferer (ADS). Therefore, three from ADRS-RC, Lagos, 3 from NLSHRC, Abuja, 3 from 180DC, Port Harcourt and 3 from NPHS, Enugu making a total of 12 participants. Also, the study used observation guides and checklists to record data on the available TACs in the four facilities that influence the patient’s psychosocial well-being. The authors used a semi-structured questionnaire to identify the psychosocial well-being needs (PWNs) of ADSs. The breakdown of the number of questionnaires administered and the responses are in Table 1. These questionnaires were designed to be completed by the patients (ADSs). Four research assistants undertook the data gathering process for twelve weeks during the morning and evening, during weekends (Fridays to Sundays). Data collection started on July 15 and ended on September 30, 2022.\n\nAccording to Table 1, The National Psychiatric Hospital Service, Enugu had a 100% response rate, 180 Degrees Centre Agip Estate, Port-Harcourt, Rivers returned 75% of the questionnaires. The New Life Specialist Hospital and Rehabilitation Centre, Kurudu, Abuja, had a 60% response rate, and the A&D Referral Services - Rehabilitation Centre, Surulere, Lagos, returned only 50% of the questionnaires.\n\nFigure 2 shows the respondents’ percentile from the analysed data, of which 46.8% are male and 53.2% female. The respondents ranged across different age groups. Youths aged 18–29 years were the largest group, accounting for 70.1% of responses, whilst the smallest group was those under 18 years old (5.2%). The composition of rehabilitation centre users in Nigeria shows that 75.3% of respondents were medical staff, and 7.8% were missing (7.8% of the questionnaires from medical staff were not recovered). The remaining 16.9% were patients, particularly in the treatment planning and administration phase. Hence most of the responses obtained were from medical staff, validating the expert opinion required for the study. Of the respondents, 74.0% were single, 22.1% were married, 2.6% were widows, and 1.3% were divorced. Degree/Higher National Diploma (HND) holders made up 58.4% of the respondents, while 27.3% were postgraduate degree holders, 7.8% were National Certificate on Education- (NCE)/Ordinary National Diploma (OND) holders, 5.2% held other educational qualifications, and 1.3% had no formal education. The figure reveals that 49.4% were employed, 14.3% were self-employed, 18.2% were students, and 6.5% were retired. The 5,000–50,000 NGN income bracket was the most common (46.8% of respondents), 18.2% of participants fell within the 50,000–100,000 bracket, and 24.7% earnt between 100,000–200,000, while 6.5% of respondents fell within the 200,000–300,000 bracket, and 2.6% earnt between 300,000–500,000.\n\nThe study used the explanatory sequential mixed approach in the analysis (i.e., collecting quantitative data first, then using qualitative data to explain the quantitative findings). The psychosocial well-being needs were analysed using descriptive statistical analysis of the 7-point Likert scale, and the result was illustrated in charts, screen plots, and graphs. The questionnaire survey employed four volunteering staff of the selected facilities. SPSS version 21 (RRID: SCR_002865) was used to code and analyse the data. The study ascertained the TACs of an ADRC through observation guides and checklists (checklist obtained from literature and personal experience and observation and adapted for this study. Following objective two of the study, which is to identify the therapeutic architectural components (TACs) of an ADRC, a TACs checklist would be vital in explaining and creating a prototype healing environment. The search for a TACs checklist led us to review the following literature (Davies, 2020; DuBose, MacAllister, Hadi, & Sakallaris, 2018; Iyendo, Uwajeh & Ikenna, 2016; Youssef, 2014; Thompson, Robinson, Dietrich, Farris & Sinclair, 1996).\n\nDavies (2020) was very helpful in identifying the TACs in ADRC. Thompson et al. (1996) provided the table format used as a checklist. In the sample table, the researchers retained the three columns, but the researcher replaced the content in each column with the TACs and TASs items. The authors used Figure 2 content in Youssef (2014), Figures 1 and 2 contents in Iyendo, Uwajeh and Ikenna (2016), and Figure 4 content in DuBose, MacAllister, Hadi, and Sakallaris (2018).\n\nBased on the observations recorded in the four (4) rehabilitation facilities, column 3 of the table, the authors assessed the rehabilitation facilities on the scale of “A” – applicable; “NA” – not applicable; “SA” – slightly applicable.) to record the components in the selected rehabilitation facilities. In analysing the effect of TASs on the recovery process of substance abuse patients, content analysis on data collected through previous literature (books, academic journals, periodicals, and reports) and interviews with addiction therapists and specialist doctors from the four Nigerian case studies were carried out to ensure an optimum result.\n\n\nResults\n\nThe data analysis relies on the research objectives presented. The assessment technique for quantitative and qualitative data depends on research objectives, methodology, and analysis. Therefore, the research objectives include: identifying the psychosocial well-being needs of ADS in the selected rehabilitation centres, examining the TACs of an ADRC and analysing the effect of TACs on the recovery process of substance abuse patients. The authors presented results in sequential order of the study objectives (Ekhaese & Ezeora, 2023).\n\nIn an interview, the Chief Consultant of the National Psychiatric Hospital Service, Enugu, said “psychosocial is a combination of psychological and social behaviour”. He further stated, “psychosocial studies the link between fears and how people relate to others in a social setting”. Thus psychosocial well-being encompasses the mental, emotional, social, and spiritual dimensions of being healthy. Accordingly, Ekhaese and Hussain (2022) believe that psychosocial well-being and substance abuse in the Sustainable Development Agenda is a historical turning point. Psychosocial well-being is a complex interaction between history, thoughts, and interpretations of the past and what it means to the present. However, identifying the PWNs of ADSs in the selected rehabilitation centres would require understanding PWNs. Below are the words of a specialist nurse in A&D Referral Services - Rehabilitation Centre, Surulere Lagos, “PWNs are any need essential to mental health and generated through interactions between the individual and the environment, such as the need for satisfaction, social approval, or justice. Consequently, psychosocial well-being needs to correlate with mental health disorders such as depression, worry, dementia, and hallucination”. She added, “psychosocial well-being needs are a dynamic experience that influences capability, social connections and support systems (including access to basic services), and cultural norms and value systems as validated by the psychosocial well-being as a conceptual framework”.\n\nFrom the literature, psychosocial well-being needs (PWNs) are at the bottom level of Maslow’s hierarchy of needs. Psychosocial well-being integrates among others mental, social, emotional, spiritual and cultural determinants of health. According to Vansteenkiste, Ryan and Soenens (2020), there are 8 PWNs: 1. affiliation (relatedness), 2. power, 3. cognitive, 4. achievement, 5. autonomy, 6. competence, 7. meaning, and 8. closure.\n\nExamples of PWNs in an ADRC include the need for symptom control, the need to maintain poise and self-esteem, to prevent rejection and isolation, to provide a comfortable and serene environment, to promote spiritual comfort, and the need for therapeutic communication. These needs require psychosocial well-being treatment and the appropriate setting. These include 1. assertive community treatment (ACT) such as a counselling room, treatment room, and community halls; 2. self-help and support groups, which can be in an indoor or outdoor space, including open spaces, parks and recreational spaces, multipurpose halls and conference rooms; 3. individual placement and support (IPS) supported employment in indoor and outdoor spaces (recovery room, worship spaces, and open spaces); 4. psychotherapy needs an indoor area such as a treatment room, sleeping room, common room/lounges, consultation rooms, lecture room, counselling room; 5. psychosocial rehabilitation in an indoor or outdoor space (meeting rooms, treatment spaces, open spaces, green gardens, and counselling room), 6. psychoeducation can be carried out in indoor or outdoor areas, such as lecture spaces, seminal rooms, multipurpose halls, workshop spaces, and open spaces for sports; 7. vocational rehabilitation (VR) requires indoor spaces such as training spaces, conference halls, seminar rooms, classrooms, and workshops; and 8. clubhouses need an indoor space (dance halls, lounges/bars and restaurants). Therefore, Olawande, Ajayi, Amoo and Iruonagbe (2019) agree that psychosocial interference and services for the reintegration of mentally ill patients into a rehabilitation centre are factors in relieving their caregivers’ burdens.\n\nA psychosocial environment can be positive or negative. A positive psychosocial environment should be friendly, sweet, warm, caring, supporting, pleasing, and encouraging. In contrast, a negative one can be cold, uncaring, cluttered, harsh, punitive, aloof, sarcastic, and threatening. However, the study has made some adjustments to help keep the therapeutic experience positive for all categories of users, especially ADSs. The built environment represents a flexible feature, which supports mental health service delivery if we engage in intelligent and sensitive design practice, as shown in Figure 4.\n\nThe rehabilitation facility comprises three drivers: people, place, and process. For the therapeutic architect to create a design that is effective for people, they must understand user behaviour. It may require working with data (information) to actualise an efficient process and utilise sustainable built environment strategies to create a healthy place. However, between people (user-behaviour) and the built environment, there is the engagement of building applications through therapeutic architecture, which may affect the built environment’s impact on the people. The flow from the built environment (place) to the process needs design competence for green building technology, and the resultant effect is the impact of the built environment (place) on the process. Ultimately, the process for the people requires the execution of the healthcare procedure that can initiate the process impact on the people through engaging the healthcare requirements. Therefore, the knowledge and manipulation of this therapeutic concept, properties, practice, and components may produce a healing rehabilitation environment required for a smooth and comfortable recovery rate for ADSs in an ADRC.\n\nFrom Table 2, nine TACs/elements were identified from the literature and interviewed experts/professionals in four selected rehabilitation centres in Nigeria. These nine elements comprise the checklist of TAC in healthcare facilities. These include:\n\n1. Wayfinding and privacy is a TAC that guides interior and exterior continuity through positive kinesthesis improvement and diversity of use to apply atmosphere, nature, colours, and light.\n\n2. Colour as a TAC is used to change space impression, promote healing, sense of sight interaction, stimulate feelings, and colour quality use. Colour application in scenery can provoke feelings of either tranquillity or anxiety. Bright colours increase blood pressure, pulse rate and open functions. However, dark and softer colours produce a calmer effect.\n\n3. Access to views and nature is an element that ensures that the patients in the centre are not feeling enclosed.\n\n4. Healthy lighting creates warm emotions during the day meals and improves light from the hall window to view the adjoining scenery in a design environment.\n\n5. Materials such as a TAC are used for installations, it is energy-saving. The design of rehabilitation centres requires easy-to-maintain natural materials such as green, multi-use, and carefully-knit buildings inspiring TACs.\n\n6. Healthy buildings as a TAC, are organised for patients’ comfort and to provide a sense of social belonging in floors, spaces, and room connections. The buildings are designed to enhance patients’ sense of unity and encourage holistic environment use.\n\n7. Cultural responsiveness. It is best to locate common-use amenities such as a swimming pool, eatery, gym, and theatre at the entrance to inspire cultural responsiveness. The local community members and patients’ families use the amenities. The environment provides deep attachment and enables the patients to feel re-integrated since facility owners permit the locals to use the amenities at the rehabilitation centre. Access to social support as a TAC means one resident cares for another to avoid isolation in the community. Accordingly, architects design the building and the spaces to inspire such connections.\n\n8. Positive distraction as a TAC aims to make the patients more responsible and have a degree of self-awareness about their concerns through personal participation and direct group communication. A prepared environment as a TAC promotes self-confidence and awareness through a designed open environment that emphasises recreation activities and art expression therapy. Home-like environment involves creating direct and alternative routes between floors to prevent isolation in the building.\n\n9. Physical security to achieve community spirit and a positive sense of physical movement through a therapeutic purpose-built rehabilitation centre.\n\nThe analysis shows the patients’ PWNs in a rehabilitation centre that requires therapeutic architecture solutions. The results reveal that the patient PWNs, that the selected rehabilitation caters for, may guide the research in determining what aspects need more focus. Using the TACs/elements as a benchmark, Table 2 presents elements assessed in the facility. For instance, in A&D Referral Services - Rehabilitation Centre (ADRS-RC), Surulere Lagos, the only applicable TACs are the ease of maintenance under materials. All of the other TACs are either not applicable or slightly applicable. This means that the ADRS-RC environment cannot support most PWNs, so there is a need for the centre to focus on all TACs. In New life Specialist Hospital and Rehabilitation Centre, Kurudu, Abuja (NLSHRC), all nine of the TACs were identified, only healthy lighting (sensory stimulation) and positive distraction (artwork and healing process and home mobility barriers) elements are not applicable, with the remaining seven TACs either applicable or slightly applicable. This means that in NLSHRC at Abuja, the PWNs of ADSs are adequately provided for. Consequently, the patients here are likely to enjoy a speedy recovery process. In 180 Degrees Centre Agip Estate, Port-Harcourt, Rivers (180DC) the situation is very similar to the NLSHRC at Abuja. Thus, the ADSs’ recovery rate here is also high. However, in the National Psychiatric Hospital Service, Enugu (NPHS), the facility meets all nine TACs in all the observation guide lists and inventories taken. The researchers recorded only applicable and slightly applicable. It is only in positive distraction that the researchers observed components that were considered not applicable. Thus, it is clear that the PWNs of ADSs are provided for, implying a high recovery rate in NPHS.\n\nThe study result analysed the effect of nine TACs on the recovery process of substance abuse patients using the survey results. Figure 5 indicates that 5.2% of the respondents considered the air quality within and around the rehabilitation facility poor, 24.7% as fair, 32.5% indicated average, 24.7% described it as good, 3.9% as very good and 9.1% as excellent. The survey results revealed that a larger percentage of people considered the air quality in the rehabilitation facility adequate. On water quality served within the rehabilitation facility, 6.5% of respondents considered it as very poor, 7.8% as poor, and 28.9% indicated that it was average. Meanwhile, 9.1% described it as good, 13.0% as very good, and 6.5% as excellent. The result requires more consideration given the water quality in rehabilitation centres today. Regarding the thermal comfort within the rehabilitation facility, 2.6% of respondents stated that it was very poor, 5.2% considered it poor, 32.5% as fair, and 35.1% as average. In contrast, 13.0% indicated that it was good, 5.2% very good, and 6.5% excellent. The quality of sleep while in the facility varied with 1.3% of respondents indicating that it was poor, 14.3% considered it fair, and 37.7% average. Conversely, 36.4% indicated that it was good, 2.6% stated that it was very good, and 7.8% considered it excellent. Thirteen per cent of respondents considered the facility poor in providing an intimate atmosphere, 9.1% stated that it was poor, 20.8% described it as average, 18.2% considered it good and 3.9% thought it was excellent. Furthermore, 5.2% of respondents described the security/sense of safety within the rehabilitation facility as very poor, 3.9% thought it was poor, 9.1% considered it fair, 31.2% indicated that it was average, 26.0% described it as good, 18.2% thought it was very good and 6.5% stated that it was excellent. The data on orderliness within the facility revealed that 1.3% of respondents considered it very poor, 13.0% poor, 14.3% fair, 26.0% indicated average, 33.8% good, 5.2% very good, and 6.5% excellent. This study indicates that orderliness is a concern in rehabilitation centres, therefore, should be a priority in the design.\n\nFigure 6 indicates that 2.6% of respondents considered the facility’s sense of trust and acceptance as very poor, 3.9% as poor, 11.7% as fair, 55.8% as average, 13.0% as good, 5.2% as very good, and 7.8% indicated it as excellent. Similarly, 5.2% of respondents described the value of lasting friendships within the facility as very poor, 9.1% as poor, 24.7% as fair, 31.2% as average, 18.2% as good, 10.4% as very good, and 1.3% as excellent. The results indicate that rehabilitation facilities should provide more spaces and activities that foster social interaction and improve the value of lasting friendships as a TAC for patients’ healing process. The result on elements (available amenity) that meets patient’ status/needs reveal that 5.2% considered it as very poor, 9.1% as poor, 24.7% as fair, 31.2% as average, 18.2% as good, 10.4% as very good, and 1.3% as excellent. Likewise, 2.6% of respondents indicated that the facility poorly boosted their self-esteem psychologically. In contrast, 16.9% stated that its ability to boost their self-esteem was fair, 20.8% as average, 28.6% as good, 13.0% as very good, and 18.2% as excellent. For a sense of belongingness, 2.6% of respondents considered it very poor, 3.9% as poor, 23.4% as fair, 36.4% as average, 23.4% as good, 5.2% as very good, and 5.2% as excellent.\n\nFigure 7 indicates that 5.2% of respondents strongly disagreed that the rehabilitation centres convey a sense of home. Meanwhile, 7.8% disagreed, 11.7% somewhat disagreed, 11.7% neither agreed nor disagreed, 23.4% somewhat agreed, 31.2% agreed, and 9.1% strongly agreed. This study indicated that most rehabilitation centres convey a sense of home to their users. On rehabilitation centres boosting social ties, relationships, and the ability to work in groups, 5.2% of respondents strongly disagreed, 5.2% disagreed, 20.8% somewhat disagreed, 14.3% neither disagreed nor agreed, 18.2% somewhat agreed, 28.6% agreed, and 7.8% strongly agreed. Regarding the sense of place and privacy, 2.6% of respondents strongly disagreed, 3.9% disagreed, 16.9% somewhat disagreed, 16.9% neither agreed nor disagreed, 23.4% somewhat agreed, 19.5% agreed, and 16.9% strongly agreed. The result indicates that most people considered rehabilitation centres today to convey a sense of place and privacy.\n\nAs shown in Figure 8, almost half of the respondents are satisfied with the treatment options in the rehabilitation centre (44.2%), 28.6% are neutral, and 26.0% as not satisfied with the treatment options in the rehabilitation centre.\n\nBased on the importance of rehabilitation centres and their facilities in our communities today, 5.2% see their availability as very unimportant, while 3.9% consider them unimportant. Meanwhile, 14.3% are uncertain, 18.2% view them as important, and 57.1% describe them as very important, as shown in Figure 9. The summary of these findings proves that for 75.3% of rehabilitation centre users and experienced medical practitioners, the availability of rehabilitation centres is vital in our communities today.\n\n\nDiscussion\n\nTherefore, to create a therapeutic environment, the architect should use the power of design to provide solutions for patients and staff throughout the facility: from the parking lot, approach entrance, public spaces, clinical spaces, and ultimately the patient room. The specific design criteria include: reduce or eliminate environmental stressors, provide a positive distraction, enable social support and give a sense of control. This study has analysed the effect of TACs on the recovery process of substance abuse patients. However, therapeutic architectural amenities in a rehabilitation centre include transitional living spaces, discussion lounges, training/lecture/seminar spaces, indoor and outdoor swimming pools, therapy gyms, therapeutic gardens, and a mobility court for patient comfort. Rehabilitation centres should engage TASs to design a structured environment to facilitate the speedy recovery of patients. A structural environment is a construct that combines aesthetics, designs, colour, nature, layout, spaces, and physical, social, and environmental needs of patients as well as their symbolic requirements to help boost psychosocial well-being, decrease infections, and improve positive therapeutic effects. Therapeutic is a term connected to psychiatric hospitals and rehabilitation centres. Therapeutic elements have influenced an architectural approach known as evidence-based design (EBD). EBD is a precise, intelligent, and cautious use of current best evidence from practice and research to make vital decisions about a building’s design (Abdelhay and Dewidar, 2016). EBD allows healthcare facilities to construct a healing setting and use the data on the therapeutic impact of physical design elements on patients, experts, and guests as a guide. The concept of TASs embodies the vision of green architectural spaces that promote healing. It involves architectural manipulation of structures, space, and environmental factors such as sound, colour, views, smells, and light to create a therapeutic environment for healing purposes. Occupants experiencing mental stress and fatigue can feel better in spaces with favourable colours, large windows for outdoor views, and restrictions on loud noise. TASs have a far-reaching effect on ADSs’ psychosocial well-being. ADSs experience denial, deteriorating mental capacity, withdrawal symptoms, and susceptibility to high-stress levels and low moods. TASs considers the impact of illness and services on ADSs’ overall health since substance-use treatment requires conducive, attractive, comfortable, and functionally designed architectural facilities for rehabilitation programs. The environmental setting is one of the factors linked to increased stress in rehabilitating ADSs, and stress triggers are a primary cause of relapse. It is possible to eliminate stress triggers through therapeutic architectural design. Therefore, a therapeutic purpose-built ADRC can facilitate ADSs’ recovery process, thus reducing the length of stay.\n\nEvery healthcare project (including rehab facility) should begin with a review of existing literature on design interventions to improve patient outcomes, staff effectiveness and patient safety, users’ decision on the project, and expected outcomes/benefits. Checklists can assist designers and users in evaluating existing conditions and in setting goals for new facilities planning and design. Design goals set and clearly defined at the beginning of a project can serve as research questions to be answered by post-occupancy surveys, data collection, and evaluation. Early healthcare organizations’ operational model process alignment with the design goals creates a positive collaborative, emotionally, spiritually, and socially supportive environment. Research plays a vital role in helping us continue to understand the healthcare environment’s effects better and identifying opportunities to make it an active agent for healing. Three kinds of research are Medical Model, which evaluates environmental impacts using biologically measurable data; Social Science Model, which evaluates user perception and behaviour; and the Holistic Model, which embraces an organization and its facility. The TACs checklist from this study has identified four factors in a healthcare environment design that can measurably improve patient outcomes which include- 1. reducing or eliminating environmental stressors, 2. providing positive distractions, 3. enabling social support and 4. giving a sense of control.\n\n\nConclusion\n\nThe study results indicate a need for rehabilitation centres in our communities. Access to community healthcare practices accelerates patient recovery rates in communities (Dominic, Ogundipe and Ogundipe, 2019). However, architects should appraise the impact of the centres on their users. Hence, the ADRC design should focus on TASs to foster the speedy recovery of patients and satisfy the PWNs of the facility users. There is limited accessible information on therapy options for substance misuse sufferers. The treatment of addicts relies on the medical paradigm, with minimal emphasis on rehabilitation or encouraging “real” attempts to kick the habit. There is a correlation between ADSs’ recovery rates and a well-designed therapeutic environment. There is also a trend toward a steady reduction in the age of first drug exposure, and multiple substance misuse is becoming more widespread. Evidence suggests that infections are more likely in persons with substance use disorders (SUD). Priority should be on addiction treatment to minimise SUD and other consequences. Reducing the demand for illicit drugs in society depends on the successful treatment of current drug users. Consequently, it has become critical in Nigeria to care for these addicts in purpose-built rehabilitation facilities with adequate care. Hence the need for the design of rehabilitation centres with full compliments of a therapeutic architectural environment.\n\nThe ethical approval was granted by the institutional review committee at Covenant University, Canaan Land, Nigeria known as Covenant University Health and Research Ethics Committee (CUHREC). The Certificate of Project Approval from the CUHREC (No.: CU/HREC/EE/162/22) was issued before the data collection. All the procedures performed in this study were under the 1964 Helsinki declaration and its later amendments. Written Informed consent was taken from all the respondents of the study.\n\nWritten informed consent was obtained from all the participants through specialist nurses in the facilities.", "appendix": "Data availability\n\nFigshare: Dataset of Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study, https://doi.org/10.6084/m9.figshare.22078487.v1 (Ekhaese and Ezeora, 2023).\n\nThis project contains the following underlying data:\n\n- Excel workbook for Psychosocial Well-being Needs.csv\n\nFigshare: Dataset of Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study, https://doi.org/10.6084/m9.figshare.22078487.v1 (Ekhaese and Ezeora, 2023).\n\nThis project contains the following extended data:\n\n- APPENDIX 1-Questionnaire.pdf\n\n- APPENDIX 2-Interview Guide.pdf\n\n- APPENDIX 3-Observation Guide.pdf\n\n- APPENDIX 4-Checklist.pdf\n\nFigshare: Dataset of Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study, https://doi.org/10.6084/m9.figshare.22078487.v1 (Ekhaese and Ezeora, 2023).\n\nThis project contains the following reporting guidelines:\n\n- Dr Ekhaese_STROBE_checklist_cross-sectional.pdf\n\n- Dr Ekhaese_STROBE_checklist_cross-sectional.doc\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgement\n\nThe author sincerely appreciates Covenant University’s financial assistance in publishing this article. We are indeed grateful for the opportunity to do this research. Appreciation goes to all authors, patients and experts who provided data for the study. For Dr Eghosa Ekhaese, who validated the results, prepared the initial draft, ideas conceptualisation, study aim and objective, methodology development, project administration, research supervision, final writing and collation of all the paper sections together. Also, special appreciation to Francis Ezeora for his involvement in the literature reviews; his valuable contribution to conducting and investigating the data collection.\n\n\nReferences\n\nAbdelhay M, Dewidar K: Effect of applying therapeutic architecture on the healing of drug addicts. Second International Conference on Sustainability and the future. At the British University; 2016.\n\nAdeloye D, Abaa DQ, Owolabi EO, et al.: Prevalence of hypercholesterolemia in Nigeria: a systematic review and meta-analysis. Public Health. 2020; 178: 167–178. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAdeloye D, Auta A, Fawibe A, et al.: Current prevalence pattern of tobacco smoking in Nigeria: a systematic review and meta-analysis. BMC Public Health. 2019a; 19(1): 1714–1719. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAdeloye D, Olawole-Isaac A, Auta A, et al.: Epidemiology of harmful use of alcohol in Nigeria: a systematic review and meta-analysis. Am. J. Drug Alcohol Abuse. 2019b; 45(5): 438–450. PubMed Abstract \| Publisher Full Text\n\nAni PN, Ngwu EK, Ani BU: Alcohol use disorders and associated factors among adults in rural communities in Enugu State, Nigeria: A cross-sectional survey. J. Ethn. Subst. Abus. 2020; 21: 1043–1062. PubMed Abstract \| Publisher Full Text\n\nAweh O, Bello OA, Omemu J: A framework for tracking the distribution of increasingly abused pharmaceutical medications. ABUAD International Journal of Natural and Applied Sciences. 2022; 2(1): 1–11. Publisher Full Text\n\nDavies N: Designing the therapeutic space: Using layout, colour, and other elements to get patients in the right frame of mind. Therapy Rooms. 2020.\n\nDominic A, Ogundipe A, Ogundipe O: Determinants of women access to healthcare services in Sub-Saharan Africa. Open Public Health J. 2019; 12(1): 504–514. Publisher Full Text\n\nDuBose J, MacAllister L, Hadi K, et al.: Exploring the concept of healing spaces. HERD: Health Environments Research & Design Journal. 2018; 11(1): 43–56. PubMed Abstract \| Publisher Full Text\n\nEbada Elsayed R, Mohamed YM: Effect of Multimodal Cardiac Rehabilitation Program on Patients after Acute Myocardial Infarction: Nursing Sensitive Outcomes. Egypt. J. Nurs. Health Sci. 2021; 2(2): 54–80. Publisher Full Text\n\nEkhaese E, Ezeora I: Dataset of Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study. [Data]. figshare. 2023. Publisher Full Text\n\nEkhaese EN, Hussain WS: Psychosocial Well-Being Determinants and Occupants’ Happiness in a Green Neighbourhood/Community. Front. Built Environ. 2022; 8: 816390. Publisher Full Text\n\nFusar-Poli P, de Pablo GS , Rajkumar RP, et al.: Diagnosis, prognosis, and treatment of brief psychotic episodes: a review and research agenda. Lancet Psychiatry. 2022; 9(1): 72–83. PubMed Abstract \| Publisher Full Text\n\nGale MJA: Prevention of Drug Use and Tension of Drug Use and Treatment of Drug Use Disorder Treatment of Drug Use Disorders in Rural Settings. United Nations Office on Drugs and Crime.2017. Reference Source\n\nGupta A, Howell ST, Yannelis C, et al.: Does private equity investment in healthcare benefits patients? Evidence from nursing homes (No. w28474). National Bureau of Economic Research. Publisher Full Text\n\nIbrahem B, Abouelmagd D, Amer A: Toward a Sustainable Design of the Rehabilitation Centers for Addiction. Towards Implementation of Sustainability Concepts in Developing Countries. Cham: Springer; 2021; (pp. 193–205). Publisher Full Text\n\nIyendo TO, Uwajeh PC, Ikenna ES: The therapeutic impacts of environmental design interventions on wellness in clinical settings: a narrative review. Complement. Ther. Clin. Pract. 2016; 24: 174–188. PubMed Abstract \| Publisher Full Text\n\nKennedy HG: Models of care in forensic psychiatry. BJPsych Adv. 2022; 28(1): 46–59. Publisher Full Text\n\nLasebikan VO, Ayinde O, Odunleye M, et al.: Prevalence of alcohol consumption and alcohol use disorders among outdoor drinkers in public open places in Nigeria. BMC Public Health. 2018; 18(1): 400–410. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLegg JT, Newman T: What Is an Alcoholic? How to Treat Alcoholism. Medical News Today. 2022. Reference Source\n\nLombardi MP Jr: New England Pathway to Recovery: Drug and Alcohol Addiction Treatment Centre around Nature in Rocky Hill, Connecticut.2018. Reference Source\n\nMarques B, Freeman C, Carter L: Adapting Traditional Healing Values and Beliefs into Therapeutic Cultural Environments for Health and Well-Being. Int. J. Environ. Res. Public Health. 2021; 19(1): 426. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcIntosh J, Rodgers M, Marques B, et al.: The Use of VR for Creating Therapeutic Environ-ments for the Health and Wellbeing of Military Personnel, Their Families and Their Communities. J. Digit. Landsc. Archit. 2019; 185–194.\n\nMerz F: United Nations Office on Drugs and Crime: World Drug Report 2017. 2017. SIRIUS-Zeitschrift für Strategische Analysen. 2018; 2(1): 85–86. Publisher Full Text\n\nMetzger IW, Anderson RE, Are F, et al.: Healing interpersonal and racial trauma: Integrating racial socialization into trauma-focused cognitive behavioural therapy for African American youth. Child Maltreat. 2021; 26(1): 17–27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMissouridou E, Fradelos EC, Kritsiotakis E, et al.: Containment and therapeutic relationships in acute psychiatric care spaces: the symbolic dimensions of doors. BMC Psychiatry. 2022; 22(1): 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMondiale de la Santé O; World Health Organization: 2021 Annual global public health intelligence report–Rapport mondial annuel de veille en santé publique, 2021. Wkly. Epidemiol. Rec.2022; 97(33): 393–396.\n\nObadeji A, Kumolalo BF, Oluwole LO, et al.: Substance use among adolescent high school students in Nigeria and its relationship with psychosocial factors. J. Res. Health Sci. 2020; 20(2): e00480. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOlawande TI, Ajayi MP, Amoo EO, et al.: Variations in family attitudes towards coping with people living with mental illness. Open Access Maced. J. Med. Sci. 2019; 7(12): 2010–2016. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOsayomi T, Iyanda AE, Adeleke R, et al.: Geographical analysis of illicit drug use in Nigeria: evidence from the first national drug use survey, 2018. Prof. Geogr. 2021; 73(3): 377–391. Publisher Full Text\n\nPergolizzi JV Jr, Raffa RB, Rosenblatt MH: Opioid withdrawal symptoms, a consequence of chronic opioid use and opioid use disorder: Current understanding and approaches to management. J. Clin. Pharm. Ther. 2020; 45(5): 892–903. PubMed Abstract \| Publisher Full Text\n\nPhillips M, Turner-Stokes L, Wade D, et al.: Rehabilitation in the wake of Covid-19-a Phoenix from the ashes. Br. Soc. Rehabil. Med. 2020; 1(2): 1–20.\n\nReitz SM, Scaffa ME: Occupational Therapy in the Promotion of Health and Well-Being. AJOT. Am. J. Occup. Ther. 2020; 74(3): 7403420010–7403420014. Reference Source\n\nSimpson V: Community resilience: One community’s view of recovery from the opioid epidemic. Int. J. Com. WB. 2021; 4(1): 3–15. Publisher Full Text\n\nSmyth BP, Elmusharaf K, Cullen W: Opioid substitution treatment and heroin-dependent adolescents: reductions in heroin use and treatment retention over twelve months. BMC Paediatrics. 2018; 18(1): 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStaton CA, Vissoci JRN, El-Gabri D, et al.: Patient-level interventions to reduce alcohol-related harms in low-and middle-income countries: A systematic review and meta-summary. PLoS Med. 2022; 19(4): e1003961. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTay AK, Riley A, Islam R, et al.: The culture, mental health and psychosocial wellbeing of Rohingya refugees: a systematic review. Epidemiol. Psychiatr. Sci. 2019; 28(5): 489–494. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThompson T, Robinson J, Dietrich M, et al.: Interdependence of architectural features and program variables in community residences for people with mental retardation. Am. J. Ment. Retard. 1996; 101(3): 315–327. PubMed Abstract\n\nTimm H, Thuesen J, Clark D: Rehabilitation and palliative care: Histories, dialectics and challenges. Wellcome Open Res. 2021; 6: 171. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVansteenkiste M, Ryan RM, Soenens B: Basic psychological need theory: Advancements, critical themes, and future directions. Motiv. Emot. 2020; 44(1): 1–31. Publisher Full Text\n\nWisdom J, Creswell JW: Mixed methods: integrating quantitative and qualitative data collection and analysis while studying patient-centred medical home models. Rockville: Agency for Healthcare Research and Quality. 2013; 13: 1–5.\n\nWorld Drug Report: 35 million people worldwide suffer from drug use disorders while only 1 in 7 people receive treatment. United Nations: Office on Drugs and Crime. 2019. Reference Source\n\nWorld Drug Report: DRUGS AND AGE Drugs and associated issues among young people and older people. United Nations Publication; 2018.\n\nYoussef O: Therapeutic Architecture Design Index. Arizona: University of Arizona; 2014.\n\nZarei S, Salimi Y, Repo E, et al.: A global systematic review and meta-analysis on illicit drug consumption rate through wastewater-based epidemiology. Environ. Sci. Pollut. Res. 2020; 27(29): 36037–36051. PubMed Abstract \| Publisher Full Text\n\nZhang Y, Tzortzopoulos P, Kagioglou M: Healing built-environment effects on health outcomes: Environment–occupant–health framework. Build. Res. Inf. 2019; 47(6): 747–766. Publisher Full Text" }	[ { "id": "184623", "date": "31 Jul 2023", "name": "Catherine Mawia Musyoka", "expertise": [ "Reviewer Expertise Alcohol and Drug Use management professional" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 the Title and throughout the text, replace the word 'sufferers', which is a stigmatizing word. There is also inconsistency in the terminologies like 'substance abuse patients'. Use words like people who use alcohol/drugs. Or people who suffer from substance/alcohol use disorder.\n'TACs' was used in the methods section first without being defined. The terminology alcohol and drug sufferers (ADS) should be replaced completely, it is not professional terminology.\n\nThe conclusion does not relate to the study findings, which are about the psychosocial well-being needs of people who use alcohol/drugs.\nin the introduction section 1st sentence refers to 'drug addicts'. This is stigmatizing and unprofessional language in the substance use arena. We have people with 'substance use disorders, 'alcohol use disorders' or 'drug use disorders', correct these terminologies throughout the text. Use recent data, World drug report 2018 reference is old data given that we have recent reports for 2022 and 2023.\n\nThe discussion section is prose and does not connect the study findings with results from previous studies. The reader needs to understand and connect your study findings with what is already known in existing literature in the field of substance use disorders rehabilitation.\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": "12273", "date": "23 Sep 2024", "name": "Ekhaese Noel", "role": "Author Response", "response": "#Authors Response to Reviewer Report 1 Manuscript title: Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study Manuscript ID: 125151 Journal: F1000Research Article type: Original Research 31 Jul 2023 \| for Version 1 Catherine Mawia Musyoka, Department of Psychiatry, University of Nairobi, Nairobi, Nairobi County, Kenya The authors appreciate your comments, observations, suggestions, recommendations, and advice on improving the work. Thank you so much. However, we promise to provide quality responses to all the issues. Thank you once again. Approved With Reservations In the Title and throughout the text, replace the word 'sufferers', which is a stigmatising word. There is also inconsistency in the terminologies like 'substance abuse patients'. Use words like people who use alcohol/drugs. Or people who suffer from substance/alcohol use disorder. Authors Response Thank you for your comments, observations and suggestions. The authors are happy to inform you that all the stigmatised words in the work have been replaced in the revised manuscript. 'TACs' were used in the methods section first without being defined. Authors Response Very well noted, although the authors ensured that every acronym was first written in full in the first part of the work, which is abstract. Anyhow, we have made the corrections in the revised manuscript. The terminology alcohol and drug sufferers (ADS) should be replaced completely; it is not professional terminology. Authors Response Again, thank you for the observation. However, we have replaced it in the revised manuscript. The conclusion does not relate to the study findings, which are about the psychosocial well-being needs of people who use alcohol/drugs. Authors Response Noted: Thank you for your kind attention to detail. The authors have re-casted the conclusion to align with the study findings in the revised manuscript. In the introduction section, 1st sentence refers to 'drug addicts'. This is stigmatising and unprofessional language in the substance use arena. We have people with 'substance use disorders, 'alcohol use disorders' or 'drug use disorders'; correct these terminologies throughout the text. Authors Response Again, the authors appreciate your observations and explanation. We have replaced all stigmatised words in the revised manuscript. Use recent data; the World Drug Report 2018 reference is old data, given that we have recent reports for 2022 and 2023. Authors Response Noted: Thank you for the comment and suggestion. We have updated the data on the World Drug Report in the revised manuscript. The discussion section is prose and does not connect the study findings with results from previous studies. The reader needs to understand and connect your study findings with what is already known in existing literature in the field of substance use disorders rehabilitation. Authors Response Thank you for the comments; however, the discussion section is prose alright, and it is supposed to relate the study to similar studies across the globe in substance use disorders rehabilitation, which we did. Nonetheless, the authors have added more existing literature in the field of study in the revised manuscript. 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? Partly If applicable, is the statistical analysis and its interpretation appropriate? Partly Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Partly Competing Interests No competing interests were disclosed. Reviewer Expertise Alcohol and Drug Use management professional Authors Response Thank you so much for the objective assessment and reviews. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. However, I have significant reservations, as outlined above. Authors Response The authors are sincerely grateful for the robust contributions to better this work. Thank you so much." } ] }, { "id": "195822", "date": "02 Oct 2023", "name": "Anishka Hettiarachchi", "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 investigators have attempted to conduct an interesting study focusing on the parameters of conducive therapeutic rehabilitation environments which can contribute to the process of healingsubstance abuse patients. The investigators have done the review of literature in a comprehensive level.\n\nHowever, there is an issue in the alignment between the proposed title, set research objectives, research design, data presentation and analysis.\nThe proposed title depicts an inquiry on the role of Therapeutic Architectural Solutions (TAS) in Alcohol and Drug Rehabilitation Centres (ADRC) to achieve Psychological Well-being Needs (PWN) of substance abuse patients. Accordingly, the study demands that the research design adopt a standard well-being scale (e.g. Building Wellbeing scale [Watson,2017] /Warwick-Edinburgh Mental Wellbeing Scale …etc) to assess the level of well-being of patients per rehab (4 cases studies) tested with reference to the respective level of presence of Therapeutic Architectural Components (TAC). Further, the investigators could have adopted the well-fitting existing model for the Parameters of therapeutic Architecture (e.g. Optimum Healing Environment [OHE] model (Sakallarix, 2015), Ulrich’s Theory of Supportive Design: (Ulrich, 2014) … etc).\nThe rationale behind the data analysis with respect to the initially developed theoretic framework is not clearly set. In the conclusion the study claims to reveal a correlation between substance abuse patients s' recovery rates and a well-designed therapeutic environment, yet the methods used in assessing the recovery rates of the patients are highly subjective. Therefore, it is suggested to realign the title and objectives with the study implemented.\n\nClarity of the logical analytical thinking framework adopted can be further improved by better explaining the line of reasoning and thereby upgrading the work to the next level of comprehension.\nIt is suggested to present the research design clearly and sequentially, elaborating the quantitative and qualitative data collection methods adopted with reference specific data types, well aligning with the research objectives.\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": [ { "c_id": "12272", "date": "23 Sep 2024", "name": "Ekhaese Noel", "role": "Author Response", "response": "#Authors Response to Reviewer Report 2 Manuscript title: Psychosocial well-being needs of alcohol/drug sufferers and therapeutic architectural solutions in rehabilitation centre, Nigeria: a cross-sectional study Manuscript ID: 125151 Journal: F1000Research Article type: Original Research 02 Oct 2023 \| for Version 1 Anishka Hettiarachchi, Department of Architecture, University of Moratuwa, Moratuwa, Western Province, Sri Lanka Approved With Reservations The investigators have attempted to conduct an interesting study focusing on the parameters of conducive therapeutic rehabilitation environments which can contribute to the process of healing substance abuse patients. The investigators have reviewed the literature at a comprehensive level. Authors Response The authors appreciate your comments and insight into the study, which resulted in the concise summary above. Thank you so much for the kind words. However, we promise to provide quality responses to all the issues. Thank you once again. However, there is an issue with the alignment between the proposed title, set research objectives, research design, data presentation, and analysis. Authors Response Thank you for the observation and comments The proposed title depicts an inquiry into the role of Therapeutic Architectural Solutions (TAS) in Alcohol and Drug Rehabilitation Centres (ADRC) to achieve the Psychological Well-being Needs (PWN) of substance abuse patients. Accordingly, the study demands that the research design adopt a standard well-being scale (e.g. Building Well-being scale [Watson,2017] /Warwick-Edinburgh Mental Well-being Scale …etc.) to assess the level of well-being of patients per rehab (4 case studies) tested with reference to the respective level of presence of Therapeutic Architectural Components (TAC). Further, the investigators could have adopted the well-fitting existing model for the Parameters of therapeutic Architecture (e.g. Optimum Healing Environment [OHE] model (Sakallarix, 2015), Ulrich’s Theory of Supportive Design (Ulrich, 2014) … etc). Authors Response Thank you for your comments and analysis of the title viz-a-viz the research design. It was enlightening. However, the scope was to go in-depth into the well-being scales because we realise that well-being can be subjective and objective. Therefore, the idea was not to go into objective well-being but to identify the users’ psychosocial well-being needs in the various rehabilitation facilities. The authors have identified in the body of the work eight (8) PWNs, just like the Human needs identified by Maslow’s Hierarchy of Needs theory. The emphasis is on well-being needs, not the well-being itself, which we clearly stated in the first objectives. Also, the data collection instrument and the method used for objective 1 showed the depth and scope we set out to cover. Again, the authors appreciate your perspective of the study, but it is hoped that your observation will be an opportunity and implication for further studies in this field of research. Thank you. The rationale behind the data analysis with respect to the initially developed theoretical framework is not set. In conclusion, the study claims to reveal a correlation between substance abuse patients’ recovery rates and a well-designed therapeutic environment. Yet, the methods used in assessing the recovery rates of the patients are highly subjective. Therefore, it is suggested that the title and objectives be realigned with the study implemented. Authors Response Again, the authors are grateful for the healthy comments and suggestions. We identified the psychosocial well-being needs (PWNs) as objective 1 and the therapeutic architectural components (TACs) as objective 2 and then correlated the effect of the TACs on the patient recovery rate as objective 3, which meets the combination of the PWNs and other needs. Again, it was indicated in our findings that a well-designed healing environment with all nine TACs facilitates a faster recovery rate than the absence of it. Thank you for your contributions and suggestions. We are open to you crafting the alignments of the title and objectives of the study the way you think they should be. The clarity of the logical, analytical thinking framework adopted can be further improved by better explaining the line of reasoning, thereby upgrading the work to the next level of comprehension. Authors Response Thank you for the comment. However, if I understand you correctly, you are asking me to guide the selection of indicators and questions that will inform the development of the assessment methodology and the data analysis plan. For instance, I know that to analyse something very broad or complex, putting a logical, analytical thinking framework in place creates an opportunity for order or linear analysis. All this we have done using the four steps, which are discovery (state in clear terms the research plan by designing a structural flow chart for the research methodology), process the data (outlining the data collection, data analysis and the likely bias control in research), generate ideas ( analysing the data and interpreting and discussing the findings and results sequentially along the objectives outlined) proffer solutions Again, the author appreciates your comment, and we have clarified the logical, analytical thinking framework adopted by the study in the revised manuscript. It is suggested that the research design be presented clearly and sequentially, elaborating on the quantitative and qualitative data collection methods adopted with reference-specific data types well aligned with the research objectives. Authors Response The author appreciates your comments and suggestions, and we have clarified the research design and explained more about the mixed data collection method adopted in the revised manuscript. Thank you. 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? Partly If applicable, is the statistical analysis and its interpretation appropriate? Partly Are all the source data underlying the results available to ensure full reproducibility? Partly Are the conclusions drawn adequately supported by the results? Partly Competing Interests No competing interests were disclosed. Authors Response The authors are grateful for the objective evaluation and reviews. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. However, I have significant reservations, as outlined above. Authors Response The authors are sincerely grateful for the robust contributions to better this work. Thank you so much." } ] } ]	1	https://f1000research.com/articles/12-705

Subsets and Splits

No community queries yet

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